Updated on 2022/04/12

写真a

 
ASANUMA, Hiroyuki
 
Organization
Graduate School of Engineering Biomolecular Engineering 1 Professor
Graduate School
Graduate School of Engineering
Undergraduate School
School of Engineering Chemistry and Biotechnology
Title
Professor
Contact information
メールアドレス

Degree 1

  1. Ph D. (Engineering) ( 1989.3   The University of Tokyo ) 

Research Interests 3

  1. Nucleic acid chemistry

  2. Photochemistry

  3. Polymer chemistry

Research Areas 1

  1. Others / Others  / Chemistry Related to Living Body

Current Research Project and SDGs 6

  1. Development of photoresponsive DNA/RNA towards the photoregulation of nucleotide functions

  2. Development of highly sensitive fluorescent probe that can recognize DNA and RNA.

  3. Design of new dye cluster by use of DNA/RNA as scaffolds

  4. Development of acyclic artificial nucleic acid; SNA and aTNA

  5. Development of artificial nucleotide for nucleic acids medicine

  6. Study on the non-enzymatic replication of artificial nucleic acid

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Research History 4

  1. Nagoya University   Professor

    2022.4

  2. Nagoya University   Innovative Research Center for Preventive Medical Engineering   Professor

    2020.5 - 2022.3

  3. Nagoya University   Department of Biomolecular Engineering, Graduate School of Engineering   Professor

    2017.4 - 2020.5

  4. Nagoya University   Graduate School of Engineering Biomolecular Engineering 1   Professor

    2017.4 - 2020.4

Education 3

  1. The University of Tokyo   Graduate School, Division of Engineering

    1986.4 - 1989.3

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    Country: Japan

  2. The University of Tokyo

    1984.4 - 1986.3

  3. The University of Tokyo

    1980.4 - 1984.3

Professional Memberships 6

  1. 生命の起源および進化学会   会員

    2021.4

  2. 日本核酸化学会   運営委員

    2017.9

  3. 高分子学会

    2011.4

  4. 日本化学会

  5. The Japanese Photochemistry Association

  6. The Japanese Photochemistry Association

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Committee Memberships 8

  1. 日本核酸化学会   運営委員  

    2017.9   

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    Committee type:Academic society

  2. Wiley-VCH   Editorial Advisory Board ChemBioChem  

    2016.1   

  3. 日本化学会生体機能関連化学・バイオテクノロジーディビジョン   幹事  

    2014.9   

  4. 日本化学会生体機能関連化学・バイオテクノロジーディビジョン   幹事  

    2014.9   

  5. 生体機能関連化学部会   部会長  

    2012.4   

  6. Organizing committee of the International Symposium on Nucleic Acids Chemistry   Executive committee  

    2011.9 - 2012.8   

  7. 高分子学会東海支部   常任幹事  

    2010.4   

  8.   Associate editor of Bulletin of the Chemical Society of Japan  

    2006.4 - 2010.3   

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    Committee type:Academic society

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Awards 4

  1. 平成29年度日本化学会 学術賞

    2018.3   公益社団法人日本化学会   非環状型核酸アナログによる機能性オリゴヌクレオチドの創製

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    Award type:Award from Japanese society, conference, symposium, etc.  Country:Japan

  2. 平成27年度高分子学会賞(科学)

    2016.5   公益社団法人高分子学会  

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    Country:Japan

  3. 部会講演賞

    2000.9   日本化学会生体機能関連化学部会   アゾベンゼン導入DNAによる二重鎖形成の光制御機構の解析

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    Country:Japan

  4. 若い世代の特別講演会講演証

    1990.4   日本化学会   乾燥高分子ゲル錯体の多孔性付与による高機能化

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    Award type:Award from Japanese society, conference, symposium, etc.  Country:Japan

 

Papers 231

  1. Nonenzymatic polymerase-like template-directed synthesis of acyclic L-threoninol nucleic acid Reviewed

    Murayama, K.; Okita, H.; Kuriki, T.; Asanuma, H.

    Nature Communications   Vol. 12   page: 804   2021.2

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    Authorship:Last author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)  

    DOI: https://doi.org/10.1038/s41467-021-21128-0

  2. Orthogonal Amplification Circuits Composed of Acyclic Nucleic Acids Enable RNA Detection Reviewed

    Chen Y., Nagao R., Murayama K., Asanuma H.

    Journal of the American Chemical Society     2022

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    Authorship:Last author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:Journal of the American Chemical Society  

    Construction of complex DNA circuits is difficult due to unintended hybridization and degradation by enzymes under biological conditions. We herein report a hybridization chain reaction (HCR) circuit composed of left-handed acyclic d-threoninol nucleic acid (d-aTNA), which is orthogonal to right-handed DNA and RNA. Because of its high thermal stability, use of an aTNA hairpin with a short 7 base-pair stem ensured clear ON-OFF control of the HCR circuit. The aTNA circuit was stable against nucleases. A circuit based on right-handed acyclic l-threoninol nucleic acid (l-aTNA) was also designed, and high orthogonality between d- and l-aTNA HCRs was confirmed by activation of each aTNA HCR via a corresponding input strand. A dual OR logic gate was successfully established using serinol nucleic acid (SNA), which could initiate both d- and l-aTNA circuits. The d-aTNA HCR was used for an RNA-dependent signal amplification system via the SNA interface. The design resulted in 80% yield of the cascade reaction in 3000 s without a significant leak. This work represents the first example of use of heterochiral HCR circuits for detection of RNA molecules. The method has potential for direct visualization of RNA in vivo and the FISH method.

    DOI: 10.1021/jacs.1c12659

    Scopus

  3. Color-Changing Fluorescent Barcode Based on Strand Displacement Reaction Enables Simple Multiplexed Labeling Reviewed

    Makino, K.; Susaki, E.; Endo, M.; Asanuma, H.; Kashida, H.

    Journal of the American Chemical Society   Vol. 144   page: 1572 - 1579   2022.1

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    Authorship:Corresponding author   Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1021/jacs.1c09844

  4. Xeno nucleic acids (XNAs) having non-ribose scaffolds with unique supramolecular properties Invited Reviewed

    Asanuma, H.; Kamiya, Y.; Kashida, H.; Murayama, K.

      Vol. 28   page: 3933   2022.3

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    Authorship:Lead author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1039/d1cc05868a

  5. Pseudo Base Pairs that Exhibit High Duplex Stability and Orthogonality through Covalent and Non-covalent Interactions Invited

    Kashida Hiromu, Asanuma Hiroyuki

    Journal of Synthetic Organic Chemistry, Japan   Vol. 79 ( 11 ) page: 1013 - 1019   2021.11

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    Authorship:Last author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:The Society of Synthetic Organic Chemistry, Japan  

    <p>Natural base pairs stabilize nucleic acid duplexes via hydrogen bonding and stacking interactions, and efforts have been made to identify artificial base pairs that stabilize duplexes through different interactions. Herein, we describe our attempts to prepare pseudo base pairs that exhibit high stability and orthogonality. Pairs of azobenzene derivatives showed unexpectedly high stability and orthogonality due to intermolecular stacking interactions. Pairs of cationic molecules showed even higher stability than natural G-C pairs through both electrostatic and stacking interactions. Duplexes can be crosslinked via [2+2] photocycloaddition between stilbene derivatives, and pairs of non-planar cyclohexane derivatives can stabilize duplexes by hydrophobic interactions rather than stacking interactions. Hetero-selective pairing can be achieved using electron donor-acceptor interactions. These pseudo base pairs would work well as building blocks in nanotechnology and biotechnology due to their unique functionalities.</p>

    DOI: 10.5059/yukigoseikyokaishi.79.1013

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  6. Perylene-Cy3 FRET System to Analyze Photoactive DNA Structures Reviewed

    Kawai H., Doi T., Ito Y., Kameyama T., Torimoto T., Kashida H., Asanuma H.

    Chemistry - A European Journal   Vol. 27 ( 50 ) page: 12845 - 12850   2021.9

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    Authorship:Last author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:Chemistry - A European Journal  

    We report a new Förster resonance energy transfer (FRET) system for structural analyses of DNA duplexes using perylene and Cy3 as donor and acceptor, respectively, linked at the termini of a DNA duplex via D-threoninol. Experimentally obtained FRET efficiencies were in good agreement with theoretical values calculated based on canonical B-form DNA. Due to the relatively long Förster radius, this system can be used to analyze large DNA structures, and duplexes containing photo-reactive molecules can be analyzed since perylene can be excited with visible light. The system was used to analyze a DNA duplex containing stilbene, demonstrating that in the region of the stilbene cluster the duplex adopts a ladder-like structure rather than helical one. Upon photodimerization between stilbene residues, FRET efficiencies indicated the reaction does not disturb DNA duplex. This FRET system will be useful for analysis of photoreactions of nucleobases as well as a wide range of nucleic acid structures.

    DOI: 10.1002/chem.202101738

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  7. Design and Hybridization Properties of Acyclic Xeno Nucleic Acid Oligomers Invited Reviewed

    Murayama K., Asanuma H.

    ChemBioChem   Vol. 22 ( 15 ) page: 2507 - 2515   2021.8

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    Authorship:Last author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:ChemBioChem  

    Xeno nucleic acids (XNAs) are analogues of DNA and RNA that have a non-ribose artificial scaffold. XNAs are possible prebiotic genetic carriers as well as alternative genetic systems in artificial life. In addition, XNA oligomers can be used as biological tools. Acyclic XNAs, which do not have cyclic scaffolds, are attractive due to facile their synthesis and remarkably high nuclease resistance. To maximize the performance of XNAs, a negatively charged backbone is preferable to provide sufficient water solubility; however, acyclic XNAs containing polyanionic backbones suffer from high entropy cost upon duplex formation, because of the high flexibility of the acyclic nature. Herein, we review the relationships between the structure and duplex hybridization properties of various acyclic XNA oligomers with polyanion backbones.

    DOI: 10.1002/cbic.202100184

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  8. Preparation of artificial hexaplex composed of non-natural nucleic acid Invited Reviewed

    Current Protocols   Vol. 1 ( 4 ) page: e106   2021.4

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    Language:Japanese  

    DOI: 10.1002/cpz1.106

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  9. Dual Crosslinking Photo-Switches for Orthogonal Photo-Control of Hybridization Between Serinol Nucleic Acid and RNA Reviewed

      Vol. 27 ( 14 ) page: 4599 - 4604   2021.3

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    Authorship:Last author, Corresponding author   Language:Japanese   Publishing type:Research paper (scientific journal)  

    DOI: 10.1002/chem.202003528

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  10. Development and modification of pre-mirnas with a fret dye pair for the intracellular visualization of processing intermediates that are generated in cells Invited Reviewed

    Kamiya Y., Kamimoto H., Zhu H., Asanuma H.

    Sensors   Vol. 21 ( 5 ) page: 1 - 14   2021.3

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    Authorship:Last author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:Sensors  

    microRNAs (miRNAs) are small non-coding ribonucleic acids (RNAs), which regulate gene expression via the RNA interference (RNAi) system. miRNAs have attracted enormous interest because of their biological significance and disease relationship. In cell systems, the generation of miRNA is regulated by multiple steps: the transfer of primary miRNA from the nucleus to the cy-tosol, the generation of the precursor-miRNA (pre-miRNA), the production of double-stranded RNA from pre-miRNA by the Dicer, the interaction with protein argonaute-2 (AGO2), and the sub-sequent release of one strand to form miRISC with AGO2. In this study, we attempt to visualize the intermediates that were generated in the miRNA-maturation step in the cells to acquire a detailed understanding of the maturation process of miRNA. To achieve this, we developed pre-miRNAs labeling with a Dicer-or AGO2-responsible fluorescence resonance energy transfer (FRET) dye pair. We observed that modifications with the dye at suitable positions did not interfere with the biological activities of pre-miRNAs. Further, imaging analyses employing these pre-miRNAs demon-strated that the processing of pre-miRNA promoted the accumulation of miRNA at the specific foci in the cytosol. The FRET-labeled pre-miRNA would further elucidate the mechanisms of the RNAi process and provide the basis for development of nucleic acid drugs working in the RNAi system.

    DOI: 10.3390/s21051785

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  11. Helical amplification system composed of artificial nucleic acids Reviewed

    Kashida, H.; Nishikawa, K.; Shi, W.; Miyagawa, T.; Yamashita, H.; Abe, M.; Asanuma, H.

    Chemical Science   Vol. 12 ( 5 ) page: 1656 - 1660   2021.2

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    Authorship:Last author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1039/d0sc05245k

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  12. Light-regulated liquid-liquid phase separation for spatiotemporal protein recruitment and cell aggregation Reviewed

    Ikeuchi, N.; Komachi, T.; Murayama, K.; Asanuma, H.; Maruyama, A.; Shimada, N.

    ACS Applied Materials & Interfaces   Vol. 13 ( 4 ) page: 5652 - 5659   2021.2

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    Language:Japanese   Publishing type:Research paper (scientific journal)  

    DOI: 10.1021/acsami.0c22314

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  13. Quantitative Analyses of Forster Resonance Energy Transfer between Identical Pyrene Chromophores (Homo-FRET) In DNA Scaffolds. Reviewed

    Kashida Hiromu, Kawai Hayato, Azuma Hidenori, Araki Yasuyuki, Wada Takehiko, Asanuma Hiroyuki

    CHEMPHOTOCHEM   Vol. 5 ( 2 ) page: 167 - 172   2021.2

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    Language:Japanese   Publishing type:Research paper (scientific journal)  

    DOI: 10.1002/cptc.202000199

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  14. A Pyrene-Modified Serinol Nucleic Acid Nanostructure Converts the Chirality of Threoninol Nucleic Acids into Circularly Polarized Luminescence Signals Reviewed

    Kashida H., Nishikawa K., Ito Y., Murayama K., Hayashi I., Kakuta T., Ogoshi T., Asanuma H.

    Chemistry - A European Journal     2021

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    Authorship:Last author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:Chemistry - A European Journal  

    Herein is reported a circularly polarized luminescent (CPL) probe that can respond to the chirality of nucleic acids. An achiral nanostructure was prepared by the hybridization of symmetric serinol nucleic acid (SNA) containing pyrene-modified residues. When chiral oligomers that were complementary to the SNA were added, they induced helicity into the SNA nanowire. Efficient circular dichroism (CD) signal amplification was observed when pyrene was attached to uracil bases through a rigid alkynyl linker. Both CPL and CD signals were observed; they depended on the chirality of the added acyclic threoninol nucleic acid (aTNA) oligomer. This system can be used to convert the chirality of chiral biomolecules into chiroptical signals.

    DOI: 10.1002/chem.202102333

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  15. Possibility of pre-RNA world with acyclic XNA before RNA Invited Reviewed

    Asanuma Hiroyuki, Okita Hikari, Murayama Keiji

    Viva Origino   Vol. 49 ( 3 ) page: 9   2021

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    Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:The Society for the Study of the Origin and Evolution of Life Japan  

    <p>  We have developed artificial <i>acyclic</i> nucleic acids composed of serinol derivatives as scaffolds. Recently, template-directed synthesis of <i>acyclic</i> <span style="font-variant: small-caps;">L</span>-threoninol nucleic acid (<span style="font-variant: small-caps;">L</span>-<i>α</i>TNA) could be achieved non-enzymatically via chemical ligation mediated by <i>N</i>-cyanoimidazole in the presence of Mn<sup>2+</sup> ion. A pseudo primer extension reaction like natural polymerase was also attained non-enzymatically using a pool of random <span style="font-variant: small-caps;">L</span>-<i>α</i>TNA trimers. In this short review, we discuss the possibility of <span style="font-variant: small-caps;">L</span>-<i>α</i>TNA as a candiate of pre-RNA before RNA world by focusing on the evolution of genetic material.</p>

    DOI: 10.50968/vivaorigino.49_9

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  16. Intrastrand backbone-nucleobase interactions stabilize unwound right-handed helical structures of heteroduplexes of L-aTNA/RNA and SNA/RNA Reviewed

      Vol. 3 ( 1 ) page: 156   2020.12

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    Authorship:Last author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1038/s42004-020-00400-2

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  17. Investigation of Strand-Selective Interaction of SNA-Modified siRNA with AGO2-MID Reviewed

    Kamiya Yukiko, Takeyama Yuuki, Mizuno Tomonari, Satoh Fuminori, Asanuma Hiroyuki

    INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES   Vol. 21 ( 15 ) page: 1 - 13   2020.8

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    Language:Japanese   Publishing type:Research paper (scientific journal)  

    DOI: 10.3390/ijms21155218

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  18. Photo-regulated trajectories of gliding microtubules conjugated with DNA Reviewed

    Akter Mousumi, Keya Jakia Jannat, Kabir Arif Md Rashedul, Asanuma Hiroyuki, Murayama Keiji, Sada Kazuki, Kakugo Akira

    CHEMICAL COMMUNICATIONS   Vol. 56 ( 57 ) page: 7953 - 7956   2020.7

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    Language:Japanese   Publishing type:Research paper (scientific journal)  

    DOI: 10.1039/d0cc03124k

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  19. Efficient Light-Harvesting Antennae Resulting from the Dense Organization of Dyes into DNA Junctions though d-Threoninol Reviewed

    Kashida Hiromu, Azuma Hidenori, Maruyama Ryoko, Araki Yasuyuki, Wada Takehiko, Asanuma Hiroyuki

    ANGEWANDTE CHEMIE-INTERNATIONAL EDITION   Vol. 59 ( 28 ) page: 11360 - 11363   2020.7

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    Authorship:Last author, Corresponding author   Language:Japanese   Publishing type:Research paper (scientific journal)  

    DOI: 10.1002/anie.202004221

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  20. A triplex-forming linear probe for sequence-specific detection of duplex DNA with high sensitivity and affinity Reviewed

    Chen Yanglingzhi, Murayama Keiji, Kashida Hiromu, Kamiya Yukiko, Asanuma Hiroyuki

    CHEMICAL COMMUNICATIONS   Vol. 56 ( 40 ) page: 5358 - 5361   2020.5

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    Language:Japanese   Publishing type:Research paper (scientific journal)  

    DOI: 10.1039/d0cc01865a

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  21. Incorporation of Pseudo-complementary Bases 2,6-Diaminopurine and 2-Thiouracil into Serinol Nucleic Acid (SNA) to Promote SNA/RNA Hybridization Reviewed

    Kamiya Yukiko, Sato Fuminori, Murayama Keiji, Kodama Atsuji, Uchiyama Susumu, Asanuma Hiroyuki

    CHEMISTRY-AN ASIAN JOURNAL   Vol. 15 ( 8 ) page: 1266 - 1271   2020.4

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    Language:Japanese   Publishing type:Research paper (scientific journal)  

    DOI: 10.1002/asia.201901728

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  22. A Quencher-Free Linear Probe from Serinol Nucleic Acid with a Fluorescent Uracil Analogue Reviewed

    Murayama Keiji, Asanuma Hiroyuki

    CHEMBIOCHEM   Vol. 21 ( 1-2 ) page: 120 - 128   2020.1

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    Language:Japanese   Publishing type:Research paper (scientific journal)  

    DOI: 10.1002/cbic.201900498

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  23. 8-Pyrenylvinyl Adenine Controls Reversible Duplex Formation between Serinol Nucleic Acid and RNA by [2+2] Photocycloaddition Reviewed

    Murayama Keiji, Yamano Yuuhei, Asanuma Hiroyuki

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   Vol. 141 ( 24 ) page: 9485 - 9489   2019.6

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    Language:Japanese   Publishing type:Research paper (scientific journal)  

    DOI: 10.1021/jacs.9b03267

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  24. cis-On/trans-Off of DNA Hybridization with Alkylthio-azobenzene on L-Threoninol Responding to Visible Light Invited Reviewed International coauthorship

    Asanuma Hiroyuki, Ishikawa Teruchika, Yamano Yuuhei, Murayama Keiji, Liang Xingguo

    CHEMPHOTOCHEM   Vol. 3 ( 6 ) page: 418 - 424   2019.6

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    Language:Japanese   Publishing type:Research paper (scientific journal)  

    DOI: 10.1002/cptc.201900060

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  25. Orthogonally Photocontrolled Non-Autonomous DNA Walker Reviewed International coauthorship

    Skugor Marko, Valero Julian, Murayama Keiji, Centola Mathias, Asanuma Hiroyuki, Famulok Michael

    ANGEWANDTE CHEMIE-INTERNATIONAL EDITION   Vol. 58 ( 21 ) page: 6948 - 6951   2019.5

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    Language:Japanese   Publishing type:Research paper (scientific journal)  

    DOI: 10.1002/anie.201901272

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  26. Isothermal double-cycle catalytic system using DNAzyme and RNase H for the highly selective one-pot detection of oligonucleotides Reviewed International coauthorship

    An Ran, Kawai Hayato, Asanuma Hiroyuki, Komiyama Makoto, Liang Xingguo

    ANALYST   Vol. 144 ( 8 ) page: 2773 - 2779   2019.4

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    Language:Japanese   Publishing type:Research paper (scientific journal)  

    DOI: 10.1039/c8an02520g

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  27. <i>N</i>-Benzoyl-protected Peptide Nucleic Acid (PNA) Monomers Expand the Range of Nucleobases Available for PNA-DNA Chimera

    Inagaki Masahito, Uematsu Ryohei, Mizutani Tatsuya, Unabara Daisuke, Araki Yasuyuki, Sakamoto Seiji, Kashida Hiromu, Nishijima Masaki, Asanuma Hiroyuki, Inoue Yoshihisa, Wada Takehiko

    Chemistry Letters   Vol. 48 ( 4 ) page: 341 - 344   2019.4

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:The Chemical Society of Japan  

    <p>We synthesized <i>N</i>-benzoyl-protected peptide nucleic acid (PNA) monomers, which are robust under the conditions for deprotecting the 9-fluorenylmethoxycarbonyl (Fmoc) group by piperidine but are removable by aqueous ammonia and hence totally compatible with Fmoc-solid phase synthesis. This new invention expands the range of available nucleobase sequences, allowing us to use acid-sensitive PNA oligomers and purine nucleotides (both of which are difficult to use in the conventional methods) in the preparation of PNA-DNA chimeras to avoid the drawbacks of traditional PNAs.</p>

    DOI: 10.1246/cl.181048

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  28. In-stem molecular beacon targeted to a 5 '-region of tRNA inclusive of the D arm that detects mature tRNA with high sensitivity Reviewed

    Miyoshi Yuichi, Ohtsuki Takashi, Kashida Hiromu, Asanuma Hiroyuki, Watanabe Kazunori

    PLOS ONE   Vol. 14 ( 1 ) page: e0211505   2019.1

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    Language:Japanese   Publishing type:Research paper (scientific journal)  

    DOI: 10.1371/journal.pone.0211505

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  29. Photo-regulatable DNA isothermal amplification by template-mediated ligation Reviewed

    Cheng Bohao, Kashida Hiromu, Shimada Naohiko, Maruyama Atsushi, Asanuma Hiroyuki

    CHEMICAL COMMUNICATIONS   Vol. 55 ( 8 ) page: 1080 - 1083   2019

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    Language:Japanese   Publishing type:Research paper (scientific journal)  

    DOI: 10.1039/c8cc09218d

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  30. Selective binding of nucleosides to gapped DNA duplex revealed by orientation and distance dependence of FRET Reviewed

    Kashida Hiromu, Kokubo Yuta, Makino Koki, Asanuma Hiroyuki

    ORGANIC & BIOMOLECULAR CHEMISTRY   Vol. 17 ( 28 ) page: 6786 - 6789   2019

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    Language:Japanese   Publishing type:Research paper (scientific journal)  

    DOI: 10.1039/c9ob00946a

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  31. The DNA Duplex as an Aqueous One-Dimensional Soft Crystal Scaffold for Photochemistry Invited

    Asanuma Hiroyuki, Murayama Keiji, Kamiya Yukiko, Kashida Hiromu

    Bulletin of the Chemical Society of Japan   Vol. 91 ( 12 ) page: 1739 - 1748   2018.12

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:The Chemical Society of Japan  

    <p>In this account, we demonstrate that DNA duplex is an ideal scaffold for photochemistry, particularly for comparison of photochemical theory with experiments. The well-defined structure of a DNA duplex can be regarded as an aqueous one-dimensional soft crystal composed of a chromophore-like base-pair assembly. When any base pair in the duplex is replaced with a chromophore, orientation, distance, and association number of chromophores can be precisely controlled. We have developed a new methodology for introduction of chromophores into DNA duplexes using <span style="font-variant: small-caps;">d</span>-threoninol. By using the DNA duplex as a scaffold, experiments on exciton interactions of chromophore assemblies can be compared with molecular exciton theory. A fluorescent resonance energy transfer (FRET) system was also constructed by introducing donor pyrene and acceptor perylene into the DNA duplex using <span style="font-variant: small-caps;">d</span>-threoninol monomers. Using this system, we demonstrated orientation-dependent FRET. We found that theories on both exciton interaction and FRET qualitatively coincide with experimental data and revealed the limitation of the point-dipole approximation. We also evaluated the intrinsic quantum yield of photodimerization of stilbene derivatives by suppressing a side reaction. We propose that there is a correlation of quantum yield of photodimerization with the energy gap of HOMO or LUMO, a hypothesis that deserves theoretical investigation.</p>

    DOI: 10.1246/bcsj.20180278

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  32. Quantitative evaluation of energy migration between identical chromophores enabled by breaking symmetry Reviewed

    Kashida Hiromu, Kawai Hayato, Maruyama Ryoko, Kokubo Yuta, Araki Yasuyuki, Wada Takehiko, Asanuma Hiroyuki

    COMMUNICATIONS CHEMISTRY   Vol. 1 ( 1 )   2018.12

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    Language:Japanese   Publishing type:Research paper (scientific journal)  

    DOI: 10.1038/s42004-018-0093-0

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  33. Bifacial Nucleobases for Hexaplex Formation in Aqueous Solution Reviewed

    Kashida Hiromu, Hattori Yuhei, Tazoe Kaho, Inoue Tadashi, Nishikawa Keiji, Ishii Kentaro, Uchiyama Susumu, Yamashita Hayato, Abe Masayuki, Kamiya Yukiko, Asanuma Hiroyuki

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   Vol. 140 ( 27 ) page: 8456 - 8462   2018.7

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    Language:Japanese   Publishing type:Research paper (scientific journal)  

    DOI: 10.1021/jacs.8b02807

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  34. DNA-assisted swarm control in a biomolecular motor system Reviewed

    Keya Jakia Jannat, Suzuki Ryuhei, Kabir Arif Md. Rashedul, Inoue Daisuke, Asanuma Hiroyuki, Sada Kazuki, Hess Henry, Kuzuya Akinori, Kakugo Akira

    NATURE COMMUNICATIONS   Vol. 9   page: 453   2018.1

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    DOI: 10.1038/s41467-017-02778-5

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  35. Does Treatment of Impaired Glucose Tolerance Improve Cardiovascular Outcomes in Patients with Previous Myocardial Infarction?

    Asakura M., Kim J., Asanuma H., Hamasaki T., Tsukahara K., Higashino Y., Ishikawa T., Nakama Y., Koba S., Maruyama Y., Tsujimoto M., Himeno H., Ohkusa T., Fujino S., Shimizu M., Endo T., Yoda S., Muroya T., Murohara T., Ohte N., Suzuki H., Kohno T., Fukui K., Shiono T., Takase H., Uzui H., Nagai Y., Hashimoto Y., Ikeda S., Mizuno S., Tamita K., Fujita M., Satake K., Kinoshita Y., Nunohiro T., Sakagami S., Higaki J., Morii I., Sawada R., Hiasa Y., Shigemasa T., Nakahama M., Sata M., Doi O., Ueda T., Yamada T., Yamanouchi T., Yamaguchi H., Morita Y., Hayashi H., Kitakaze M.

    Cardiovascular Drugs and Therapy   Vol. 31 ( 4 ) page: 401 - 411   2017.8

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    Purpose: We evaluated the effects of an alpha-glucosidase inhibitor, voglibose, on cardiovascular events in patients with a previous myocardial infarction (MI) and impaired glucose tolerance (IGT). Methods: This prospective, randomized, open, blinded-endpoint study was conducted in 112 hospitals and clinics in Japan in 3000 subjects with both previous MI and IGT receiving voglibose (0.6 mg/day, n = 424) or no drugs (n = 435) for 2 years. The Data and Safety Monitoring Board (DSMB) recommended discontinuation of the study in June 2012 after an interim analysis when the outcomes of 859 subjects were obtained. The primary endpoint was cardiovascular events including cardiovascular death, nonfatal MI, nonfatal unstable angina, nonfatal stroke, and percutaneous coronary intervention/coronary artery bypass graft. Secondary endpoints included individual components of the primary endpoint in addition to all-cause mortality and hospitalization due to heart failure. Results: The age, ratio of males, and HbA1C were 65 vs. 65 years, 86 vs. 87%, and 5.6 vs. 5.5% in the groups with and without voglibose, respectively. Voglibose improved IGT; however, Kaplan–Meier analysis showed no significant between-group difference with respect to cardiovascular events [12.5% with voglibose vs. 10.1% without voglibose for the primary endpoint (95% confidence interval, 0.82–1.86)]; there were no significant differences in secondary endpoints. Conclusion: Although voglibose effectively treated IGT, no additional benefits for cardiovascular events in patients with previous MI and IGT were observed. Voglibose may not be a contributing therapy to the secondary prevention in patients with MI and IGT. Trial Registration: Clinicaltrials.gov number: NCT00212017.

    DOI: 10.1007/s10557-017-6740-3

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  36. Antisense oligonucleotide modified with serinol nucleic acid (SNA) induces exon skipping in mdx myotubes

    Le Bao T., Murayama Keiji, Shabanpoor Fazel, Asanuma Hiroyuki, Veedu Rakesh N.

    RSC ADVANCES   Vol. 7 ( 54 ) page: 34049 - 34052   2017

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    DOI: 10.1039/c7ra06091b

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  37. Development of Pseudo Base-Pairs on D-Threoninol which Exhibit Various Functions

    Kashida Hiromu, Asanuma Hiroyuki

    Bulletin of the Chemical Society of Japan   Vol. 90 ( 5 ) page: 475 - 484   2017

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    <p>The authors have developed various kinds of pseudo base pairs using a <span style="font-variant: small-caps;">d</span>-threoninol scaffold. Although the chemical structures of the pseudo base pairs are much different from natural nucleobases, they can mimic supramolecular properties of natural base pairs. Moreover, modified DNA can possess various functions that cannot be achieved by natural nucleic acids, such as fluorescent switchability, photocrosslinking, insulating and emission color change. These pseudo base pairs can be used to prepare various functional nanomaterials. In the present account, we summarize our recent work on pseudo base pairs, focusing on molecular designs and functions.</p>

    DOI: 10.1246/bcsj.20160371

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  38. Visible-Light-Triggered Cross-Linking of DNA Duplexes by Reversible [2+2] Photocycloaddition of Styrylpyrene

    Doi T., Kawai H., Murayama K., Kashida H., Asanuma H.

    Chemistry - A European Journal   Vol. 22 ( 30 ) page: 10533 - 10538   2016.7

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    Reversible photo-cross-linking of a DNA duplex through the [2+2] photocycloaddition of styrylpyrene is reported. Styrylpyrene moieties on d-threoninol linkers were introduced into complementary positions on DNA strands. Irradiation of the styrylpyrene pair in the duplex with visible light at λ=455 nm induced a [2+2] photocycloaddition between styrylpyrenes that cross-linked the two strands of the duplex. Two diastereomers were formed after [2+2] photocycloaddition as a result of rotation of the styrylpyrene residues. Also, the cycloreversion reaction was induced by UV light at λ=340 nm, which reversibly yielded the uncross-linked strands.

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  39. Faint electric treatment-induced rapid and efficient delivery of extraneous hydrophilic molecules into the cytoplasm

    Hasan M., Nishimoto A., Ohgita T., Hama S., Kashida H., Asanuma H., Kogure K.

    Journal of Controlled Release   Vol. 228   page: 20 - 25   2016.4

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    Effective delivery of extraneous molecules into the cytoplasm of the target cells is important for several drug therapies. Previously, we showed effective in vivo transdermal delivery of naked siRNA into skin cells induced by faint electric treatment (ET) iontophoresis, and significant suppression of target mRNA levels (Kigasawa et al., Int. J. Pharm., 2010). This result indicates that electricity promoted the delivery of siRNA into cytoplasm. In the present study, we analyzed the intracellular delivery of naked anti-luciferase siRNA by faint ET, and found that the luciferase activity of cells expressing luciferase was reduced by in vitro ET like in vivo iontophoresis. Cellular uptake of fluorescent-label siRNA was increased by ET, while low temperature exposure, macropinocytosis inhibitor amiloride and caveolae-mediated endocytosis inhibitor filipin significantly prevented siRNA uptake. These results indicate that the cellular uptake mechanism involved endocytosis. In addition, voltage sensitive fluorescent dye DiBAC4 (3) penetration was increased by ET, and the transient receptor potential channel inhibitor SKF96365 reduced siRNA uptake, suggesting that faint ET reduced membrane potentials by changing intracellular ion levels. Moreover, to analyze cytoplasmic delivery, we used in-stem molecular beacon (ISMB), which fluoresces upon binding to target mRNA in the cytoplasm. Surprisingly, cytoplasmic ISMB fluorescence appeared rapidly and homogeneously after ET, indicating that cytoplasmic delivery is markedly enhanced by ET. In conclusion, we demonstrated for the first time that faint ET can enhance cellular uptake and cytoplasmic delivery of extraneous molecules.

    DOI: 10.1016/j.jconrel.2016.02.048

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  40. 天然に存在しない非環状構造の核酸アナログ-人工の非環状骨格で神の設計した環状骨格に挑む

    浅沼 浩之

    化学   Vol. 71   page: 2016   2016

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  41. Terminus-free siRNA prepared by photo-crosslinking activated via slicing by Ago2

    Kamiya Y., Iishiba K., Doi T., Tsuda K., Kashida H., Asanuma H.

    Biomaterials Science   Vol. 3 ( 12 ) page: 1534 - 1538   2015.12

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    We report the development of photo-crosslinked siRNA strands modified at each terminus with p-cyanostilbene. The siRNA was nuclease resistant and retained RNAi activity. We further studied the activation mechanism of the covalently-crosslinked siRNA. Interestingly Dicer, which is known to generate siRNA with overhanging 3′ ends from the precursor siRNA, did not cleave the crosslinked siRNA at all. Our results suggest that the activation of the crosslinked siRNAs required cleavage by Argonaute2.

    DOI: 10.1039/c5bm00231a

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  42. Pre-organized Guide RNA in the Cas9 Complex Is Ready for the Selection of Target Double-Stranded DNA

    Kamiya Y., Asanuma H.

    ChemBioChem   Vol. 16 ( 16 ) page: 2273 - 2275   2015.11

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    The 3 D structure of Cas9 bound with sgRNA was solved by X-ray crystal-structure analysis. The conformation change in SpyCas9 upon binding to sgRNA changes Cas9 to target-DNA-recognition mode in which seed segments in sgRNA are pre-ordered in an A-type conformation.

    DOI: 10.1002/cbic.201500424

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  43. Detection of DNA target with highly enhanced specificity by self-circularization rolling circle amplification

    Wang X., Wang X., Dong P., Suzuki M., Asanuma H., Liang X.

    Lecture Notes in Electrical Engineering   Vol. 251 LNEE ( VOL. 3 ) page: 1449 - 1458   2014.2

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    DNA detection is widely used for gene analysis. However, false-positive results are difficult to be avoided due to the non-specific amplification. Here, we described a novel RCA approach to improve the specificity. With the help of TspR I (endonuclease), DNA was cleaved into smaller duplex fragments, including the target DNA fragment, with 9 nt sticky ends. A duplex adaptor with two sticky ends which were complementary to that of the target fragment was designed. After hybridization of the adaptor with the target fragments, T4 DNA ligase was used to ligate them to form a circular ds DNA with a gap. Then RCA was carried out from the free 3′-end of the open strand by Phi29 DNA polymerase with two primers which were complementary to the target sequence. Different from the traditional padlock-RCA, SC-RCA showed excellent specificity by amplifying the specific DNA target other than the added probe. © Springer-Verlag Berlin Heidelberg 2014.

    DOI: 10.1007/978-3-642-37925-3_154

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  44. SNA: A nucleic acid analogue that can control the helical structure by sequence design

    Asanuma H., Murayama K., Kashida H.

    Kobunshi   Vol. 62 ( 9 ) page: 513 - 514   2013.9

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    We synthesized a unique nucleic acid analogue, Serinol Nucleic Acid (SNA), from a serinol scaffold tethering natural nucleobases through an amide bond. The SNA oligomer that is fully synthesized from four chiral SNA monomers changes its chirality by the sequence design, not by the inherent chirality of monomers: The SNA oligomer with an asymmetric sequence is chiral whereas the symmetric one is achiral. The chirality of the SNA oligomer can be inverted by reversing its sequence, i.e., two enantiomers of SNA oligomers can be synthesized from four monomers with the identical chirality. Interestingly, SNA formed a remarkably stable duplex with a complementary SNA in an antiparallel manner with its helicity depending on the sequence, which is much more stable than the corresponding DNA/DNA or RNA/RNA duplex. More interestingly, SNA also formed a stable duplex both with DNA and RNA, indicating high potential for antisense agents. These unique properties of SNA might provide an insight for why D-ribose was selected as a scaffold for natural nucleic acids. © 2013 The Society of Polymer Science, Japan.

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  45. A “sugar-deficient” G-quadruplex: Incorporation of aTNA in G4 structures

    Zhou J., Murayama K., Amrane S., Rosu F., Kashida H., Bourdoncle A., Asanuma H., Mergny J.L.

    Chemical Science   Vol. 4 ( 9 ) page: 3693 - 3698   2013.7

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    The effects of modification of the phosphodiester backbone or the guanine bases on G-quadruplex formation have been widely investigated. Only a few studies have investigated the effects of deoxyribose or ‘sugar’ modifications on G-quadruplex structure. Here, we evaluated the structural, thermodynamic, and kinetic properties of the parallel quadruplexes formed by the sequence d(TGGGGT) in which each guanine base was substituted, one at a time, with acyclic threoninol nucleic acid (aTNA). We found that all sequences were able to form G-quadruplexes; however, the presence of aTNA resulted in the formation of a mixture of quadruplex structures in some cases. Furthermore, the presence of a single substitution at any position resulted in destabilization of the G-quadruplex relative to that formed by the unmodified sequence. The introduction of the aTNA in terminal quartets was the most detrimental to stability. In addition, kinetic experiments showed that, compared to its unmodified counterpart sequence d(TGGGGT), the substitution of a normal guanine nucleotide by aTNA decelerated quadruplex formation except when the aTNA was at the 5′ most guanine of the sequence. In summary, our studies indicate that the deoxyribose sugar affects the properties of G-quadruplex structures. © 2013 The Royal Society of Chemistry.

    DOI: 10.1039/c3sc50474c

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  46. P-stilbazole moieties as artificial base pairs for photo-cross-linking of DNA duplex

    Kashida H., Doi T., Sakakibara T., Hayashi T., Asanuma H.

    Journal of the American Chemical Society   Vol. 135 ( 21 ) page: 7960 - 7966   2013.5

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    In this study, we report a photo-cross-linking reaction between p-stilbazole moieties. p-Stilbazoles were introduced into base-paring positions of complementary DNA strands. The [2 + 2] photocycloaddition reaction occurred rapidly upon light irradiation at 340 nm. Consequently, duplex was cross-linked and highly stabilized after 3 min irradiation. The CD spectrum of the cross-linked duplex indicated that the B-form double-helical structure was not severely distorted. NMR analysis revealed only one conformation of the duplex prior to UV irradiation, whereas two diastereomers were detected after the photo-cross-linking reaction. Before UV irradiation, p-stilbazole can adopt two different stacking modes because of rotation around the single bond between the phenyl and vinyl groups; these conformations cannot be discriminated on the NMR time scale due to rapid interconversion. However, photo-cross-linking fixed the conformation and enabled discrimination both by NMR and HPLC. The artificial base pair of p-methylstilbazolium showed almost the same reactivity as p-stilbazole, indicating that positive charge does not affect the reactivity. When a natural nucleobase was present in the complementary strand opposite p-stilbazole, the duplex was significantly destabilized relative to the duplex with paired p-stilbazole moieties and no photoreaction occurred between p-stilbazole and the nucleobase. The p-stilbazole pair has potential as a "third base pair" for nanomaterials due to its high stability and superb orthogonality. © 2013 American Chemical Society.

    DOI: 10.1021/ja401835j

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  47. Quencher-free linear probe with multiple fluorophores on an acyclic scaffold

    Asanuma H., Akahane M., Kondo N., Osawa T., Kato T., Kashida H.

    Chemical Science   Vol. 3 ( 11 ) page: 3165 - 3169   2012.11

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    We have developed a new quencher-free stemless linear probe involving multiple perylenes incorporated through d-threoninol; each perylene is separated by intervening natural nucleotides. Without a substrate, the flexible linear probe does not emit fluorescence due to the self-quenching of the weakly interacting fluorophores. Upon hybridization with the target, intercalation of each dye between the base pairs results in emission of strong fluorescence. The maximum signal-background ratio attained was 180, and the response rate was significantly faster than that of a classic hairpin-forming molecular beacon. © 2012 The Royal Society of Chemistry.

    DOI: 10.1039/c2sc20732j

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  48. Reversed assembly of dyes in an RNA duplex compared with those in DNA

    Fujii T., Urushihara M., Kashida H., Ito H., Liang X., Yagi-Utsumi M., Kato K., Asanuma H.

    Chemistry - A European Journal   Vol. 18 ( 42 ) page: 13304 - 13313   2012.10

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    We prepared reversed dye clusters by hybridizing two RNA oligomers, each of which tethered dyes (Methyl Red, 4'-methylthioazobenzene, and thiazole orange) on D-threoninols (threoninol nucleotides) at the center of their strands. NMR spectroscopic analyses revealed that two dyes from each strand were axially stacked in an antiparallel manner to each other in the duplex, and were located adjacent to the 3'-side of a natural nucleobase. Interestingly, this positional relationship of the dyes was completely the opposite of that assembled in DNA that we reported previously: dyes in DNA were located adjacent to the 5'-side of a natural nucleobase. This observation was also consistent with the circular dichroism of dimerized dyes in which the Cotton effect of the dyes (i.e., the winding properties of two dyes) was inverted in RNA relative to that in DNA. Further spectroscopic analyses revealed that clustering of the dyes on RNA duplexes induced distinct hypsochromicity and narrowing of the band, thus demonstrating that the dyes were axially stacked (i.e., H-aggregates) even on an A-type helix. On the basis of these results, we also prepared heterodimers of a fluorophore (thiazole orange) and quencher (Methyl Red) in an RNA duplex. Fluorescence from thiazole orange was found to be strongly quenched by Methyl Red due to the excitonic interaction, so that the ratio of fluorescent intensities of the RNA-thiazole orange conjugate with and without its complementary strand carrying a quencher became as high as 27. We believe that these RNA-dye conjugates are potentially useful probes for real-time monitoring of RNA interference (RNAi) mechanisms. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

    DOI: 10.1002/chem.201201956

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  49. Model of elongation of short DNA sequence by thermophilic DNA polymerase under isothermal conditions

    Kato T., Liang X., Asanuma H.

    Biochemistry   Vol. 51 ( 40 ) page: 7846 - 7853   2012.10

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    Short DNA sequences, especially those that are repetitive or palindromic, can be used as the seeds for synthesis of long DNA by some DNA polymerases in an unusual manner. Although several elongation mechanisms have been proposed, there is no well-established model that explains highly efficient elongation under isothermal conditions. In the present study, we analyzed the elongation of nonrepetitive sequences with distinct hairpins at each end. These DNAs were elongated efficiently under isothermal conditions by thermophilic Vent (exo -) DNA polymerase, and the products were longer than 10 kb within 10 min of the reaction. A 20-nucleotide DNA with only one hairpin was also elongated. Sequence analysis revealed that the long products are mainly tandem repeats of the short seed sequences. The thermal melting temperatures of the products were much higher than the reaction temperature, indicating that most DNAs form duplexes during the reaction. Accordingly, a terminal hairpin formation and self-priming extension model was proposed in detail, and the efficient elongation was explained. Formation of the hairpin at the 5′ end plays an important role during the elongation. © 2012 American Chemical Society.

    DOI: 10.1021/bi3010413

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  50. A photon-fueled DNA nanodevice that contains two different photoswitches

    Nishioka H., Liang X., Kato T., Asanuma H.

    Angewandte Chemie - International Edition   Vol. 51 ( 5 ) page: 1165 - 1168   2012.1

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    DNA seesaw: Photoswitchable azobenzenecarboxylic acid 1 reversibly photoisomerizes between the trans form and the thermally stable cis form upon irradiation with visible light. A photon-fueled DNA nanodevice that moves like a seesaw in response to irradiation with different wavelengths of light was made by modifying DNA oligonucleotides with a combination of 1 and a conventional azobenzene (see picture). Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

    DOI: 10.1002/anie.201106093

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  51. A polycation-chaperoned in-stem molecular beacon system

    Asanuma H., Osawa T., Kashida H., Fujii T., Liang X., Niwa K., Yoshida Y., Shimada N., Maruyama A.

    Chemical Communications   Vol. 48 ( 12 ) page: 1760 - 1762   2012.1

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    In the presence of poly(l-lysine)-graft-dextran, an in-stem molecular beacon involving three perylene–anthraquinone pairs in the stem region had a signal/background ratio of as high as 570. Response speed was also remarkable; equilibrium was attained within 5 minutes after addition of substrate DNA at 20 °C. © 2012 The Royal Society of Chemistry.

    DOI: 10.1039/c2cc16812j

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  52. Nick sealing by T4 DNA ligase on a modified DNA template: Tethering a functional molecule on D -threoninol

    Liang X., Fujioka K., Asanuma H.

    Chemistry - A European Journal   Vol. 17 ( 37 ) page: 10388 - 10396   2011.9

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    Efficient DNA nick sealing catalyzed by T4 DNA ligase was carried out on a modified DNA template in which an intercalator such as azobenzene had been introduced. The intercalator was attached to a D-threoninol linker inserted into the DNA backbone. Although the structure of the template at the point of ligation was completely different from that of native DNA, two ODNs could be connected with yields higher than 90 % in most cases. A systematic study of sequence dependence demonstrated that the ligation efficiency varied greatly with the base pairs adjacent to the azobenzene moiety. Interestingly, when the introduced azobenzene was photoisomerized to the cis form on subjection to UV light (320-380 nm), the rates of ligation were greatly accelerated for all sequences investigated. These unexpected ligations might provide a new approach for the introduction of functional molecules into long DNA strands in cases in which direct PCR cannot be used because of blockage of DNA synthesis by the introduced functional molecule. The biological significance of this unexpected enzymatic action is also discussed on the basis of kinetic analysis,. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

    DOI: 10.1002/chem.201100215

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  53. A cationic dye triplet as a unique "glue" that can connect fully matched termini of DNA duplexes

    Kashida H., Hayashi T., Fujii T., Asanuma H.

    Chemistry - A European Journal   Vol. 17 ( 9 ) page: 2614 - 2622   2011.2

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    In this study, we propose that three consecutive cationic p-methylstilbazoles tethered on D-threoninols (Z residues) at 5′ termini act as a unique "glue" connecting DNA duplexes by their interstrand cluster formation. Interstrand clustering of p-methylstilbazoles (ZZZ triplets) induces narrowing and hypsochromic shift of bands at 350nm, which can be assigned to the absorption of p-methylstilbazole. However, single-stranded DNA conjugates involving a ZZZ triplet at the 5′ terminus of 8-mer native nucleotides is found not to induce such large spectral changes, which implies that the intrinsic self-assembling property of ZZZ triplets is weak. Interestingly, when this conjugate is hybridized with a complementary 8-mer native oligonucleotide, a remarkable spectral change is observed, indicating the dimerization of a duplex through the interstrand clustering of ZZZ triplets. Dimerization of the duplex is also evidenced by cold-spray ionization mass spectrometry. This interstrand clustering is observed only when a ZZZ triplet is tethered to a 5′ rather than 3′ terminus. Furthermore, the stability of the interstrand cluster increases by increasing the number of nucleobases of the DNA portion, and when mismatched base pairs are incorporated or when a base next to the Z residue is deleted, the stability substantially drops. When we apply the ZZZ triplet to the formation of a nanowire using two complementary DNA conjugates, each of which has a ZZZ triplet at the 5′ termini as overhang, we demonstrate the successful formation of a nanowire by native PAGE analysis. Since native sticky ends that have three nucleotides do not serve as "glue", ZZZ triplets with their unique glue-like properties are prime candidates for constructing DNA-based nanoarchitectures. Stick together! A unique "glue" of cationic p-methylstilbazoles tethered on D-threoninols connects DNA duplexes by intermolecular clustering. When the "glue" is attached to both termini of a DNA duplex, a nanowire is formed (see graphic). Thus, the "glue" can be utilized for constructing DNA-based nanoarchitectures. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

    DOI: 10.1002/chem.201003059

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  54. Design of a functional nanomaterial with recognition ability for constructing light-driven nanodevices

    Liang X., Mochizuki T., Fujii T., Kashida H., Asanuma H.

    Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)   Vol. 6518 LNCS   page: 112 - 122   2011.2

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    An artificial macromolecule (foldamer) was designed as a novel nanomaterial with the backbone of phosphodiester and the side chain of functional molecules and nucleobases. The functional molecules tethered on D-threoninol and the nucleosides on D-ribose can be lined up with any sequence and ratio by using standard phosphoramidite chemistry. The nucleobases that form Watson-Crick base pairs provide the sequence recognition which is required for constructing complicate nanostructures. The multiple functional molecules give applicable and advanced functions such as photoresponsiveness when azobenzenes were used. Unexpectedly, a stable double helix was formed even in the case that the ratio of azobenzene molecules and base pairs was as high as 2:1. More interestingly, this artificial duplex showed high sequence specificity: the stability decreased greatly when a mismatched base pair was present. Furthermore, the formation and dissociation of the constructed artificial duplex were reversibly and completely modulated with light irradiation. By using this new nanomaterial, a variety of functional nanostructures and nanodevices are promising to be designed. © 2011 Springer-Verlag.

    DOI: 10.1007/978-3-642-18305-8_11

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  55. A light-driven DNA nanomachine for the efficient photoswitching of RNA digestion

    Zhou M., Liang X., Mochizuki T., Asanuma H.

    Angewandte Chemie - International Edition   Vol. 49 ( 12 ) page: 2167 - 2170   2010.3

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    "Chemical Equation Presented" Photons as fuel: A photoresponsive DNA enzyme was constructed that can work at the single-molecule level. Complete ONOFF photoswitching of RNA digestion was realized by photoregulating the topological structure of a DNAzyme/RNA complex. The key components of the photoswitch are azobenzene units. © 2010 Wiley-VCH Verlag GmbH & Co. KGaA.

    DOI: 10.1002/anie.200907082

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  56. Photoregulation of DNA transcription by using photoresponsive T7 promoters and clarification of its mechanism

    Liang X., Wakuda R., Fujioka K., Asanuma H.

    FEBS Journal   Vol. 277 ( 6 ) page: 1551 - 1561   2010.3

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    With the use of photoresponsive T7 promoters tethering two 2′-methylazobenzenes or 2′,6′-dimethylazobenzenes, highly efficient photoregulation of DNA transcription was obtained. After UV-A light irradiation (320-400 nm), the rate of transcription with T7 RNA polymerase and a photoresponsive promoter involving two 2′,6′-dimethylazobenzenes was 10-fold faster than that after visible light irradiation (400-600 nm). By attaching a nonmodified azobenzene and 2′,6′-dimethylazobenzene at the two positions, respectively, and by utilizing the different cis→trans thermal stability between cis-nonmodified azobenzene and cis-2′,6′- dimethylazobenzene, four species of T7 promoter (cis-cis, trans-cis, cis-trans, and trans-trans) were obtained. The four species showed transcriptional activity in the order of cis-cis > cis-trans > trans-cis > trans-trans. Kinetic analysis revealed that the Km for the cis-cis promoter (both of the introduced azobenzene derivatives were in the cis form) and T7 RNA polymerase was 68 times lower than that for the trans-trans form, indicating that high photoregulatory efficiency was mainly due to a remarkable difference in affinity for RNA polymerase. The present approach is promising for the creation of biological tools for artificially controlling gene expression, and as a photocontrolled system for supplying RNA fuel for RNA-powered molecular nanomachines. © 2010 FEBS.

    DOI: 10.1111/j.1742-4658.2010.07583.x

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  57. Molecular imprinting of cyclodextrin to physiologically active oligopeptides in water

    Song S., Shirasaka K., Hirokawa Y., Asanuma H., Wada T., Sumaoka J., Komiyama M.

    Supramolecular Chemistry   Vol. 22 ( 3 ) page: 149 - 155   2010.3

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    β-Cyclodextrin (β-CyD)-based polymeric receptors for γ-endorphin (γ-endor, an opioid heptadecapeptide) were prepared using the molecular imprinting method. When mono-3-(N-acrylamido)-3-deoxy-β-CyD bearing a vinyl group in the secondary hydroxyl side of the cavity of β-CyD was polymerised in water in the presence of γ-endor, the binding activity of the β-CyD polymer to this peptide in water was enormously promoted by the imprinting. By contrast, the bindings towards methionine-enkephalin (N-terminal pentapeptide of γ-endor) and its homologue leucine-enkephalin were suppressed. Thus, the binding of γ-endor by the imprinted polymer was highly selective. The imprinting towards γ-endor was also successful with the use of the β-CyD monomer bearing a vinyl group in the primary hydroxyl side of the cavity, although the recognition was less strict. Various factors affecting the imprinting efficiency (kinds of β-CyD vinyl monomer and template, as well as the pH of imprinting mixture) are discussed. © 2010 Taylor & Francis.

    DOI: 10.1080/10610270902980622

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  58. An efficient fluorescence resonance energy transfer (FRET) between Pyrene and Perylene assembled in a DNA duplex and its potential for discriminating single-base changes

    Kashida H., Takatsu T., Sekiguchi K., Asanuma H.

    Chemistry - A European Journal   Vol. 16 ( 8 ) page: 2479 - 2486   2010.2

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    To increase the apparent Stokes' shift of perylene, pyrene (donor) and perylene (acceptor) were assembled in a DNA duplex to achieve the efficient fluorescence resonance energy transfer (FRET) from pyrene to perylene. Multiple donors were introduced in the vicinity of acceptors through d-threoninol and natural base pairs were inserted between the dyes. Accordingly, donors and acceptors could be accumulated inside the DNA without forming an undesired excimer/ exciplex. When two pyrene moieties were located in proximity to one perylene with one base pair inserted between them, efficient FRET occurred within the duplex. Thus, strong emission at 460 nm was observed from perylene when excited at 345 nm at which pyrene has its absorption. The apparent Stokes' shift became as large as 115 nm with a high apparent FRET efficiency (Fφ1). However, the introduction of more than two pyrenes did not enhance the fluorescence intensity of perylene, due to the short Fçrster radius (R0) of the donor pyrene. Next, this FRET system was used to enlarge the Stokes' shift of the DNA probe, which can discriminate a one-base deletion mutant from wild type with a model system by incorporation of multiple donors into DNA. Two perylene moieties were tethered to the DNA on both sides of the intervening base, and two pyrenes were further inserted in the vicinity of the perylenes as an antenna. Hybridization of this FRET probe with a fully matched DNA allowed monomer emission of perylene when the pyrenes were excited. In contrast, excimer emission was generated by hybridization with a one-base deletion mutant. Thus, the apparent Stokes' shift was enhanced without loss of efficiency in the detection of the deletion mutant. © 2010 Wiley-VCH Verlag GmbH&Co. KGaA, Weinheim.

    DOI: 10.1002/chem.200902078

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  59. Effect of the ortho modification of azobenzene on the photoregulatory efficiency of DNA hybridization and the thermal stability of its eis form

    Nishioka H., Liang X., Asanuma H.

    Chemistry - A European Journal   Vol. 16 ( 7 ) page: 2054 - 2062   2010.2

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    We synthesized various azobenzenes methylated at their ortho positions with respect to the azo bond for more effective photoregulation of DNA hybridization. Photoregulatory efficiency, evaluated from the change of T m (ΔTm) induced by trans-cis isomerization, was significantly improved for all ortho-modified azobenzenes compared with non-modified azobenzene due to the more stabilized trans form and the more destabilized cis form. Among the synthesized azobenzenes, 4-carboxy-2',6'- dimethylazobenzene (2',6'-Me-Azo), in which two ortho positions of the distal benzene ring with respect to carboxyl group were methylated, exhibited the largest ΔTm, whereas the newly synthesized 2,6-Me-Azo (4-carboxy-2,6- dimethylazobenzene), which possesses two methyl groups on the two ortho positions of the other benzene ring, showed moderate improvement of ΔTm. Both NMR spectroscopic analysis and computer modeling revealed that the two methyl groups on 2',6'-Me-Azo were located near the imino protons of adjacent base pairs; these stabilized the DNA duplex by stacking interactions in the trans form and destabilized the DNA duplex by steric hindrance in the cis form. In addition, the thermal stability of cis-2',6'-Me-Azo was also greatly improved, but not that of cis2,6-Me-Azo. Solvent effects on the half-life of the cis form demonstrated that cis-to-trans isomerization of all the modified azobenzenes proceeded through an inversion route. Improved thermal stability of 2',6'-Me-Azo but not 2,6-Me-Azo in the eis form was attributed to the retardation of the inversion process due to steric hindrance between lone pair electrons of the π orbital of the nitrogen atom and the methyl group on the distal benzene ring. © 2010 Wiley-VCH Verlag GmbH & Co. KGaA.

    DOI: 10.1002/chem.200902789

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  60. Femtosecond photoisomerization study on azobenzene-derivative bound by DNA

    Chen T., Igarashi K., Yamaguchi A., Nakagawa N., Yamane K., Fujii T., Asanuma H., Yamashita M.

    Optics InfoBase Conference Papers     2010

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    First observation of femtosecond absorbance change in azobenzene-derivative (AzD) bound by double-strand DNA, that by single-strand DNA and Azd shows trans-to-cis photoisomerization rate per pulse in the former is much lower than in the latter. © OSA / UP 2010.

    DOI: 10.1364/up.2010.me6

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  61. Analysis of coherent heteroclustering of different dyes by Use of threoninol nucleotides for comparison with the molecular exciton theory

    Fujii T., Kashida H., Asanuma H.

    Chemistry - A European Journal   Vol. 15 ( 39 ) page: 10092 - 10102   2009.10

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    To test the molecular exciton theory for heterodimeric chromophores, various heterodimers and clusters, in which two different dyes were stacked alternately, were prepared by hybridizing two oligodeoxyribonucleotides (ODNs), each of which tethered a different dye on D-threoninol at the center of the strand. NMR analyses revealed that two different dyes from each strand were stacked antiparallel to each other in the duplex, and were located adjacent to the 5'-side of a natural nucleobase. The spectroscopic behavior of these heterodimers was systematically examined as a function of the difference in the wavelength of the dye absorption maxima (Δλmax). We found that the absorption spectrum of the heterodimer was significantly different from that of the simple sum of each monomeric dye in the single Strand. When azobenzene and Methyl Red, which have λmax at 336 and 480 nm, respectively, in the single strand (Δλmax= 144nm), were assembled on ODNs, the band derived from azobenzene exhibited a small hyperchromism, whereas the band from Methyl Red showed hypochromism and both bands shifted to a longer wavelength (bathochromism). These hyper- and hypochromisms were further enhanced in a heterodimer derived from 4'-methylthioazobenzene and Methyl Red, which had a much smaller Δλmax (82 nm; λmax = 398 and 480 nm in the single-strand, respectively). With a combination of 4'-dimethyl-amino-2- nitroazobenzene and Methyl Red, which had an even smaller Δλ max (33 nm), a single sharp absorption band that was apparently different from the sum of the single-stranded spectra was observed. These changes in the intensity of the absorption band could be explained by the molecular exciton theory, which has been mainly applied to the spectral behavior of H- and/or Jaggregates composed of homo dyes. However, the bathochromic band shifts observed at shorter wavelengths did not agree with the hypsochromism predicted by the theory. Thus, these data experimentally verify the molecular exciton theory of heterodimerization. This coherent coupling among the heterodimers could also partly explain the bathochromicity and hypochromicity that were observed when the dyes were intercalated into the duplex. © 2009 Wiley-VCH Verlag GmbH & Co. KGaA.

    DOI: 10.1002/chem.200900962

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  62. In-stem molecular beacon containing a pseudo base pair of threoninol nucleotides for the removal of background emission

    Kashida H., Takatsu T., Fujii T., Sekiguchi K., Liang X., Niwa K., Takase T., Yoshida Y., Asanuma H.

    Angewandte Chemie - International Edition   Vol. 48 ( 38 ) page: 7044 - 7047   2009.9

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    Off means off: An in-stem molecular beacon in which Dthreoninol units tether perylene and anthraquinone in the stem region effectively detected target sequences and was able to discriminate a one-base-deletion mutant from the wild-type (full-match) sequence without background emission (see picture). © 2009 Wiley-VCH Verlag GmbH & Co. KGaA.

    DOI: 10.1002/anie.200902367

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  63. A supra-photoswitch involving sandwiched DNA base Pairs and azobenzenes for light-driven nanostructures and nanodevices

    Liang X., Mochizuki T., Asanuma H.

    Small   Vol. 5 ( 15 ) page: 1761 - 1768   2009.8

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    A supra-photoswitch is designed for complete ON/OFF switching of DNA hybridization by light irradiation for the purpose of using DNA as a material for building nanostructures. Azobenzenes, attached to D-threoninols that function as scaffolds, are introduced into each DNA strand after every two natural nucleotides (in the form (NNX)n whereNandXrepresent the natural nucleotide and the azobenzene moiety, respectively). Hybridization of these two modified strands forms a supra-photoswitch consisting of alternating natural base pairs and azobenzene moieties. In this newly designed sequence, each base pair is sandwiched between two azobenzene moieties and all the azobenzene moieties are separated by base pairs. When the duplex is irradiated by visible light, the azobenzene moieties take the trans form and this duplex is surprisingly stable compared to the corresponding native duplex composed of only natural oligonucleotides. On the other hand, when the azobenzene moieties are isomerized to the cis form by UV light irradiation, the duplex is completely dissociated. Based on this design, a DNA hairpin structure is synthesized that should be closed by visible light irradiation and opened by UV light irradiation at the level of a single molecule. Indeed, perfect ON/OFF photoregulation is attained. This is a promising strategy for the design of supra-photoswitches such as photoresponsive sticky ends on DNA nanodevices and other nanostructures. © 2009 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

    DOI: 10.1002/smll.200900223

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  64. Positively charged base surrogate for highly stable "base pairing" through electrostatic and stacking interactions

    Kashida H., Ito H., Fujii T., Hayashi T., Asanuma H.

    Journal of the American Chemical Society   Vol. 131 ( 29 ) page: 9928 - 9930   2009.7

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    (Figure Presented) "Base pairs" of cationic dyes (p-methylstilbazole) were incorporated into oligodeoxyribonucleotides (ODNs). This "base pair" greatly stabilized the duplex through electrostatic and stacking interactions. The melting temperature of modified ODN was higher than those of neutral dyes and native base pairs. Further stabilization of the duplex was observed when the number of cationic dyes increased. © 2009 American Chemical Society.

    DOI: 10.1021/ja9013002

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  65. Modulation of pK<inf>a</inf> of Brooker's merocyanine by DNA hybridization

    Kashida H., Sano K., Kara Y., Asanuma H.

    Bioconjugate Chemistry   Vol. 20 ( 2 ) page: 258 - 265   2009.2

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    Brocker's merocyanine (BM), which changes its emission and absorption maxima upon protonation, was introduced into oligodeoxyribonucleotide (ODN) via D-threoninol by postsynthetic modification on a CPG (controlled-pore glass) support. The pKa of BM in the modified ODN increased from 9.5 to 10.1 upon hybridization. As a result, absorption maxima shifted from 492 to 432 nm at pH 10.0 by the presence of its complementary strand. This spectral shift was sufficiently large so that DNA hybridization could easily be discriminated even by the naked eye; the color of the solution changed from orange to yellow upon hybridization. In addition, the fluorescence emission was strongly quenched upon hybridization, demonstrating that this probe can also detect the target DNA by the fluorescence change. Ratiometric detection of hybridization was also possible by simultaneous excitation of both protonated and deprotonated BMs. Furthermore, we could also modulate its pKa by the antiparallel stacking of two BM molecules in the duplex; the pKa of BM decreased from 10.1 to 9.7 by the stacking of two BMs in an antiparallel manner. Thus, control of the microenvironment around the BM molecule allowed modulation of its pKa, which is applicable to the sequence-specific recognition of target DNA. © 2009 American Chemical Society.

    DOI: 10.1021/bc800335h

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  66. Rational design of functional DNA with a Non-Ribose acyclic scaffold

    Kashida H., Liang X., Asanuma H.

    Current Organic Chemistry   Vol. 13 ( 11 ) page: 1065 - 1084   2009

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    The growing field of DNA technology requires new modified DNAs that can perform advanced functions. No matter how we optimize the length and sequence of DNA using only the four naturally occurring nucleotides, potential performance is limited. In this review, we describe a facile and effective method of rationally designing new functional DNA by focusing on acyclic scaffolds, especially threoninols, which are utilized to incorporate functional molecules into DNA. Wedge-type insertion of a functional molecule with a planar structure of proper size in D-threoninol to DNA does not destabilize the duplex, although the backbone structure is changed. Rather, intercalation offsets such distortions and significantly raises the melting temperature of the DNA duplex. Based on the wedge-type insertion, photoresponsive DNA (tethering azobenzenes) and fluorescent probes that can detect single nucleotide polymorphisms (SNPs) and insertion/deletion (indel) polymorphisms have been designed. Furthermore, a variety of molecular clusters of dyes have also been prepared from acyclic scaffolds tethering dyes. © 2009 Bentham Science Publishers Ltd.

    DOI: 10.2174/138527209788680736

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  67. 名古屋コンファレンス報告

    浅沼 浩之, 早川 芳宏

    化学と工業 = Chemistry and chemical industry   Vol. 60 ( 4 )   2007.4

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  68. 2′,6′-Dimethylazobenzene as an efficient and thermo-stable photo-regulator for the photoregulation of DNA hybridization

    Nishioka H., Liang X., Kashida H., Asanuma H.

    Chemical Communications   ( 42 ) page: 4354 - 4356   2007

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    The introduction of methyl groups into two ortho positions (2′ and 6′ positions) of the same benzene ring in an azobenzene remarkably raised both its photoregulation ability and the thermal stability of the cis-form. © The Royal Society of Chemistry.

    DOI: 10.1039/b708952j

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  69. Unexpected efficient ab initio DNA synthesis at low temperature by using thermophilic DNA polymerase.

    Liang X., Kato T., Asanuma H.

    Nucleic acids symposium series (2004)   ( 51 ) page: 351 - 352   2007

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    DNA was synthesized in the absence of DNA or RNA as template (or primer) from dNTPs at relatively low temperatures (25 approximately 50 degrees C) by thermophilic Vent DNA polymerase whose proper reaction temperature for primer extension is 70 approximately 80 degrees C. Unexpectedly, the ab initio DNA synthesis was even more efficient at 50 degrees C as compared with that at 70 degrees C. Interestingly, the ab initio DNA synthesis by Vent (exo), a mutant version of Vent DNA polymerase lacking of 3' --> 5' exonuclease activity, became much less efficient, and it could only carry out ab initio DNA synthesis after a long incubation time. This remarkable difference between Vent and Vent (exo) indicates that the exonuclease activity domain of Vent may play an important role at the initiation step of ab initio DNA synthesis.

    DOI: 10.1093/nass/nrm176

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  70. Effective photoregulation of DNA hybridization by the introduction methyl group into azobenzene

    Nishioka H., Kashida H., Komiyama M., Asanuma H.

    Polymer Preprints, Japan   Vol. 55 ( 1 )   2006.10

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    We have synthesized azobenzene-tethered DNA and have successfully photoregulated various DNA functions. In the present study, we synthesized various azobenzenes substituted with methyl group for still more effective photoregulation, as shown in Fig. 1. The melting temperatures of 1a/S 0 duplex are listed in Table 1. When an azobenzene took trans-form, mono-substituted one at ortho position exhibited larger Tm compared with other mono-substituted ones. In contrast, Tm of ortho-substituted azobenzene was the smallest in Tm-form. As a result, change of T m (ΔTm) induced by trans-cis isomerization was as large as 10.6°C, which was 4.9°C higher than previous non-substituted azobenzene (Azo: 5.7°C). Quite interestingly, di-substituted azobenzene at both ortho positions (2,6-Azo) exhibited even larger ΔTm (14.6°C). Thus, we succeeded in the efficient photoregulation of DNA hybridization by the modification of azobenzene at ortho position.

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  71. Preparation of new dye supramolecule by the spontaneous aggregation

    Yamada A., Kashida H., Komiyama M., Asanuma H.

    Polymer Preprints, Japan   Vol. 55 ( 1 )   2006.10

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    In the previous study, we introduced cationic dyes (Naphthyl Reds) and spacers alternately into the middle of 12mer oligonucleotides and prepared dye cluster by using DNA hybridization. The melting temperature (Tm) of this duplex was much higher than native DNA due to electrostatic and stacking interaction. Therefore, there is a possibility of forming dye cluster without the aid of natural bases. In this study, we decreased the number of natural bases at the terminal from 12 to 6 and 2 (see Scheme 1) and investigated the formation of dye cluster. Circular dichroism of 3C/3D and 3G/3G showed very strong symmetrical positive and negative Cotton effect at around 500 nm, suggesting the formation of dye cluster. The melting temperature (Tm) determined from the change of CD at 536 nm of 3C/3D was about 30°C, which almost coincided with the Tm from absorbance change at 260nm. Similarly, melting curve of 3C/3D of CD intensity at 536 nm also showed loose sigmoid, suggesting that 3G/3G also forms dye cluster.

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  72. Preparation of active DNA enzymes by introduction of intercalator

    Hayashi H., Zhao J., Komiyama M., Liang X., Asanuma H.

    Polymer Preprints, Japan   Vol. 55 ( 1 )   2006.10

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    The RNA cleaving 10-23 DNA enzyme, which is expected to be used as an antisense agent to suppress gene activity, shows dependence of activity on the sequence at the active site. We already showed that the cleavage efficiency of 10-23 DNA enzyme with lower activity was improved by attaching an azobenzene residue close to the active site. In this study, we introduced several planar molecules instead of azobenzene as intercalators and checked their activation (Fig. 1). We found that structures of introduced intercalators and linkers greatly influenced the cleavage activity. When anthraquinone was used as the intercalator, catalytic activation was increased more than six folds in comparison with the native DNA enzyme (Table 1). Our finding is helpful for understanding the mechanism of cleavage by DNA enzymes.

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  73. Recognition of bioactive oligopeptide by imprinted cyclodextrin polymer in water

    Sumaoka J., Shirasaka K., Katayama M., Song S., Nagaoka S., Asanuma H., Komiyama M.

    Polymer Preprints, Japan   Vol. 55 ( 1 )   2006.10

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    We prepared molecularly imprinted polymers of β-cyclodextrin using three bioactive oligopeptides as templates; (a) angiotensin I (10-mer), (b) γ-endorphin (17-mer), and (c) leucine-enkephalin (Leu-Enk: 6-mer). With both angiotensin I and Leu-Enk as the templates, highly precise imprinting effects were observed. The present finding strongly indicates that we can prepare artificial antibodies by imprinting of CyD to a conformationally restrained part of a protein.

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  74. Synthesis of peptide nucleic acid conjugated with carbohydrate

    Noguchi A., Yamada Y., Nishida Y., Asanuma H.

    Polymer Preprints, Japan   Vol. 55 ( 1 )   2006.10

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    Peptide nucleic acid (PNA) is composed of non-charged N-2-aminoethylglycine as a scaffold, and thus it strongly hybridizes with natural DNA. But due to its high hydrophobic property, large PNA oligomers prefer to make aggregates rather than form duplex with DNA. Therefore, incorporation of functional molecules such as intercalators is difficult because such modification should raise the hydrophobicity of PNA. In order to modify the PNA without increasing its hydrophobicity, we designed a new monomer involving carbohydrate for the introduction of PNA oligomer. Here, we successfully synthesized a lysine monomer tethering mannose unit according to the Scheme 1. In the present paper, effect of mannose on the stability of PNA/DNA duplex is examined.

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  75. Synthesis of fluorescent DNA probe by use of dye polarization

    Sano K., Tanaka M., Kashida H., Komiyama M., Asanuma H.

    Polymer Preprints, Japan   Vol. 55 ( 1 )   2006.10

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    DNA duplex involves hydrophobic inside in which water molecules are excluded, and its exterior is surrounded with the anions of phosphodiester linkages. Since the inside is not shielded by water molecules, strong electric field is formed by the phosphodiester anion and thus the molecules bound to the duplex should be easily polarized. In the present study, we tethered Dansyl moiety as a fluorophore through amide bond to DNA (Dco in Scheme 1), and fluorescence change by duplex formation was investigated. Single-stranded S showed fluorescence emission at around 550 nm (Blue line in Fig.1). When it was hybridized with native S0, small but distinct decrease in the fluorescence by the phosphodiester anion was observed (Red line). On the contrary, hybridization with M56 (Green line), in which two phosphodiesters nearest to Dansyl moiety are replaced with non-charged methyl phosphonate, slightly increased the fluorescence.

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  76. Stabilization of DNA duplex by introducing intercalators into DNA through D-threoninol

    Kashida H., Komiyama M., Asanuma H.

    Polymer Preprints, Japan   Vol. 55 ( 1 )   2006.10

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    We have introduced various dyes into DNA through D-threoninol and successfully functionalized DNA. However, little has been known on the relationship between the structure of intercalators and the stability of duplex. In this study, various intercalators (1 to 7 as shown in Scheme 1) were incorporated into DNA and the melting temperatures (TmS) of duplexes were measured. As shown in Table 1, azobenzene (1) stabilized duplex strongly compared with native duplex. However, larger molecules (2 and 3) and a smaller molecule (4) did not stabilize duplex. Therefore, molecular size is one of the most significant factors for the duplex stability.

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  77. Importance of the position of vinyl group on β-cyclodextrin for the effective imprinting of amino acid derivatives and oligopeptides in water

    Osawa T., Shirasaka K., Matsui T., Yoshihara S., Akiyama T., Hishiya T., Asanuma H., Komiyama M.

    Macromolecules   Vol. 39 ( 7 ) page: 2460 - 2466   2006.4

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    Two kinds of vinyl monomers of β-cyclodextrin (β-CyD) that tether a vinyl group on either wider rim of the truncated cone or its smaller rim were synthesized and applied to the imprinting toward amino acid derivatives and oligopeptides in water. Mono-3-(N-acrylamido)-β-deoxy-altro-β- cyclodextrin (3-AAm-CyD) showed a remarkable imprinting effect for the enantioselective recognition of protected amino acids such as N-benzyloxycarbonyltyrosine (Z-Tyr). However, the imprinted polymer from mono-6-(N-acrylamido)-6-deoxy-βcyclodextrin (6-AAm-CyD) hardly showed enantioselectivity. According to NOESY analysis on the preorganized β-CyD/Z-Tyr complex in D2O, the aromatic moieties of Z-Tyr were included into the cavity of β-CyD from its wider rim. Since the vinyl group of 3-AAm-CyD protruded toward the template and was polymerized there, the detailed shape of the template was precisely copied on the polymer by the imprinting. In the case of 6-AAm-CyD, however, the shape of template could not be well transcribed because its vinyl group was located at opposite side of the cavity, and thus copolymerization occurred far from the template molecule. On the other hand, the imprinted polymers from both β-CyD vinyl monomers were effective for the recognition of sequences of tetrapeptides composed of two glycines and two phenylalanines, although the selectivity itself was not remarkable. In these polymers, even the β-CyD residues of 6-AAm-CyD were immobilized complementarily to the phenyl rings and bound them. © 2006 American Chemical Society.

    DOI: 10.1021/ma060064f

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  78. Photo- and thermoregulation of DNA nanomachines

    Takahashi K., Yaegashi S., Asanuma H., Hagiya M.

    Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)   Vol. 3892 LNCS   page: 336 - 346   2006

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    We have been investigating DNA state machines, especially those based on the opening of hairpin molecules in which state transitions are realized as hairpin loops are opened by molecules called openers. This paper introduces photo- and thermoregulation of such hairpin-based DNA machines, in which the openers become active by sensing external signals in the form of light or heat. We conducted fluorescence experiments and show that photo- and thermoregulation is possible. In the experiments, the openers become active when they are irradiated by UV light or when they receive heat as external input. For photoregulation, we use azobenzene-bearing oligonucleotides developed by the third author. © Springer-Verlag Berlin Heidelberg 2006.

    DOI: 10.1007/11753681_26

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  79. Functionalization of DMA by using DNA-pyrene conjugates

    Kashida H., Komiyama M., Asanuma H.

    Polymer Preprints, Japan   Vol. 54 ( 2 ) page: 5092 - 5093   2005.12

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    We have successfully introduced functional molecules into DNA and prepared various aggregates by intercalation between base-pairs. Here, we synthesized DNA-pyrene conjugates through D-threoninol and investigated their properties. Excimer emission of pyrene was not observed when two pyrene moieties were intervened by one base-pair. On the other hand, strong excimer emission was observed at around 480 nm with complementary strand which lacks one base. Sequence dependence and linker modification are also investigated.

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  80. Photo- and Thermoregulation of DNA Nanomachines

    浅沼 浩之, 萩谷 昌己

    DNA11, Eleventh International Meeting on DNA Based Computers, Preliminary Proceedings     page: 147 - 156   2005

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  81. バイオナノデバイスとしての人工DNA Reviewed

    浅沼 浩之

    化学と教育 53     page: 12 - 15   2005

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  82. NMR study on the photoresponsive DNA tethering an azobenzene. Assignment of the absolute configuration of two diastereomers and structure determination of their duplexes in the trans-form.

    Liang X, Asanuma H, Kashida H, Takasu A, Sakamoto T, Kawai G, Komiyama M

    Journal of the American Chemical Society   Vol. 125 ( 52 ) page: 16408 - 15   2003.12

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    DOI: 10.1021/ja037248j

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  83. DNA-Naphthyl Red conjugate as a visualizing probe of DNA hybridization.

    Asanuma H, Kashida H, Liang X, Komiyama M

    Chemical communications (Cambridge, England)   ( 13 ) page: 1536 - 7   2003.7

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    DOI: 10.1039/b302875e

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  84. DNA-dye conjugates for controllable H aggregation(1).

    Asanuma H, Shirasuka K, Takarada T, Kashida H, Komiyama M

    Journal of the American Chemical Society   Vol. 125 ( 8 ) page: 2217 - 23   2003.2

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    DOI: 10.1021/ja021153k

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  85. Development of a probe DNA which accompanies color change on hybridization.

    Kashida H, Asanuma H, Komiyama M

    Nucleic acids research. Supplement (2001)   ( 3 ) page: 143 - 4   2003

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    DOI: 10.1093/nass/3.1.143

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  86. Photo-regulation of DNA function by azobenzene-tethered oligonucleotides.

    Asanuma H, Matsunaga D, Liu M, Liang X, Jhao J, Komiyama M

    Nucleic acids research. Supplement (2001)   ( 3 ) page: 117 - 8   2003

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    DOI: 10.1093/nass/3.1.117

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  87. Effective photo-regulation of transcription reaction by SP6 RNA polymerase with modified DNA tethering multiple azobenzenes.

    Liu M, Asanuma H, Komiyama M

    Nucleic acids research. Supplement (2001)   ( 3 ) page: 265 - 6   2003

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    DOI: 10.1093/nass/3.1.265

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  88. Photoregulation of the transcription reaction of T7 RNA polymerase by tethering an azobenzene to the promoter.

    Asanuma H, Tamaru D, Yamazawa A, Liu M, Komiyama M

    Chembiochem : a European journal of chemical biology   Vol. 3 ( 8 ) page: 786 - 9   2002.8

  89. Photoregulation of DNA triplex formation by azobenzene.

    Liang X, Asanuma H, Komiyama M

    Journal of the American Chemical Society   Vol. 124 ( 9 ) page: 1877 - 83   2002.3

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    DOI: 10.1021/ja011988f

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  90. Spectroscopic anatomy of molecular-imprinting of cyclodextrin. Evidence for preferential formation of ordered cyclodextrin assemblies.

    Hishiya T, Asanuma H, Komiyama M

    Journal of the American Chemical Society   Vol. 124 ( 4 ) page: 570 - 5   2002.1

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    DOI: 10.1021/ja011305w

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  91. Photo-regulation of transcription by RNA polymerase with azobenzene-tethered promoter.

    Asanuma H, Liu M, Tamaru D, Liang X, Komiyama M

    Nucleic acids research. Supplement (2001)   ( 2 ) page: 75 - 6   2002

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    DOI: 10.1093/nass/2.1.75

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  92. Enantioselective Incorporation of Azobenzenes into Oligodeoxyribonucleotide for Effective Photoregulation of Duplex Formation This work was partially supported by a Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology, Japan (Molecular Synchronization for Design of New Materials System). The support by the Grant from "Research for the Future" Program of the Japan Society for the Promotion of Science (JSPS-RFTF97I00301) is also acknowledged.

    Asanuma H, Takarada T, Yoshida T, Tamaru D, Liang X, Komiyama M

    Angewandte Chemie (International ed. in English)   Vol. 40 ( 14 ) page: 2671 - 2673   2001.7

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    Language:English  

    PubMed

  93. Enantioselective Incorporation of Azobenzenes into Oligodeoxyribonucleotide for Effective Photoregulation of Duplex Formation.

    Asanuma H, Takarada T, Yoshida T, Tamaru D, Liang X, Komiyama M

    Angewandte Chemie (International ed. in English)   Vol. 40 ( 14 ) page: 2671 - 2673   2001.7

  94. Acceleration of influenza virus clearance by Th1 cells in the nasal site of mice immunized intranasally with adjuvant-combined recombinant nucleoprotein

    Tamura S.I., Miyata K., Matsuo K., Asanuma H., Takahashi H., Nakajima K., Suzuki Y., Aizawa C., Kurata T.

    Journal of Immunology   Vol. 156 ( 10 ) page: 3892 - 3900   1996.5

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    The protective roles of influenza viral nucleoprotein (NP), together with the cellular mechanism of the protection in the nasal site, were examined in BALB/c mice immunized intranasally with an adjuvant (cholera toxin B subunit containing 0.2% of the whole toxin)-combined A or B virus recombinant NP. The NP-immune mice, when challenged intranasally with a sublethal dose of the virus 3 wk after immunization, had accelerated virus clearance from the nasal site in both an influenza type-specific and a nonspecific manner, as shown by the protection from high morbidity from the second day after challenge. Both type-specific and nonspecific acceleration of recovery was confirmed by the increased survival rate after challenge with a lethal dose of virus in mice immunized and boosted with adjuvant-combined NP. The acceleration of nasal virus clearance was accompanied with acceleration of type-specific systemic delayed-type hypersensitivity (DTH) and with IFN-γ production by nasal lymphocytes. The nasal lymphocytes from the immunized and challenged mice generated a significantly high level of DTH when transferred locally, but no class I MHC-restricted CTL response. Moreover, nasal CD4+ T cells, induced by NP immunization and increased in number by the subsequent challenge, were involved in the accelerated IFN-γ production. These results suggest that nasal Th1 cells, capable of producing IFN-γ and mediating DTH, are involved in the type-specific acceleration of recovery from influenza after challenge in mice immunized intranasally with adjuvant-combined NP, although the nonspecific mechanism of accelerated recovery remains to be solved.

    Scopus

  95. Signal Amplification Circuit Composed of Serinol Nucleic Acid for RNA Detection Reviewed

    Chen, Y.; Murayama, K.; Asanuma, H.

    Chemistry Letters   Vol. 51   page: 330 - 333   2022.2

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    Authorship:Last author, Corresponding author   Language:English  

    DOI: 10.1246/cl.210813

  96. Renewable DNA proportional-integral controller with photoresponsive molecules Invited Reviewed

    Tamba, M.; Murayama, K.; Asanuma, H.; Nakakuki, T.

    Micromachines   Vol. 13   page: 193   2022.1

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    DOI: doi.org/10.3390/mi13020193

  97. Unexpected Dissociation of Photoresponsive UV-ON DNA Carrying p-tert-Butyl Azobenzene under UV Light Irradiation Reviewed

    Ishii, S.; Murayama, K.; Sada, K.; Asanuma, H.; Kakugo, A.

    Chemistry Letters   Vol. 51   page: 292 - 295   2022.1

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    Authorship:Corresponding author   Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1246/cl.210788

  98. 光駆動型DNAナノマシン Invited Reviewed

    浅沼浩之, 村山恵司, 神谷由紀子, 樫田 啓

    高分子   Vol. 70   page: 550 - 552   2021.10

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    Authorship:Lead author, Corresponding author   Language:Japanese   Publishing type:Research paper (scientific journal)  

  99. Microheater-integrated zinc oxide nanowire microfluidic device for hybridization-based detection of target single-stranded DNA Reviewed

    Nanotechnology     2021.3

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  100. Development of pre-miRNAs modification with FRET dye pair for intracellular visualization of processing intermediates generated in cells Reviewed

    Kamiya, Y.; Kamimoto, H.; Zhu, H. ; Asanuma, H.

    Sensors   Vol. 21   page: 1785   2021.3

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    DOI: doi.org/10.3390/s21051785

  101. Pyrene modified serinol nucleic acid nanostructure converts chirality of threoninol nucleic acids into circularly polarized luminescence signals Invited Reviewed

    Kashida, H.; Nishikawa, K.; Ito Y.; Murayama, K.; Hayashi, I.; Kakuta, T.; Ogoshi, T.; Asanuma, H.

        2021.1

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1002/chem.202102333

  102. Microheater-integrated zinc oxide nanowire microfluidic device for hybridization-based detection of target single-stranded DNA Reviewed

    Takahashi, H.; Yasui, T.; Kashida, H.; Makino, K.; Shinjo, K.; Liu, Q.; Shimada, T.; Rahong, S.; Kaji, N.; Asanuma, H.; Baba, Y.

    Nanotechnology   Vol. 32   page: 255301   2021

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1088/1361-6528/abef2c

  103. 核酸医薬の創製に向けた人工核酸の開発 Invited Reviewed

    樫田啓、村山恵司、浅沼浩之

    バイオマテリアル   Vol. 38 ( 2 ) page: 124 - 129   2020.4

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  104. The Use of Serinol Nucleic Acids as Ultrasensitive Molecular Beacons Invited Reviewed

    Murayama Keiji, Kashida Hiromu, Asanuma Hiroyuki

    NON-NATURAL NUCLEIC ACIDS: METHODS AND PROTOCOLS   Vol. 1973   page: 261-279   2019

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    Authorship:Last author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1007/978-1-4939-9216-4_17

    Web of Science

  105. Development of Visible-Light-Responsive RNA Scissors Based on a 10-23 DNAzyme Reviewed

    Kamiya Yukiko, Arimura Yu, Ooi Hideaki, Kato Kenjiro, Liang Xing-Guo, Asanuma Hiroyuki

    CHEMBIOCHEM   Vol. 19 ( 12 ) page: 1305 - 1311   2018.6

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    DOI: 10.1002/cbic.201800020

    Web of Science

  106. DNA Microcapsule for Photo-Triggered Drug Release Systems

    Kamiya Yukiko, Yamada Yoshinobu, Muro Takahiro, Matsuura Kazunori, Asanuma Hiroyuki

    CHEMMEDCHEM   Vol. 12 ( 24 ) page: 2016-2021   2017.12

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1002/cmdc.201700512

    Web of Science

  107. Introduction of 2,6-Diaminopurines into Serinol Nucleic Acid Improves Anti-miRNA Performance Reviewed

    Kamiya Yukiko, Donoshita Yuka, Kamimoto Hiroshi, Murayama Keiji, Ariyoshi Jumpei, Asanuma Hiroyuki

    CHEMBIOCHEM   Vol. 18 ( 19 ) page: 1917-1922   2017.10

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    DOI: 10.1002/cbic.201700272

    Web of Science

  108. Chaperone-Polymer-Assisted, Photodriven DNA Strand Displacement

    Cheng Bohao, Kashida Hiromu, Shimada Naohiko, Maruyama Atsushi, Asanuma Hiroyuki

    CHEMBIOCHEM   Vol. 18 ( 16 ) page: 1568-1572   2017.8

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    DOI: 10.1002/cbic.201700202

    Web of Science

  109. D-aTNA Circuit Orthogonal to DNA Can Be Operated by RNA Input via SNA

    Murayama Keiji, Nagao Ryuya, Asanuma Hiroyuki

    CHEMISTRYSELECT   Vol. 2 ( 20 ) page: 5624-5627   2017.7

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1002/slct.201701126

    Web of Science

  110. Antisense oligonucleotide modified with serinol nucleic acid (SNA) induces exon skipping in mdx myotubes Reviewed

    Le, B. T.; Murayama, K.; Shabanpoor, F.; Asanuma, H.; Veedu, R. N.

    RSC Advances   Vol. 7   page: 34049-34052   2017.7

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: DOI: 10.1039/c7ra06091b

  111. 光応答性DNAの開発―ナノ環境を汚染しない分子マシンへの応用― Invited

    浅沼浩之

    現代化学   Vol. 556 ( 7 ) page: 50-55   2017.7

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  112. DNA二重鎖の高い安定性と直交性をもつ疑似塩基対の開発 Invited Reviewed

    樫田啓、浅沼浩之

    高分子論文集   Vol. 74 ( 4 ) page: 257-264   2017.7

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  113. Orientation-dependent FRET system reveals differences in structures and flexibilities of nicked and gapped DNA duplexes

    Kashida Hiromu, Kurihara Ayako, Kawai Hayato, Asanuma Hiroyuki

    NUCLEIC ACIDS RESEARCH   Vol. 45 ( 11 )   2017.6

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    DOI: 10.1093/nar/gkx200

    Web of Science

  114. Development of pseudo base-pairs on D-threoninol which exhibit various functions Invited Reviewed

    Kashida, H.; Asanuma, H.

    Bull. Chem. Soc. Jpn.   Vol. 90   page: 475   2017.5

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  115. Design of photo-functional oligonucleotide by "copolymerization" of natural nucleobases with base-surrogate prepared from acyclic scaffold Invited Reviewed

    Asanuma, H.; Murayama, K.; Kamiya, Y.; Kashida, H.

    Polymer J.   Vol. 49   page: 279-289   2017.3

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    Authorship:Lead author   Language:English  

    DOI: doi:10.1038/pj.2016.120

  116. DNA二重鎖による色素会合体の精密位置配向制御と光化学への展開 Invited Reviewed

    浅沼浩之、樫田啓

    固体物理   Vol. 52 ( 3 ) page: 149-158   2017.3

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  117. Effect of Methyl Group on Acyclic Serinol Scaffold for Tethering Dyes on the DNA Duplex Stability

    Murayama Keiji, Asanuma Hiroyuki

    CHEMBIOCHEM   Vol. 18 ( 1 ) page: 142-149   2017.1

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1002/cbic.201600558

    Web of Science

  118. Orientation-dependent FRET system reveals differences in structures and flexibilities of nicked and gapped DNA duplexes Reviewed

    Kashida, H.; Kurihara, A.; Kawai, H.; Asanuma, H.

    Nucleic Acids Res.   Vol. 45 ( 11 ) page: e105   2017

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  119. Development of Pseudo Base Pairs Which Show High DNA Duplex Stabilities and Orthogonality

    KASHIDA Hiromu, ASANUMA Hiroyuki

    KOBUNSHI RONBUNSHU   Vol. 74 ( 4 ) page: 257 - 264   2017

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    Language:Japanese   Publishing type:Research paper (scientific journal)   Publisher:The Society of Polymer Science, Japan  

    Natural nucleobases of DNA exhibit high duplex stability and high orthogonality, which are attractive from chemical viewpoints. If artificial base pairs are developed, it would be possible to develop novel functional materials. We have developed pseudo base pairs by incorporating non-natural molecules into DNA through <small>D</small>-threoninol. Although our pseudo bases are much different from natural nucleobases, they show high duplex stability and high orthogonality similarly to the natural ones. In this paper, we summarize our recent work on pseudo base pairs, focusing on the stability of DNA duplexes containing pseudo base pairs.

    DOI: 10.1295/koron.2017-0009

    Web of Science

    Scopus

  120. 天然に存在しない非環状構造の核酸アナログ-人工の非環状骨格で神の設計した環状骨格に挑む Invited

    村山恵司、浅沼浩之

    化学   Vol. 71 ( 3 ) page: 66-67   2016

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  121. Acyclic artificial nucleic acids with phosphodiester bonds exhibit unique functions Invited Reviewed

    H. Kashida, K. Murayama, H. Asanuma

    Polymer J.   Vol. 48   page: 781-786   2016

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  122. A stem-less probe using spontaneous pairing between Cy3 and quencher for RNA detection Invited Reviewed

    Kashida, H., Morimoto, K., Asanuma, H.

    Sci. Technol. Adv. Mater.   Vol. 17   page: 267-273   2016

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  123. Faint electric treatment-induced rapid endosomal escape for efficient delivery of functional macromolecules into the cytoplasm Reviewed

    Hasan, M., Nishimoto, A., Ohgita, T., Hama, S., Kashida, H., Asanuma, H., Kogure, K.

    J. Control. Release   Vol. 228   page: 20-25   2016

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  124. Visible Light-Triggered Crosslinking of DNA Duplex by Reversible [2+2] Photocycloaddition of Styrylpyrene Reviewed

    Doi, T., Kawai, H., Murayama, K., Kashida, H., Asanuma, H.

    Chem. Eur. J.     page: 0000-0000   2016

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    DOI: 0000-0000

  125. Strand-invading linear probe combined with unmodified PNA Reviewed

    Aasanuma, H., Niwa, R., Akahane, M., Murayama, K., Kashida, H., Kamiya, Y.

    Bioorg. Med. Chem.     2016

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    DOI: DOI:10.1016/j.bmc.2016.06.055

  126. Dynamics of Inter-DNA Chain Interaction of Photoresponsive DNA Reviewed

    Nakasone, Y., Ooi, H., Kamiya, Y., Asanuma, H., Terazima, M.

    J. Am. Chem. Soc.     page: 0000-0000   2016

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  127. 新規人工核酸SNAを用いたRNAイメージング Invited

    樫田 啓、村山恵司、浅沼浩之

    生体の科学   Vol. 66 ( 2 ) page: 145-150   2015

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  128. Reversible photo-switching of DNA fuction with azobenzene-tethered DNA Invited

    Y. Kamiya, H. Asanuma

    The Glen Report   Vol. 27   page: 1-3   2015

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  129. Pre-organized guide RNA in Cas9 complex is ready for selection of the target double-stranded DNA Invited Reviewed

    Y. Kamiya, H. Asanuma

    ChemBioChem   Vol. 16   page: 2273-2275   2015

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  130. Terminus-free siRNA prepared by photo-crosslinking activated via slicing by Ago2 Reviewed

    Y. Kamiya, K. Iishiba,T. Doi, K. Tsuda, H. Kashida, H. Asanuma,

    Biomater. Sci.   Vol. 3   page: 1534-1538   2015

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  131. Azobenzene C-nucleosides for photo-controlled hybridization of DNA at room temperature Reviewed

    T. Goldau, K. Murayama, C. Brieke, H. Asanuma, A. Heckel

    Chem. Eur. J.   Vol. 21   page: 17870-17876   2015

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    DOI: DOI: 10.1002/chem.201503303

  132. Hetero-Selective DNA-like Duplex Stabilized by Donor-Acceptor Interaction Reviewed

    T. Doi, T. Sakakibara,H. Kashida, Y. Araki, T. Wada, H. Asanuma

    Chem. Eur. J.   Vol. 21   page: 15974-15980   2015

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    DOI: DOI: 10.1002/chem.201502653

  133. Ultra-Sensitive Molecular Beacon Designed with Totally Serinol Nucleic Acid (SNA) for Monitoring mRNA in Cell Invited Reviewed

    K. Murayama, Y. Kamiya, H. Kashida, H. Asanuma

    ChemBioChem   Vol. 16   page: 1298-1301   2015

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    DOI: DOI: 10.1002/cbic.201500167

  134. Molecular design of Cy3 derivative for highly sensitive in-stem molecular beacon and its application to the wash-free FISH Reviewed

    H. Kashida, T. Osawa, K. Morimoto, Y. Kamiya, H. Asanuma

    Bioorg. Med. Chem.   Vol. 23   page: 1758-1762   2015

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  135. Efficiency of [2+2] photodimerization of various stilbene derivatives within the DNA duplex scaffold Reviewed

    T. Doi, H. Kashida, H. Asanuma

    Org. Biomol. Chem.   Vol. 13   page: 4430-4437   2015

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  136. Highly sensitive and robust linear probe for detection of mRNA in cells Reviewed

    H. Asanuma, M. Akahane, R. Niwa, H. Kashida, Y. Kamiya

    Angew. Chem. Int. Ed.   Vol. 54   page: 4315-4319   2015

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  137. Acyclic L-Threoninol Nucleic Acid (L-aTNA) with Suitable Structural Rigidity Cross-pairs with DNA and RNA Reviewed

    K. Murayama, H. Kashida, H. Asanuma,

    Chem. Commun.   Vol. 51   page: 6500-6503   2015

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  138. Reversible photoswitching of RNA hybridization at room temperature with an azobenzene C-nucleoside Reviewed

    T. Goldau, K. Murayama, C. Brieke, S. Steinwand, P. Mondal, M. Biswas, I. Burghardt, J. Wachtveitl, H. Asanuma, A. Heckel

    Chem. Eur. J.   Vol. 21   page: 2845-2854   2015

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  139. Synthetic gene involving azobenzene-tethered T7 promoter for the photocontrol of gene expression by visible light Reviewed

    Y. Kamiya, T. Takagi, H. Ooi, H. Ito, X.G. Liang, H. Asanuma,

    ACS Synth. Biol.   Vol. 4   page: 365-370   2015

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  140. Orientation-dependent FRET by use of DNA duplex as a scaffold Invited

    Hiroyuki Asanuma, Ayako Kurihara, Hiromu Kashida

    Photochemistry   Vol. 45   page: 146-147   2014.12

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  141. De Novo Design of Functional Oligonucleotides with Acyclic Scaffolds Invited Reviewed

    Asanuma, H.; Kashida, H.; Kamiya, Y.

    Chem. Rec.     2014

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    DOI: DOI:10.1002/tcr.201402040

  142. Light-driven DNA nanomachine with a photoresponsive molecular engine Invited Reviewed

    Kamiya, Y.; Asanuma, H.

    Accounts of Chemical Research   Vol. 47   page: 1663-1672   2014

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  143. Enhancement of stability and activity of siRNA by terminal substitution with Serinol Nucleic Acid (SNA) Reviewed

    Y. Kamiya, J. Takai, H. Ito, K. Murayama, H. Kashida, H. Asanuma.

    ChemBioChem   Vol. 15   page: 2549-2555   2014

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  144. Highly specific DNA detection from massive background nucleic acids based on rolling circle amplification of target dsDNA Reviewed

    X. Wang, X. Yu, X. Wand, M. Suzuki, H. Asanuma, P. Dong, W. Wu, X.G. Liang,

    RSC Adv.   Vol. 4   page: 38293-38299   2014

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  145. Selective labeling of mature RISC using siRNA carrying fluorophore-quencher pair Reviewed

    Kamiya, Y.; Ito, A.; Ito, H.; Urushihara, M.; Takai, J.; Fujii, T.; Liang, X.G.; Kashida, H.; Asanuma, H.

    Chem. Sci.     2013

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    DOI: DOI:10.1039/C3SC51197A

  146. A "sugar-deficient" G-quadruplex: incorporation of aTNA in G4 structures Reviewed

    Zhou, J.; Murayama, K.; Amrane, S.; Kashida, H.; Bourdoncle, A.; Asanuma, H.; Mergny, J. L.

    Chem. Sci.   Vol. 4   page: 3693-3698   2013

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  147. Highly stable duplex formation by artificial nucleic acids aTNA and SNA with acyclic scaffolds Reviewed

    Murayama, K.; Tanaka, Y.; Toda, T.; Kashida, H.; Asanuma, H.

    Chem. Eur. J.     2013

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    DOI: 10.1002/chem.201301578

  148. p-Stilbazole moieties as artificial base pairs for photocrosslinking of DNA duplex Reviewed

    Kashida, H.; Doi, T.; Sakakibara, T.; Hayashi, T.; Asanuma, H.

    J. Am. Chem. Soc.   Vol. 135   page: 7960-7966   2013

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  149. Evaluation of intrinsic spectroscopic properties of chromophore assemblies by shielding with cyclohexyl base pairs within a DNA duplex Reviewed

    Kashida, H.; Higashiyama, N.; Kato, T.; Asanuma, H.

    Bioorg. Med. Chem.     2013

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    DOI: 10.1016/j.bmc.2013.04.032

  150. Photoswitch nucleic acid catalytic activity by regulating topological structure with a universal supra-photoswitch Reviewed

    Liang, X.G.; Zhou, M.G.; Kato, K.; Asanuma, H.

    ACS Synth. Biol   Vol. 2   page: 194-202   2013

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  151. Development of a robust model system of FRET using base-surrogates tethering fluorophores for strict control of their position and orientation within DNA duplex Reviewed

    Kato, T.; Kashida, H.; Kishida, H.; Yada, H.; Okamoto, H.; Asanuma, H.

    J. Am. Chem. Soc.   Vol. 135   page: 741-750   2013

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  152. Polycation-chaperoned in-stem molecular beacon system Reviewed

    Asanuma, H.; Osawa, T.; Kashida, H.; Fujii, T.; Liang, X. G.; Niwa, K.; Yoshida, Y.; Shimada, N.; Maruyama, A

    Chem. Commun.   Vol. 48   page: 1760-1762   2012

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  153. Quencher-free linear probe with multiple fluorophores on acyclic scaffold Reviewed

    Asanuma, H.; Akahane, M.; Kondo, N.; Osawa, T.; Kato, T.; Kashida, H.

    Chem. Sci.     page: in press   2012

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  154. Reversed assembling of dyes in RNA duplex compared with those in DNA Reviewed

    Fujii, T.; Urushihara, M.; Kashida, H.; Ito, H.; Liang, X.G.; Yagi-Utsumi, M.; Kato, K.; Asanuma, H.

    Chem. Eur. J.     page: in press   2012

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  155. Bulge-like asymmetric hetero dye-clustering in DNA duplex results in efficient quenching of background emission based on the maximized excitonic interaction Reviewed

    Fujii, T.; Hara, Y.; Osawa, T.; Kashida, H.; Liang, X.G.; Yoshida, Y.; Asanuma, H.

    Chem. Eur. J.     page: in press   2012

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  156. Quencher-free molecular beacon tethering 7-hydroxycoumarin detects targets through protonation/deprotonation Reviewed

    Kashida, H.; Yamaguchi K.; Hara, Y.; Asanuma, H.

    Bioorg. Med. Chem.   Vol. 20   page: 4310-4315   2012

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  157. Coherent Interactions of Dyes Assembled on DNA Invited Reviewed

    Asanuma, H.; Fujii, T.; Kato, T.; Kashida, H.

    J. Photochem. Photobiol. C   Vol. 13   page: 1065-1084   2012

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  158. Preparation of supramolecular chromophoric assemblies using a DNA duplex Invited Reviewed

    Kashida, H.; Asanuma, H.

    Phys. Chem. Chem. Phys.   Vol. 14   page: 7196-7204   2012

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  159. Design of an Artificial Functional Nanomaterial with High Recognition Ability Invited Reviewed

    Liang, X. G.; Mochizuki, T.; Fujii, T.; Kashida, H.; Asanuma, H.

    Natural Computing   Vol. 11   page: 231-238   2012

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  160. A model of elongation of short DNA sequence by thermophilic DNA polymerase under isothermal conditions Reviewed

    Kato, T.; Liang, X. G.; Asanuma, H.

    Biochemistry   Vol. 51   page: 7846-7853   2012

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  161. Preparation of photoresponsive DNA tethering ortho-methylated azobenzene as a supraphotoswitch Invited Reviewed

    Asanuma, H.; Nishioka, H.; Ishikawa, T.; Liang, X. G.

    Current Protocols in Nucleic Acid Chemistry     page: accepted   2011.9

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  162. Detection of three-base deletion by exciplex formation with perylene derivatives Reviewed

    Kashida, H.; Kondo, N.; Sekiguchi, K.; Asanuma, H.

    Chem. Commun.     page: accepted   2011.7

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  163. Control of the Chirality and Helicity of Oligomers of Serinol Nucleic Acid (SNA) by Sequence Design Reviewed

    Kashida, H.; Murayama, K.; Toda, T.; Asanuma, H.

    Angew. Chem. Int. Ed.,   Vol. 50   page: 1285-1288   2011.3

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  164. Cationic dye-triplet as unique "glue" that can connect full-matched termini of the duplexes Reviewed

    Kashida, H.; Hayashi, T.; Fujii, T.; Asanuma, H.

    Chem. Eur. J.   Vol. 17   page: 2614-2622   2011.2

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  165. Improvement of RNAi activity and strand-selectivity of RISC formation by modified siRNA involving intercalators near 5'-termini Reviewed

    Hiroshi Ito, Masaaki Urushihara, Xingguo Liang, Hiroyuki Asanuma

    ChemBioChem     page: ***-***   2011

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  166. Photon-fueled DNA nanodevice carrying two different photoswitches Reviewed

    Hidenori Nishioka, Xingguo Liang, Tomohiro Kato, Hiroyuki Asanuma

    Angew. Chem. Int. Ed.     page: ***-***   2011

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  167. Cyclohexyl "base pairs" stabilize duplexes and intensify pyrene fluorescence by shielding it from natural base pairs Reviewed

    Kashida, H.; Sekiguchi, K.; Higashiyama, N.; Kato, T.; Asanuma, H.

    Org. Biomol. Chem.     page: ***-***   2011

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  168. Ultrafast photoisomerization and its single-shot pump pulse efficiency of trans-azobenzene derivative: Compound for photosensitive DNA Reviewed

    T. Chen, A. Yamaguchi, K. Igarashi, N. Nakagawa, H. Nishioka, H. Asanuma, M. Yamashita

    Opt. Commun.     2011

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    DOI: 10.1016/j.optcom.2011.10.032

  169. Femtosecond photoisomerization of azobenzene-derivative binding to DNA Reviewed

    T. Chen, K. Igarashi, N. Nakagawa, K. Yamane, T. Fujii, H. Asanuma, M. Yamashita

    J. Photochem. Photobiol. A   Vol. 223   page: 119-123   2011

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  170. Nick Sealing by T4 DNA Ligase on a Modified DNA Template Tethering a Functional Molecule on D-Threoninol Reviewed

    Liang Xingguo, Kenta Fujioka, Hiroyuki Asanuma

    Chem. Eur. J.   Vol. 17   page: 10388-10396   2011

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  171. An interstrand-wedged duplex composed of alternating DNA base pairs and covalently attached intercalators Reviewed

    Liang, X.G.; Nishioka H.; Mochizuki, T.; Asanuma, H.

    J. Mater. Chem.   Vol. 20   page: 575-581   2010.1

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    An interstrand-wedged duplex involving alternating base pairs and covalently attached intercalators via D-threoninols was constructed. In this novel duplex structure, natural DNA base pairs and artificially introduced planar molecules such as azobenzene derivatives are lined up one by one. Although each base pair is sandwiched by two intercalators and vice versa, the duplex is extremely stable compared with the corresponding native DNA duplex.

  172. An efficient FRET between pyrene and perylene assembled in a DNA duplex and its potential for discriminating single base changes Reviewed

    Kashida, H.; Takatsu,T.; Sekiguchi, K.; H. Asanuma

    Chem. Eur. J.   Vol. 16   page: 2479-2486   2010

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    In order to increase the apparent Stokes' shift of perylene, pyrene (donor) and perylene (acceptor) were assembled in a DNA duplex to achieve the efficient fluorescence resonance energy transfer (FRET) from pyrene to perylene. Multiple donors were introduced in the vicinity of acceptors via D-threoninol and natural base pairs were inserted between the dyes. Accordingly, donors and acceptors could be accumulated inside the DNA without forming undesired excimer/exciplex. When two pyrene moieties were located in proximity to one perylene with one base pair inserted between them, efficient FRET occurred within the duplex. Thus, strong emission at 460 nm was observed from perylene when excited at 345 nm where pyrene has its absorption. The apparent Stokes' shift became as large as 115 nm with a high apparent FRET efficiency.

  173. Construction of photoresponsive RNA for photoswitching RNA hybridization Reviewed

    Ito, H.; Liang, X.G.; Nishioka, H.; Asanuma, H.

    Org. Biomol. Chem.     page: in press   2010

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  174. Robust and photo-controllable DNA capsules using azobenzenes Reviewed

    Tanaka, F.; Mochizuki, T.; Liang, X.G.; Asanuma, H.; Tanaka, S.; Suzuki, K.; Kitamura, S.; Nishikawa, A.; Ui-Tei, K.; Hagiya, M

    Nano Lett.   Vol. 10   page: 3560-3565   2010

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  175. Unexpectedly stable artificial duplex from flexible acyclic threoninol. Reviewed

    Asanuma, H.; Toda, T.; Murayama, K.; Liang, X.G.; Kashida, H.

    J. Am. Chem. Soc.   Vol. 132   page: 14702-14703   2010

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  176. Insulator base pairs for lighting-up perylenediimide in a DNA duplex Reviewed

    Hiromu Kashida,Koji Sekiguchi,and Hiroyuki Asanuma

    Chem. Eur. J.   Vol. 16   page: 11554-11557   2010

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    Perylenediimide (PDI) is highly quenched by nucleobases, which greatly restricts its application as a fluorescent probe. Here, we propose “insulator base pairs" tethering cyclohexane ring through D-threoninol. When “insulator base pairs" were inserted between PDI and nucleobases, the quantum yield of PDI drastically increased several thousand-fold. The “insulator base pairs" reported here also have the potential to increase the quantum yields of other fluorophores.

  177. Coherent Quenching of a Fluorophore for the Design of a Highly Sensitive In-Stem Molecular Beacon. Reviewed

    Yuichi Hara, Taiga Fujii, Hiromu Kashida, Koji Sekiguchi, Xingguo Liang, Kosuke Niwa, Tomokazu Takase, Yasuko Yoshida, and Hiroyuki Asanuma

    Angew. Chem. Int. Ed.   Vol. 49   page: 5502-5506   2010

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    Excitonic interaction (coherency) was utilized to design a highly sensitive In-Stem molecular beacon (ISMB) in which both a fluorophore and a quencher on D-threoninols are incorporated into the stem region as a pseudo “base-pair". A systematic study indicated that minimization of the difference of &#61548;max between the fluorophore and the quencher maximized quenching efficiency due to maximization of coherency. A highly sensitive ISMB could be prepared using the excitonically optimized pair of Cy3 and modified Methyl Red.

  178. Accumulation of fluorophores into DNA duplexes to mimic the properties of quantum dots Reviewed

    Hiromu Kashida, Koji Sekiguchi, Xingguo Liang, Hiroyuki Asanuma

    J. Am. Chem. Soc.   Vol. 132   page: 6223-6230   2010

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    By using perylene and pyrene as fluorophores, we have designed various fluorophore assemblies that mimic inorganic quantum dots in showing a high emission intensity, a large Stokes' shift, and a modulated emission maximum. For this purpose, we utilized two kinds of duplex motifs with D-threoninols as scaffolds: cluster and interstrand-wedged motifs. In the cluster motif, fluorophores are introduced into both strands to produce tentative pseudo-“base-pairs", in which the dyes strongly interact with each other and form dimers, trimers or hexamers. In the interstrand-wedged motif, a base-pair is inserted between the fluorophores to suppress their direct interaction. These two motifs were applied to accumulate dyes within a DNA duplex depending on their emission properties. Since pyrene exhibits strong excimer emission, the emission at 500 nm of a pyrene cluster motif strongly increased as the number of accumulated dyes increased, whereas interstrand-wedged motif quenched pyrene monomer emission. In contrast, assembled perylenes, which are mostly quenched by dimerization, showed intense monomer emission in the interstrand-wedged motif whereas perylene cluster motifs strongly suppressed perylene emission. These two motifs were then applied to the hetero-assembly of pyrenes and perylenes. Both a large Stokes' shift and a modulation of the emission maximum, which are also characteristics of inorganic quantum dots, were successfully realized using fluorescent resonance energy transfer (FRET) and exciplex formation. These fluorophore assemblies thus obtained could be enzymatically ligated to longer DNA, demonstrating that this technique has the potential to be a versatile labeling agent for biomolecules.

  179. *Photoregulation of DNA transcription by using photoresponsive T7 promoter and clarification of its mechanism Reviewed

    Xingguo Lianga, Ryuji Wakuta, Kenta Fujioka, Hiroyuki Asanuma

    FEBS Journal   Vol. 277   page: 1551-1561   2010

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    Using photoresponsive T7 promoters tethering two 2&#61602;-methylazobenzenes or 2&#61602;,6&#61602;-dimethylazobenzenes, highly efficient photoregulation of DNA transcription was attained. Under UV-A irradiation (320-400 nm), the rate of transcription with T7 RNA polymerase and a photoresponsive promoter involving two 2&#61602;,6&#61602;-dimethylazobenzenes was 10-fold faster than that after visible light irradiation (400-600 nm). By attaching a non-modified azobenzene (Azo) and 2&#61602;,6&#61602;-dimethylazobenzene (DM-azo) at the two positions, respectively, and by utilizing the different cis-to-trans thermal stability between cis Azo and cis DM-azo, four species of T7 promoter (cis-cis, trans-cis, cis-trans, and trans-trans) were obtained. The four species showed transcriptional activity in the order of cis-cis > cis-trans > trans-cis > trans-trans. Kinetic analysis revealed that the Km for the cis-cis promoter (both of the introduced azobenzene derivatives were in the cis form) and T7 RNA polymerase was 68 times larger than that of the trans-trans form, indicating that high photoregulatory efficiency was mainly due to a remarkable difference in affinity with RNA polymerase. The present approach is promising for the creation of biological tools for artificially controlling gene expression, and as a photo-controlled system for supplying RNA fuel for RNA-powered molecular nanomachines.

  180. *A light-driven DNA nanomachine for efficiently photoswitching RNA digestion Reviewed

    Zhou M.G.; Liang, X.G.; Mochizuki, T.; Asanuma, H.

    Angew. Chem. Int. Ed.   Vol. 49   page: 2167-2170   2010

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    A machine-like photoresponsive DNA enzyme was constructed that can work for us at a single molecule level. The complete ON-OFF photoswitching of RNA digestion was realized by photoregulating the topological structure of DNAzyme/RNA complex. The interstrand-wedged duplex was used as the supra-photoswitch.

  181. Effect of the ortho modification of azobenzene on the photoregulatory efficiency of DNA hybridization and thermal stability of its cis-form Reviewed

    Nishioka H.; Liang, X.G.; Asanuma, H.

    Chem. Eur. J.   Vol. 16   page: 2054-2062   2010

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    We synthesized various azobenzenes methylated at their ortho-positions with respect to the azo bond for more effective photoregulation of DNA hybridization. Photoregulatory efficiency, evaluated from the change of Tm (&#61508;Tm) induced by trans-cis isom-erization, was significantly improved for all ortho-modified azobenzenes compared with non-modified azoben-zene due to the more stabilized trans-form and more destabilized cis-form. Among the synthesized azobenzenes, 4-carboxy-2&#61602;,6&#61602;-dimethylazobenzene (2&#61602;,6&#61602;-Me-Azo), in which two ortho-positions of the distal benzene ring with respect to carboxyl group were methy-lated, exhibited the largest &#61508;Tm, whereas newly synthesized 2,6-Me-Azo (4-carboxy-2,6-dimethylazobenzene), which possesses two methyl groups on the two ortho-positions of the other benzene ring, showed moderate im-provement of &#61508;Tm.

  182. Line up base pairs and intercalators one by one in a stable duplex

    Liang, X.G.; Mochizuki T.; Nishioka H.; Asanuma, H.

    Nucleic Acids Symp. Ser.   Vol. 53   page: 189-190   2009.11

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    A stable double helix involving alternating base pairs and azobenzene moieties was constructed. In this supramolecule, base pairs and azobenzenes are lined up one by one to form an interstrand-wedged motif: each base pair is sandwiched with two azobenzenes, and each azobenzene intercalates between two base pairs. This motif was formed by the hybridization of two modified DNA tethering multiple azobenzene moieties at a frequency of one azobenzene for every two nucleotides. Furthermore, this structure could be simply dismantled by UV light irradiation and reformed with the irradiation of visible light. By using this new duplex motif, construction of a variety of photoresponsive nanostructures and nanodevices is highly expected.

  183. Efficient energy transfer from pyrene to perylene assembled inside DNA duplex

    Kashida, H.; Takatsu, T.; Asanuma, H.

    Nucleic Acids Symp. Ser.,   Vol. 53   page: 29-30   2009.11

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    Pyrene (donor) and perylene (acceptor) were assembled in a DNA duplex to increase the apparent Stokes' shift of perylene. Plural Multiple donors were introduced in the vicinity of acceptors via D-threoninol and natural base pairs were inserted between donors and acceptors in order to suppress undesired interactions between them. When two pyrene moieties were located in proximity to one perylene with one base pair inserted between them, efficient FRET occurred within the duplex. Thus, strong emission at 495 nm was observed from perylene when excited at 345 nm where pyrene has its absorption. The apparent Stokes' shift became as large as 115 nm with a high FRET efficiency (&#61510;>1). However, the introduction of more than two pyrenes did not enhance the fluorescence intensity of perylene, due to the short F&ouml;rster radius (R0) of the donor pyrene.

  184. *Analysis of Coherent Heteroclustering of Different Dyes by Use of Threoninol-Nucleotides for Comparison with the Molecular Exciton Theory Reviewed

    Taiga Fujii, Hiromu Kashida, Hiroyuki Asanuma

    Chem. Eur. J.   Vol. 15   page: 10092-10102   2009.10

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    To test the molecular exciton theory for heterodimeric chromophores, various heterodimers and clusters, in which two different dyes were stacked alternately, were prepared by hybridizing two oligodeoxyribo-nucleotides (ODNs), each of which tethered a different dye on D-threoninol at the center of the strand. NMR analyses revealed that two different dyes from each strand were stacked antiparallel to each other in the duplex, and were located adjacent to the 5'-side of a natural nucleobase. Spectroscopic behaviors of these heterodimers were systematically examined as a function of the difference in the wavelength of the dye absorption maxima (&#61508;&#61548;max). We found that the absorption spectrum of the heterodimer was significantly different from that of the simple sum of each monomeric dye in the single-strand. When azobenzene and Methyl Red, which have &#61548;max at 336 nm and 480 nm in the single-strand, respectively, (&#61508;&#61548;max = 144 nm), were assembled on ODNs, the band derived from azobenzene exhibited a small hyperchromism whereas the band from Methyl Red showed hypochromism and both bands shifted to a longer wavelength (bathochromism). These hyper- and hypochromisms were further enhanced in a heterodimer derived from 4'-methylthioazobenzene and Methyl Red that had a much smaller &#61508;&#61548;max (82 nm) (&#61548;max = 398 and 480 nm in the single-strand, respectively). With a combination of 4'-dimethylamino-2-nitroazobenzene and Methyl Red, which had an even smaller &#61508;&#61548;max (33 nm), a single sharp absorption band that was apparently different from the sum of the single-stranded spectra was observed. These changes in the intensity of the absorption band could be explained by the molecular exciton theory that has been mainly applied to the spectral behavior of H- and/or J-aggregates composed of homo dyes. However, the bathochromic band shifts observed at shorter wavelengths did not agree with the hypsochromism predicted by the

  185. *In-Stem Molecular Beacon containing a Pseudo Base Pair of Threoninol Nucleotides for Removal of Background Emission Reviewed

    Hiromu Kashida, Tomohiko Takatsu, Taiga Fujii, Koji Sekiguchi, Xingguo Liang, Kosuke Niwa, Tomokazu Takase, Yasuko Yoshida, and Hiroyuki Asanuma

    Angew. Chem. Int. Ed.   Vol. 48   page: 7044-7047   2009.9

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    An in-stem molecular beacon (IS-MB), which tethers perylene and anthraquinone in the stem region via D-threoninol, effectively detected target sequences. This design of IS-MB is also applicable to the discrimination of a one-base deletion mutant from wild type (full-match) without background emission.

  186. Photoisomerization dynamics study on cis-azobenzene derivative using ultraviolet-to-visible tunable femtosecond pulses Reviewed

    Yamaguchi, N.; Nagasawa, N.; Igarashi, K.; Sekikawa, T.; Asanuma, H.; Yamashita, M.

    Appl. Surf. Sci.   Vol. 255   page: 9864-9868   2009.7

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    We performed the transient absorption measurement and the first rate equation (RE) analysis for cis isomer of 4-carboxy-20,60-dimethylazobenzene to clarify the quantitative difference between the photoisomerization process and the thermal relaxation process from the SC
    1 excited state. The RE analysis enabled us to determine the cis-to-trans photoisomerization rate per each pump pulse to be 3% under the condition of the 430 nm, 150 fs pump pulse with energy of 200 nJ. Moreover, the signal due to the yielded trans molecules appearing in the transient absorption was assigned from the following observed result: the transient absorbance change at the 380 nm probe mostly decreased within 300 fs after the 430 nm pulse pumping and then slowly decreased to zero, while the absorbance change at the 350 nm probe had a positive constant component in the over one picosecond time region. The RE analysis showed
    that this constant component is due to the yielded transmolecules, and its positive value is due to the fact
    that the absorption cross-section of the ST 0 -to- ST
    2 transition in their trans molecules is larger than that of
    the SC0 -to- SC 2 transition in the original cis molecules.

  187. Positively charged base surrogate for highly stable “base-pairing" through electrostatic and stacking interactions. Reviewed

    Hiromu Kashida, Hidehiro Ito, Taiga Fujii, Takamitsu Hayashi, Hiroyuki Asanuma

    J. Am. Chem. Soc.   Vol. 131   page: 9928-9930   2009.7

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    “Base pairs" of cationic dyes (p-methylstilbazole) were incorporated into oligodeoxyribonucleotides (ODNs). This “base pair" greatly stabilized the duplex through electrostatic and stacking interactions. The melting temperature of modified ODN was higher than those of neutral dyes and native base pairs. Further stabilization of the duplex was observed when the number of cationic dyes increased.

  188. *A Supra-Photoswitch Involving Sandwiched DNA Base Pairs and Azobenzenes for Light-Driven Nanostructures and Nanodevices Reviewed

    Liang, X.G.; Mochizuki, T.; Asanuma, H.

    Small   Vol. 5 ( 15 ) page: 1761-1768   2009.6

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    A supra-photoswitch was designed for complete ON / OFF switching of DNA hybridization by light irradiation for the purpose of using DNA as a material for building nanostructures. Azobenzenes, attached to D-threoninols that function as scaffolds, were introduced into each DNA strand after every two natural nucleotides (in the form (NNX)n where N and X represent the natural nucleotide and the azobenzene moiety, respectively). Hybridization of these two modified strands formed a supra-photoswitch consisting of alternating natural base pairs and azobenzene moieties. In this newly designed sequence, each base pair is sandwiched between two azobenzene moieties and all the azobenzene moieties are separated by base pairs. When the duplex is irradiated by visible light, the azobenzene moieties take the trans form and this duplex is surprisingly stable compared to the corresponding native duplex composed of only natural oligonucleotides. On the other hand, when the azobenzene moieties are isomerized to the cis form by UV light irradiation, the duplex is completely dissociated. Based on this design, a DNA hairpin structure was synthesized that should be closed by visible light irradiation and opened by UV light irradiation at the level of a single molecule. Indeed, perfect ON-OFF photoregulation was attained. This design is a promising strategy for the design of supra-photoswitches such as photoresponsive sticky ends on DNA nano devices and other nanostructures.

  189. Construction of Photon-Fueled DNA Nanomachines by Tethering Azobenzenes as Engines Reviewed

    Liang, X.G.; Nishioka, H.; Takenaka, N.; Asanuma, H.

    Lecture Note in Computer Science   Vol. 5347   page: 21-32   2009

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    Nanoscale DNA tweezers operated by photo-irradiation were constructed by using azobenzene-modified DNA as materials. The azobenzenes that can photoisomerize between trans and cis form were used as the engines to open and close the tweezers. The work principle is based on the reversible photoregulation of DNA hybridization. When non-substituted azobenzene was used, the tweezers were open after UV light irradiation ((330-350 nm, cis form), and closed after visible light irradiation (440-460 nm, trans form). More interestingly, the operation reversed when an azobenzene derivative with a para-isopropyl group was used: UV light irradiation closed the tweezers and visible light irradiation opened them. As compared with the oligonucleotide-fuelled DNA machines, the nanomachines constructed here were “environment-friendly" because no dsDNA waste was produced. Furthermore, the operation can be repeated many times simply by switching the photoirradiation without any decrease of the cycling efficiency.

  190. DNAを切断するはさみ

    西岡英則、浅沼浩之

    化学   Vol. 64   page: 70-71   2009

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    遺伝子工学(遺伝子組み換え技術)は、1)遺伝子であるDNAの特定の位置での“裁断”、2)得られたDNA断片の、ベクターと呼ばれる遺伝子の“運び屋”への“縫製”、そして3)ベクターの細胞内への導入(形質転換)、という3つの基本技術に基づいている。この中でも1)のDNAを“裁断”する “はさみ”=制限酵素 の発見が、現在の遺伝子工学を可能にしたと言っても過言ではない。この天然由来の“はさみ”に相当する制限酵素には様々な種類が存在し、その多くは4~6塩基程度の塩基配列を認識してDNAを切断する。したがって数千塩基程度の短い遺伝子ならば、天然の制限酵素を用いることで特定の1~2箇所を切断することが可能である。しかしながら、高等生物のような巨大なゲノムDNAに対して利用すると非常に多くの断片が生じてしまう。例えば、30億塩基を持つヒトゲノムに対して6塩基しか認識しない制限酵素を利用すると、おおよそ73万 (= 30億÷46)もの断片が生じてしまうことになる。すなわち、天然の制限酵素では、高等生物のDNAを配列特異的に1箇所で切断することは不可能である。このような問題点を克服するために近年、認識配列に制限が無い人工的な “はさみ”=「人工制限酵素」に関する様々な研究が活発に行われている。ここでは、DNAを配列特異的に切断する人工制限酵素について紹介する。

  191. *Rational Design of Functional DNA with a Non-Ribose Acyclic Scaffold Invited Reviewed

    H. Kashida, X.G. Liang, H. Asanuma

    Current Organic Chemistry   Vol. 13 ( 11 ) page: 1065-1084   2009

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    The growing field of DNA technology requires new modified DNAs that can perform advanced functions. No matter how we optimize the length and sequence of DNA using only the four naturally occurring nucleotides, potential performance is limited. In this review, we describe a facile and effective method of rationally designing new functional DNA by focusing on acyclic scaffolds, especially threoninols, which are utilized to incorporate functional molecules into
    DNA. Wedge-type insertion of a functional molecule with a planar structure of proper size in D-threoninol to DNA does
    not destabilize the duplex, although the backbone structure is changed. Rather, intercalation offsets such distortions and significantly raises the melting temperature of the DNA duplex. Based on the wedge-type insertion, photoresponsive DNA (tethering azobenzenes) and fluorescent probes that can detect single nucleotide polymorphisms (SNPs) and insertion/
    deletion (indel) polymorphisms have been designed. Furthermore, a variety of molecular clusters of dyes have also been prepared from acyclic scaffolds tethering dyes.

  192. Glucuronidase-assisted transglycosylation for the synthesis of highly functional disaccharides: β-D-Glucuronyl 6-O-sulfo-β-D-gluco- and -β-D-Galactopyranosides Reviewed

    Nagatsuka T.; Uzawa H.; Asanuma H., Nishida, Y.

    J. Carbohydrate Chem.   Vol. 28   page: 94-106   2009

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    The substrate specificity of snail, limpet, and bovine glucuronidases was examined by using p-nitrophenyl glucuronide and p-nitrophenyl 6-O-sulfo-D-glycopyranosides as the glycosyl donor and acceptors, respectively. When the donor was treated with these enzymes in the absence of the acceptors, beta(1-3) glucuronyl disaccharides were obtained as the major products together with beta(1-2) isomers as the result of an enzymatic "self-transglycosylation"reaction.

  193. Modulation of pKa of Brooker's Merocyanine by DNA Hybridization Reviewed

    Kashida, H.; Sano, K.; Hara, Y.; Asanuma, H.

    Bioconjugate Chem.   Vol. 20   page: 258-265   2009

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    Brooker's merocyanine (BM), which changes its emission and absorption maxima upon protonation, was introduced into oligodeoxyribonucleotide (ODN) via D-threoninol by postsynthetic modification on a CPG (Controlled-Pore Glass) support. The pKa of BM in the modified ODN increased from 9.5 to 10.1 upon hybridization. As a result, absorption maxima shifted from 492 nm to 432 nm at pH 10.0 by the presence of its complementary strand. This spectral shift was sufficiently large so that DNA hybridization could easily be discriminated even by the naked eye; the color of the solution changed from orange to yellow upon hybridization. In addition, the fluorescence emission was strongly quenched upon hybridization, demonstrating that this probe can also detect the target DNA by the fluorescence change. Ratiometric detection of hybridization was also possible by simultaneous excitation of both protonated and deprotonated BMs. Furthermore, we could also modulate its pKa by the anti-parallel stacking of two BM molecules in the duplex; the pKa of BM decreased from 10.1 to 9.7 by the stacking of two BMs in an anti-parallel manner. Thus, control of the microenvironment around the BM molecule allowed modulation of its pKa, which is applicable to the sequence specific recognition of target DNA.

  194. Light driven open/close operation of an azobenzene-modified DNA nano-pincette

    Liang, X.G.; Takenaka, N.; Nishioka, H.; Asanuma, H.

    Nucleic Acids Res. Symp. Ser.   Vol. 52   page: 697-698   2008.9

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    A photoresponsive DNA nano-pincette was constructed by using azobenzene-modified DNA as materials. When the azobenzene-modified part hybridizes with its complementary sequence on the pincette, the duplex formation closes it. On the contrary, the pincette is opened after the formed duplex dissociates. Based on reversible photoswitching of this DNA hybridization, the pincette involving non-substituted azobenzene can be opened simply by UV light irradiation and closed by visible light irradiation. Interestingly, the operation can be reversed by using para-isopropyl group substituted azobenzene: visible light opens the pincette, and UV light closes it. In both cases, the azobenzene-modified part was attached to the pincette throughout the open/close operation, which makes single molecular operation possible. Furthermore, the operation can be repeated many times without any decrease of the cycling efficiency and no DNA waste was produced.

  195. Preparation of coherent hetero clusters with threoninol scaffold.

    Fujii, T.; Kashida, H.; Asanuma, H.

    Nucleic Acids Symp. Ser.   Vol. 52   page: 699-700   2008.9

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    New hetero aggregates where different dyes stacked alternately were prepared by hybridizing two DNAs, each of which tethered a different dye in the centre of strand. Spectral changes due to exciton coupling between different kinds of dyes were observed. Especially, hetero aggregates of Methyl Red and 2-nitro-4'-dimethylaminoazobenzene showed substantial narrowing of the band, demonstrating coherent coupling occurred in these aggregates.

  196. Incorporation of cationic dyes into DNA for distinct stabilization of duplex

    Kashida, H.; Itoh, H.; Fujii, T.; Asanuma, H.

    Nucleic Acids Symp. Ser.   Vol. 2008   page: 701-702   2008.9

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    In this study, cationic dyes (methylstilbazole) were introduced into ODN. When two complementary ODNs, both of which tethered thise dye, were hybridized, the melting temperature drastically increased. Furthermore, The duplex was further stabilized by introducing multiple dyes.

  197. Construction of a photo-switchable gene for turning on and off gene expression with light irradiation

    Liang, X.G.; Fujioka, K.; Tsuda, Y.; Wakuda, R.; Asanuma, H.

    Nucleic Acids Res. Symp. Ser.   Vol. 52   page: 19-20   2008.9

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    A photoresponsive GFP gene was constructed by attaching a T7 promoter that involves two azobenzene moieties as the photoswitch. The azobenzene moieties tethered on D-threoninol were inserted precisely into the sequence of T7 promoter at two positions in the non-template strand. By using azobenzene-tethered DNA as a primer, azobenzene was attached to GFP gene after PCR amplification. However, a single-stranded overhang involving azobenzene was formed because primer extension stopped at the position of azobenzene moiety. Interestingly we found that oligonucleotide complementary to the overhang could be ligated by T4 DNA ligase at the stopped position, and the intact photoresponsive T7 promoter was attached onto GFP gene. Furthermore, the in vitro expression of the constructed photoresponsive GFP gene was successfully switched on and off with light irradiation.

  198. A DNA Nanomachine Powered by Light Irradiation Reviewed

    Liang, X.G.; Takenaka, N.; Nishioka, H.; Asanuma, H.

    ChemBioChem   Vol. 9 ( 5 ) page: 702-705   2008.5

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    The photoresponsive DNA tweezers as a nanomachine fuelled with photons were constructed by using azobenzene-modified DNA. The tweezers were photoswitched to be open with the UV light irradiation (335-345 nm) and to be closed with the visible light irradiation (445-455 nm) without further adding oligonucleotides as the fuel.

  199. Postsynthetic modification of DNA via threoninol on a solid support by means of allylic protection Reviewed

    Hiroyuki Asanuma, Yuichi Hara, Akira Noguchi, Kanae Sano, Hiromu Kashida

    Tetrahedron Letters   Vol. 49   page: 5144-5146   2008

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    We have developed a facile but versatile method to introduce functional molecules into DNA on a CPG support. Threoninol, whose amino group was protected with an (allyloxy)carbonyl (Alloc) group, was introduced into DNA via the corresponding phosphoramidite monomer. After selective deprotection of the Alloc group by treatment with palladium(0), a dye with a carboxyl group could be introduced into the DNA on the CPG support through an amide bond.

  200. Threoninol as a Scaffold of Dyes (Threoninol-nucleotide) and Their Stable Interstrand Clustering in Duplexes Reviewed

    Hiromu Kashida, Taiga Fujii, Hiroyuki Asanuma

    Org. Biomol. Chem.   Vol. 6 ( 16 ) page: 2892 - 2899   2008

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    Functional molecules such as dyes (Methyl Red, azobenzene, and Naphthyl Red) were tethered on D-threoninol as base surrogates (threoninol-nucleotide), which were consecutively incorporated at the center of natural oligodeoxyribonucleotides (ODNs). Hybridization of two ODNs involving threoninol-nucleotides allowed interstrand clustering of the dyes on D-threoninol and greatly stabilized the duplex. When two complementary ODNs, both of which had tethered Methyl Reds on consecutive D-threoninols, were hybridized, the melting temperature increased proportionally to the number of Methyl Reds, due to stacking interactions. Clustering of Methyl Reds induced both hypsochromicity and narrowing of the band, demonstrating that Methyl Reds were axially stacked relative to each other (H-aggregation). Since hybridization lowered the intensity of circular dichroism peaks at the p-p* transition region of Methyl Red (300 nm – 500 nm), clustered Methyl Reds were scarcely wound in the duplex. Alternate hetero dye clusters could also be prepared only by hybridization of two ODNs with different threoninol-nucleotides, such as Methyl Red / azobenzene and Methyl Red / Naphthyl Red combinations. A combination of Methyl Red and azobenzene induced bathochromic shift and broadening of the band at the Methyl Red region due to the disturbance of exciton interaction among Methyl Reds. But interestingly, the Methyl Red and Naphthyl Red combination induced merging of each absorption band to give a single sharp band, indicating that exciton interaction occurred among the different dyes. Thus, D-threoninol can be a versatile scaffold for introducing functional molecules into DNA for their ordered clustering.

  201. Molecular Design for Reversing the Photoswitching Mode of Turning ON and OFF DNA Hybridization Reviewed

    Xingguo Liang, Nobutaka Takenaka, Hidenori Nishioka, Hiroyuki Asanuma

    Chem. Asian J.   Vol. 9   page: 702-705   2008

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    A new photoswitch of DNA hybridization involving para-substituted azobenzene (such as isopropyl or tert-butyl substituted one) on L-threoninol as a linker was synthesized. When visible light was irradiated to the modified DNA, the duplex was dissociated due to the destabilization effect of the bulky substituent on trans-azobenzene. In contrast, trans-to-cis isomerization (UV light irradiation) facilitated the duplex formation. The direction of this photoswitching mode was entirely reversed as compared with the previous one carrying an unmodified azobenzene on D-threoninol whose trans-form turned on the hybridization, and cis-form turned it off. Such reversed and reversible photoswitching of DNA hybridization was directly demonstrated by using fluorophore- and quencher-attached oligonucleotides. Furthermore, it was revealed that the cis-to-trans thermal isomerization was greatly suppressed in the presence of the complementary strand due to the formation of more stable duplex in cis-form.

  202. Diastereomer Separation of Azobenzene-Tethered Oligodeoxyribonucleotides and Determination of Their Absolute Configurations by Enzymatic Digestion. Reviewed

    Xingguo Liang, Makoto Komiyama, Hiroyuki Asanuma

    Nucleosides, Nucleotides & Nucleic Acids   Vol. 27   page: 332-350   2008

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    Two diastereomers were produced by the introduction of azobenzene-tethering prochiral linker (2,2-bis(hydroxymethyl)propionic acid) in the modified ODN, which had been used for the photo-regulation of DNA functions. We found that this modified ODN with sequence 5&cent;-…pNpXpN…-3&cent; (p = phosphate; N = nucleoside; X = azobenzene residue) could be digested to pX (the phosphate at the 5&cent; side of X was left) by an over excess of Phosphodiesterase I. By comparing the retention time of pX from the separated diastereomer with that of authentic R- or S-pX on chiral HPLC, absolute configuration could be easily determined.

  203. Photoregulation of DNA hybridization by introducing an azobenzene: Molecular design for more stabilization of DNA duplex with cis-azobenzene than with its trans-form.

    Xingguo Liang, Nobutaka Takenaka, Hidenori Nishioka, Hiroyuki Asanuma

    Nucleic Acids Symp. Ser.   Vol. 51   page: 169-170   2007.11

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    Previously, photoregulation of DNA hybridization was achieved by introducing nonsubstituted azobenzene via a D-threoninol linker: DNA duplex formed (ON) after visible light irradiation (planar trans-form), whereas the duplex dissociated (OFF) after UV light irradiation (non-planar cis-form). In this study, for more efficient photoregulation of DNA functions, the reverse switch that can turn on duplex formation with UV, and turn off it with visible light irradiation was designed. When para-isopropylazobenzene (p-iPrAzo) was introduced into DNA via a L-thereoninol linker, the photoswitching direction was completely reversed: the duplex involving non-planar cis-p-iPrAzo was much more stable than that involving planar trans-form.

  204. Unexpected efficient ab initio DNA synthesis at low temperature by using thermophilic DNA

    Xingguo Liang, Tomohiro Kato, Hiroyuki Asanuma

    Nucleic Acids Symp. Ser.   Vol. 51   page: 351-352   2007.11

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    DNA was synthesized in the absence of DNA or RNA as template (or primer) from dNTPs at relatively low temperatures (25~50oC) by thermophilic Vent DNA polymerase whose proper reaction temperature for primer extension is 70~80oC. Unexpectedly, the ab initio DNA synthesis was even more efficient at 50oC as compared with that at 70oC. Interestingly, the ab initio DNA synthesis by Vent (exo-), a mutant version of Vent DNA polymerase lacking of 3&cent;&reg;5&cent; exonuclease activity, became much less efficient, and it could only carry out ab intio DNA synthesis after a long incubation time. This remarkable difference between Vent and Vent (exo-) indicates that the exonuclease activity domain of Vent may play an important role at the initiation step of ab initio DNA synthesis.

  205. Effective photoregulation of gene expression by photoresponsive T7 promoter

    Xingguo Liang, Ryuji Wakuda, Yuichiro Tsuda, Hidenori Nishioka, Hiroyuki Asanuma

    Nucleic Acids Symp. Ser.   Vol. 51   page: 349-350   2007.11

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    We constructed a photoresponsive T7 promoter by tethering two 2,6-dimethyl azobenzenes (4-(2,6-dimethyl-phenlylazo)-benzoic acids) via D-threoninol linkers. Under UV light irradiation, the rate of transcription with T7 RNA polymerase (RNAP) on the photoresponsive promoter was 10-fold faster than that under visible light irradiation. Kinetic analysis revealed that Km of cis-cis-promoter (both of the introduced azobenzenes are in cis-form) with T7 RNAP was more than 60 times larger than that of trans-trans-form, indicating that the high photoregulatoryion efficiency was obtained mainly due to the remarkable difference in their affinity with RNAP. By attaching a photoresponsive promoter to the GFP gene, we also showed that photoregulation of gene expression became practicable.

  206. Development of photoresponsive RNA towards photoswitching of RNA functions

    Hiroshi Ito, Hidenori Nishioka, Xingguo Liang, Hiroyuki Asanuma

    Nucleic Acids Symp. Ser.   Vol. 51   page: 171-172   2007.11

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    By introducing azobenzene into RNA via a D-threoninol linker, the photoresponsive RNA was developed for the photoswitching of RNA hybridization. The Tm measurements showed that RNA/RNA duplex formation and dissociation could be efficiently photoregulated. The difference in Tm between trans- and cis-form (DTm) was as large as 9~12oC when azobenzene was tethered at the central position of a 10-nt-long RNA. Interestingly, photoregulation ability of the azobenzene introduced in RNA was even greater than that in DNA for photoswitching the corresponding duplex formation. The constructed photoresponsive RNA is promising to be applied for the photoregulation of RNA functions such as Ribozyme activity, RNAi, pre-mRNA editing, and aptamer complex formation.

  207. Design of peptide nucleic acid by introduction of carbohydrate on lysine linker.

    Akira Noguchi, Hiroyuki Asanuma

      Vol. 51   page: 261-262   2007.11

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    We synthesized “cartridge" type monomer involving mannose unit on lysine as a linker and additionally in-serted it to peptide nucleic acid (PNA) oligomer. Ad-vantage of this procedure is that functional molecule could be easily introduced into anywhere position of PNA without sacrificing base-pairs, although such in-sertion lowered stability of the duplex with DNA.

  208. Development of high-sensitive DNA probe by using perylene

    Hiromu Kashida, Tomohiko Takatsu, Hiroyuki Asansuma

    Nucleic Acids Symp. Ser   Vol. 51   page: 279-280   2007.11

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    Modified oligodeoxyribonucleotides (ODNs) involving two perylene moieties are synthesized. By using this ODN, one-base deletion can easily be distinguished with high sensitivity. In addition, emission color of the solution greatly changed so that the detection was possible even by naked eyes.

  209. Preparation of "comb-type" hetero aggregates by DNA-dye conjugation

    Taiga Fujii, Hiromu Kashida, Hiroyuki Asanuma

    Nucleic Acids Symp. Ser.   Vol. 51   page: 277-278   2007.11

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    New alternating hetero aggregates (``comb-type'' hetero aggregates) were successfully prepared by hybridizing two single-stranded DNAs, each of which tethered different homo-dye aggregates in the centre of the strand. When excitonically inert dyes (Methyl Red and azobenzene) were alternately assembled, broadening of the spectrum was observed. On the other hand, alternating aggregates of Methyl Red and Naphthyl Red showed substantial narrowing of the band. Although the peak maxima of these two dyes were different, strong exciton coupling occurred.

  210. Detection of genetic polymorphisms with high sensitivity by DNA-perylene conjugate Reviewed

    Hiromu Kashida, Tomohiko Takatsu, Hiroyuki Asanuma

    Tetrahedron Letters   Vol. 48   page: 6759-6762   2007

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    Modified oligodeoxyribonucleotides (ODNs) involving two perylene moieties are synthesized. By using this ODN, one-base deletion can easily be distinguished with high sensitivity. In addition, emission color of the solution greatly changed so that the detection was possible even by naked eyes.

  211. 2&cent;,6&cent;-Dimethylazobenzene as an efficient and thermo-stable photo-regulator for the photoregulation of DNA hybridization Reviewed

    Hidenori Nishioka, Xingguo Liang, Hiromu Kashida, and Hiroyuki Asanuma

    Chem. Commun.   Vol. 2007   page: 4354-4356   2007

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    The introduction of methyl groups into two ortho positions (2&cent; and 6&cent; positions) of the same benzene ring in an azobenzene remarkably raised both its photoregulation ability and the thermal stability of the cis-form.

  212. Recognition of Solution Structures of Peptides byMolecularly Imprinted Cyclodextrin Polymers Reviewed

    Shi-hui Song, Kazumi Shirasaka, Mami Katayama,Suguru Nagaoka, Shinji Yoshihara, Tomo Osawa,Jun Sumaoka, Hiroyuki Asanuma, andMakoto Komiyama

    Macromolecules   Vol. 40   page: 3530-3532   2007

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  213. Synthesis of azobenzene-tethered DNA for reversible photo-regulation of DNA functions: hybridization and transcription Invited Reviewed

    Hiroyuki Asanuma, Xingguo Liang, Hidenori Nishioka, Daijiro Matsunaga, Minghe Liu, Makoto Komiyama

    Nature Protocols   Vol. 2 ( 1 ) page: 203-212   2007

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    A phosphoramidite monomer bearing an azobenzene is synthesized from D-threoninol. By using this monomer, azobenzene moieties can be introduced into oligodeoxyribonucleotide (DNA) at any position on a conventional DNA synthesizer. With this azobenzene-tethered DNA, formation and dissociation of DNA duplex can be reversibly photo-regulated by cis-trans isomerization of the azobenzene. When the azobenzene takes trans-form, a stable duplex is formed. Upon isomerization of the trans-azobenzene to its cis-form by UV-light irradiation (300 nm < l < 400 nm), the duplex can be dissociated to two strands. The duplex is re-formed on photo-induced cis→trans isomerization (l > 400 nm). By introducing azobenzenes into T7 promoter at specific positions, transcription by T7-RNA polymerase is also efficiently and reversibly photo-regulated. The reversible regulation can be repeated many times without causing damage to DNA or the azobenzene moiety. All these procedures take about 10 days to complete.

  214. Construction of novel dye aggregates based on "comb-type" sequence

    Hiromu Kashida, Taiga Fujii, Hiroyuki Asanuma

    Nucleic Acids Symp. Ser.   Vol. 51   page: 11-12   2007

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    Novel dye aggregates (“comb-type" aggregates) was prepared by hybridizing modified oligodeoxyribo-nucleotides (ODNs), in which dyes were introduced consecutively. From NMR structural analysis, dye molecules were intercalated between base pairs and stacked in anti-parallel manner. When ODNs containing three Methyl Red moieties were hybridized, strong exciton coupling was observed. In addition, thermal stability of duplex was substantially enhanced due to the intermolecular stacking.

  215. Exciplex Formation between Pyrene and N,N-Dimethylaniline in DNA for the Detection of One-base Deletion Reviewed

    Hiromu Kashida, Makoto Komiyama, Hiroyuki Asanuma

    Chem. Lett.   Vol. 35 ( 8 ) page: 934-935   2006

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    Exciplex emission from pyrene and N,N-dimethylaniline moieties was observed in aqueous solution by incorporating them into DNA. By using exciplex formation, one-base deletion was successfully detected.

  216. Azobenzene-tethered T7 promoter for Efficient Photoregulation of Transcription Reviewed

    Minghe Liu, Hiroyuki Asanuma, Makoto Komiyama

    J. Am. Chem. Soc.   Vol. 128   page: 1009-1015   2006

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    Azobenzene was additionally introduced into side chain of T7 promoter for the photoregulation of transcription reaction by T7 RNA polymerase (T7 RNAP). When single azobenzene molecule was introduced into the T7 promoter either at the loop binding region of the RNAP (–7 to –11 position) or at the unwinding region (+1 to –4 position), transcription was suppressed in the trans-form but proceeded faster in the cis-form. The amount of transcripts after UV irradiation with respect to that under dark was only 1.5 – 2.0-fold. Kinetic analysis of the transcription reaction revealed that photoregulatory mechanism was different in these positions. The photoisomerization of an azobenzene at the loop binding region primarily affected Km. On the other hand, the isomerization of an azobenzene at unwinding region mainly affected kcat. Still more clear-cut photoregulation was achieved when two azobenzenes were introduced into both loop binding and unwinding regions, respectively: transcription proceeded 7.6-fold faster after UV irradiation than that under dark. This synergistic effect was observed only when two azobenzenes were introduced into these two different regions, respectively, and introduction into the same loop binding region drastically lowered the transcription activity. The cooperation of two azobenzenes at loop binding and unwinding region would contribute to the clear-cut photoregulation of transcription.

  217. Importance of the Position of Vinyl Group on b-Cyclodextrin for the Effective Imprinting of Amino Acid Derivatives and Oligopeptides in Water Reviewed

    Osawa, T.; Shirasaka, K.; Matsui, T.; Akiyama, T.; Yoshihara, S.; Hishiya, T.; Asanuma, H.; Komiyama, M.

    Macromolecules   Vol. 39   page: 2460-2466   2006

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    Two kinds of vinyl monomers of b-cyclodextrin (b-CyD) that tether a vinyl group on either wider rim of the truncated cone or its smaller rim were synthesized and applied to the imprinting towards amino acid derivatives and oligopeptides in water. Mono-3-(N-acrylamido)-3-deoxy-altro-b-cyclodextrin (3-AAm-CyD) showed remarkable imprinting effect for the enantioselective recognition of protected amino acids such as N-benzyloxycarbonyltyrosine (Z-Tyr). However, the imprinted polymer from mono-6-(N-acrylamido)-6-deoxy-b-cyclodextrin (6-AAm-CyD) hardly showed enantioselectivity. According to NOESY analysis on pre-organized b-CyD/Z-Tyr complex in D2O, the aromatic moieties of Z-Tyr were included into the cavity of b-CyD from its wider rim. Since the vinyl group of 3-AAm-CyD protruded towards the template and was polymerized there, detailed shape of the template was precisely copied on the polymer by the imprinting. In case of 6-AAm-CyD, however, the shape of template could not be well transcribed because its vinyl group was located at opposite side of the cavity and thus co-polymerization occurred far from the template molecule. On the other hand, the imprinted polymers from both b-CyD vinyl monomers were effective for the recognition of sequences of tetrapeptides composed of two glycines and two phenylalanines, although the selectivity itself was not remarkable. In these polymers, even the b-CyD residues of 6-AAm-CyD were immobilized complementarily to the phenyl rings and bound them.

  218. Improved Method of Molecular Imprinting of Cyclodextrin on Silica-gel Surface for the Preparation of Stable Stationary HPLC Phase Reviewed

    Matsui, T. , Osawa , T.; Shirasaka , K.; Katayama, M.; Hishiya, T.; Asanuma H., Komiyama, M.

    J. Inclu. Phenom. Macrocyclic Chem.   Vol. 56   page: 39-44   2006

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    By using N-(3-triethoxysilyl)propylacrylamide (TPAAm), vinyl groups were introduced onto the surface of silicagel.
    On the surface of this silica-gel, b-CyD was molecularly imprinted by using a redox initiator, and the composite
    was used as stationary phase of high performance liquid chromatography (HPLC). The pump pressure was sufficiently
    low and did not increase even after continuous elution for 24 h. In order to prepare still more stable columns,
    a new polymerization process was developed. There, the redox initiator was first mixed with the surface-modified
    silica-gel and then vinylated b-CyD, crosslinker, and the template were added. This modification promoted the
    immobilization of b-CyD copolymer to the silica-gel, resulting in still lower pump pressure. Concurrently, the
    imprinting efficiency was increased in comparison with previous method where the redox initiator was directly
    added to the mixture of the b-CyD–template complex, crosslinker, and surface-modified silica-gel. The molecularly
    imprinted b-CyD column, prepared by this new method, efficiently discriminated the enantiomers of
    N-benzyloxycarbonyltyrosine.

  219. Enhancement of RNA cleavage activity of 10-23 DNAzyme by covalently introduced intercalator Reviewed

    H. Asanuma, H. Hayashi, J. Zhao, X. Liang, A. Yamazawa, T. Kuramochi, D. Matsunaga, Y. Aiba, H. Kashida, M. Komiyama

    Chem. Commun.     page: 5062-5064   2006

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    By introducing an intercalator through D-threoninol to the 10-23 DNAzyme at the junction between its catalytic loop and the binding arm, the RNA cleavage activity was greatly improved.

  220. Insertion of Two Pyrene Moieties to Oligodeoxyribonucleotides for the Efficient Detection of Insertion/Deletion Polymorphisms Reviewed

    Hiromu Kashida, Hiroyuki Asanuma, Makoto Komiyama

    Chem. Commun.     page: 2768-2770   2006

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    For the detection of deletion polymorphisms, two pyrene moieties are tethered to oligodeoxyribonucleotide (ODN) on both sides of the intervening base. When this probe ODN was hybridized with wild type ODN, both pyrenes intercalated between base pairs and only monomer emission was observed. In contrast, strong excimer emission was generated by hybridization with one-base deletion mutant. Similarly, two-base deletion was also detected.

  221. Covalent Incorporation of Methyl Red Dyes into Double-Stranded DNA for Their Ordered Clustering Reviewed

    Kashida, H.; Tanaka, M.; Baba, S.; Sakamoto, T.; Kawai, G.; Asanuma, H.; Komiyama, M.

    Chem. Eur. J.   Vol. 12   page: 777-784   2006

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    Ordered dye cluster of Methyl Reds was formed in double-stranded DNA by hybridizing two complementary DNA-dye conjugates that involve Methyl Red moiety on threoninol linker and 1,3-propanediol as a spacer alternately in the middle of the sequence. In the duplex, Methyl Reds from each strand were axially stacked anti-parallel to each other as determined from NMR analysis. This clustering of Methyl Reds induced distinct change of both UV-Vis and CD spectra. Single-stranded DNA-Methyl Red conjugate on D-threoninol linkers and (1,3-propanediol) spacers exhibited broad absorption spectrum having lmax at around 480 nm, and almost no CD was observed at around absorption maximum of Methyl Red. However, when Methyl Reds were clustered by hybridization, lmax shifted towards shorter wavelength with respect to its monomeric transition. This hypsochromic shift increased with the number of Methyl Reds. Furthermore, positive couplet was also strongly induced here. These dye clusters are H-aggregates, in which molecular excitons are coupled. The positive couplet demonstrates that the clusters on D-threoninol forms right-hand helix. In contrast, induced CD became much weaker with Methyl Red on L-threoninol, which intrinsically prefers counterclockwise winding. Thus, mutual orientation of the stacked dyes was controlled by the chirality of the linker.

  222. Incorporation of methyl group on azobenzene for the effective photo-regulation of hybridization and suppression of thermal isomerization

    H. Nishioka, H. Kashida, M. Komiyama, X. Liang, and H. Asanuma

    Nucleic Acids Res. Supple.   Vol. 50   page: 85-86   2006

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  223. Activation of DNA enzyme 10-23 by tethering an intercalator to its backbone

    H. Hayashi, X. Liang, J. Zhao, M. Komiyama, and H. Asanuma

    Nucleic Acids Res. Supple   Vol. 50   page: 167-168   2006

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  224. Design of Light-switchable Phage Promoter for Efficient Photo-regulation of Gene-expression

    Minghe Liu, Hiroyuki Asanuma, Makoto Komiyama

    Nucleic Acids Res. Supple.   Vol. 49   page: 283-284   2005

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  225. Clear-cut photo-regulation of the formation and dissociation of the DNA duplex by modified oligonucleotide involving multiple azobenzenes

    Hiroyuki Asanuma, Daijiro Matsunaga, Makoto Komiyama

    Nucleic Acids Res. Supple.   Vol. 49   page: 35-36   2005

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  226. Efficient Separation of Hydrophobic Biomolecules by Molecularly Imprinted Cyclodextrins Reviewed

    Hishiya, T.; Asanuma, H.; Komiyama, M.

    J. Inclu. Phenom. Macrocyclic Chem.   Vol. 50   page: 51-55   2004

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  227. Photo-regulation of RNA Digestion by RNase H with Azobenzene-Tethered DNA Reviewed

    Daijiro Matsunaga, Hiroyuki Asanuma, Makoto Komiyama

    J. Am. Chem. Soc.   Vol. 126 ( 37 ) page: 11452-11453   2004

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    RNA digestion by RNase H, which is responsible for the antisense effect, was efficiently photo-regulated by use of the duplex of azobenzene-tethered sense DNA and native antisense DNA. Under dark, RNA digestion was suppressed because antisense DNA was strongly hybridized with azobenzene-tethered sense DNA, and accordingly RNA was isolated. On UV light irradiation, antisense DNA was released from the azobenzene-tethered DNA due to the trans to cis isomerization and hybridized with RNA, which was digested by RNase H.

  228. Alternating hetero H-aggregation of different dyes by interstrand stacking from two DNA-dye conjugates

    Hiromu Kashida, Hiroyuki Asanuma, Makoto Komiyama

    Angew. Chem. Int. Ed.   Vol. 43 ( 47 ) page: 6522-6525   2004

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    New hetero aggregates in which Methyl Reds and Naphthyl Reds are stacked alternately were successfully prepared by hybridization of two DNA-dye conjugates. When the Naphthyl Red conjugate was hybridized with Methyl Red conjugate, a new sharp absorption band (H-band) appeared at 480 nm that was different from the lmax of each dye conjugate in the single-stranded state. In addition to this new band in the UV-Vis spectrum, strong circular dichroism was also induced by interstrand hetero-stacking of these dyes. These results demonstrated that even different dyes as well as identical dyes could exhibit H-band.

  229. Interstrand H aggregation of cationic dyes for narrowing the absorption spectra and stabilizing the duplex Reviewed

    Hiromu Kashida, Hiroyuki Asanuma, Makoto Komiyama

    Supramol. Chem.   Vol. 16 ( 6 ) page: 459-464   2004

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    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)  

    Interstrand H-aggregates of cationic dyes are prepared by hybridization of the two DNA-dye conjugates involving Naphthyl Red moiety and spacer alternately in the middle of the sequence. At pH 5.0 where Naphthyl Red is positively charged, single-stranded DNA-Naphthyl Red conjugate involving three dye groups and three spacer residues exhibited broad absorption spectrum having lmax at around 530 nm. But hybridization of two DNA-Naphthyl Red conjugates that are complementary provided rather different spectrum: much narrower absorption band appeared at 507 nm, which is 23 nm shorter than the single stranded conjugates. These spectroscopic behaviors indicate that dyes in the duplex are H-aggregated and excitons are strongly coupled in the aggregate. In addition to the appearance of narrow H-band, melting temperature dramatically increased by the H-aggregation of stacked cationic dyes compared with that of natural duplex without dye and spacer residues. Thus, positive charges on the stacked dyes did not interfere the duplex formation by the electrostatic repulsion, and moreover fairly promoted the hybridization.

  230. Real time monitoring of the interaction of T7 RNA polymerase with azobenzene-tethered T7 promoter by biosensor

    Minghe Liu, Hiroyuki Asanuma, Makoto Komiyama

    Nucleic Acids Res. Supple. 4   Vol. 4   page: 221-222   2004

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    Authorship:Lead author   Language:English  

  231. Photoregulation of in vitro transcription/translation of GFP by tethering an azobenzene to T7 promoter

    Jing Zhao, J. Zhou, Minghe Liu, Hiroyuki Asanuma, Makoto Komiyama

    Nucleic Acids Res. Supple. 4   Vol. 4   page: 199-120   2004

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    Authorship:Lead author   Language:English  

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Books 27

  1. 生体材料化学 : 基礎と応用

    浅沼 浩之, 樫田 啓, 神谷 由紀子

    コロナ社  2015  ( ISBN:9784339067507

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    Language:Japanese

    CiNii Books

  2. 光応答性DNAの搭載によるナノマシンとナノ構造体の光制御

    浅沼浩之, 神谷由紀子( Role: Joint author)

    化学同人  2021 

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    Language:Japanese

  3. DNA機能の拡張 Reviewed

    浅沼浩之( Role: Sole author)

    講談社  2020.12  ( ISBN:978-4-06-520786-4

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    Language:Japanese Book type:Scholarly book

  4. 核酸の直交性

    浅沼浩之、村山恵司( Role: Joint author)

    CBI学会出版  2019.4  ( ISBN:978-4-9909076-4-8

  5. ナノマテリアルとしての光応答性DNA

    浅沼浩之、神谷由紀子( Role: Joint author)

    エヌ・ティー・エス  2018.12 

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    Total pages:806   Responsible for pages:7   Language:Japanese Book type:Scholarly book

  6. 遺伝子を蛍光検出するナノプローブ開発 Reviewed

    浅沼浩之、樫田 啓( Role: Joint author)

    丸善プラネット(株)  2017.12 

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    Language:Japanese

  7. 非環状骨格型人工核酸:aTNA, SNA

    神谷由紀子、村山恵司、樫田 啓、浅沼浩之( Role: Joint author)

    シーエムシー出版  2016 

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    Language:Japanese

  8. 非環状骨格型人工核酸:aTNA, SNA

    神谷由紀子, 村山恵司, 樫田 啓, 浅沼浩之( Role: Joint author)

    シーエムシー出版  2016 

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    Responsible for pages:79-86   Language:Japanese

  9. 生体材料化学-基礎と応用―

    浅沼浩之、樫田啓、神谷由紀子( Role: Joint author)

    (株)コロナ社  2015.11  ( ISBN:978-4-339-06750-7

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    Language:Japanese

  10. プローブへの応用を目指した人工ヌクレオチドの設計

    浅沼浩之、樫田 啓( Role: Joint author)

    一粒書房  2014 

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    Language:Japanese

  11. 核酸医薬を目指した機能性siRNA

    神谷由紀子、浅沼浩之( Role: Joint author)

    一粒書房  2014 

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    Language:Japanese

  12. ナノ環境に優しい光応答性DNAの設計

    神谷由紀子、浅沼浩之( Role: Joint author)

    コロナ社   2013 

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    Language:Japanese

  13. Oligonucleotide Conjugates for Detection of Specific Nucleic Acid Sequences

    Hiromu Kashida, Hiroyuki Asanuma( Role: Joint author)

    RSC publishing   2012.12 

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    Language:English

  14. Oligonucleotide Conjugates for Detection of Specific Nucleic Acid Sequences

    Hiromu Kashida, Hiroyuki Asanuma( Role: Joint author)

    2012 

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    Language:English

  15. カートリッジ型人工ヌクレオチドによる光応答性DNAの設計

    浅沼浩之, 梁興国( Role: Joint author)

    化学同人  2011 

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    Language:Japanese

  16. 人工核酸を利用したプローブDNAの調製と遺伝子多型検出

    樫田啓、浅沼浩之( Role: Joint author)

    NTS  2010.4 

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    Language:Japanese

    これまでに様々な蛍光色素で修飾した核酸プローブが合成されており、溶液中での遺伝子多型の検出に関しては数多くの報告がなされてきた。しかしながら、それに比べて基板にこれらの核酸プローブを固定化した例は必ずしも多くない。その原因としては、プローブ自身の蛍光によるバックグラウンドが挙げられる。蛍光色素で修飾した核酸プローブを基板上に固定化する場合、プローブ自身が発する蛍光により検出が阻害されてしまう。そのため、蛍光性核酸プローブを固定化したDNAチップを調製するためには、ターゲット非存在下でプローブ自身の蛍光を抑制することが必要となる。そこで、本節ではこのようなプローブ単体でのバックグラウンドが抑制された核酸プローブの例として1)モレキュラービーコン及び2)レシオメトリックプローブについて述べる。

  17. 人工核酸を利用したプローブDNAの調製と遺伝子多型検出

    樫田啓, 浅沼浩之( Role: Joint author)

    NTS  2010.4 

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    Responsible for pages:603-610   Language:Japanese

    これまでに様々な蛍光色素で修飾した核酸プローブが合成されており、溶液中での遺伝子多型の検出に関しては数多くの報告がなされてきた。しかしながら、それに比べて基板にこれらの核酸プローブを固定化した例は必ずしも多くない。その原因としては、プローブ自身の蛍光によるバックグラウンドが挙げられる。蛍光色素で修飾した核酸プローブを基板上に固定化する場合、プローブ自身が発する蛍光により検出が阻害されてしまう。そのため、蛍光性核酸プローブを固定化したDNAチップを調製するためには、ターゲット非存在下でプローブ自身の蛍光を抑制することが必要となる。そこで、本節ではこのようなプローブ単体でのバックグラウンドが抑制された核酸プローブの例として1)モレキュラービーコン及び2)レシオメトリックプローブについて述べる。

  18. DNAのダイナミックな光制御(超分子サイエンスー基礎から材料への展開ー

    浅沼浩之、梁興国( Role: Joint author)

    NTS  2009.5 

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    Language:Japanese

    天然のDNAの更なる機能化を目的としてこれまでに様々な化学修飾がDNAに対して行われてきたが、上述のようにDNAの応用分野が多様化したことで、DNAの化学修飾の重要性は更に増しつつある。もちろん天然の4つの核酸塩基だけでも多彩なナノ構造を形成し様々な機能を発揮するが、化学修飾によって天然のDNAでは実現不可能な機能を補うことが出来れば、DNAの応用範囲は飛躍的に拡大するであろう。本稿ではこのような観点から筆者らが開発したアゾベンゼン導入型光応答性DNAと、これを用いたDNAナノマシンのダイナミックな光制御について解説したい。

  19. 光機能化DNAファイバー(”ファイバー”スーパーバイオミメティックス)

    浅沼浩之( Role: Sole author)

    NTS  2006.10 

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    Language:Japanese

  20. 光による核酸機能の制御(図解 高分子新素材の全て)

    浅沼浩之( Role: Sole author)

    工業調査会  2005 

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    Language:Japanese

  21. 光による核酸機能の制御(図解 高分子新素材の全て)

    浅沼浩之( Role: Sole author)

    工業調査会  2005 

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    Responsible for pages:50-53   Language:Japanese

  22. Molecular imprinting – from fundamentals to applications-

    Makoto Komiyama, Toshifumi Takeuchi, Takashi Mukawa, Hiroyuki Asanuma( Role: Joint author)

    Wiley-VCH  2003 

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    Language:English

  23. Molecular imprinting – from fundamentals to applications-

    Makoto Komiyama, Toshifumi Takeuchi, Takashi Mukawa, Hiroyuki Asanuma( Role: Joint author)

    Wiley-VCH  2003 

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    Responsible for pages:47-64, 119-138   Language:English

  24. Encyclopedia of Separation Science

    Naoki Toshima, and Hiroyuki Asanuma( Role: Joint author)

    Academic Press Ltd.  2000 

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    Language:English

  25. Synthesis of Hybrid Polymers Which Bind Guests in Water by Hydrogen Bond Formation

    Makoto Komiyama and Hiroyuki Asanuma( Role: Joint author)

    2000 

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    Language:English

  26. Polymer for Gas Separation

    Naoki Toshima, Hiroyuki Asanuma( Role: Joint author)

    VHC Publishers  1992 

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    Language:English

  27. Polymer for Gas Separation

    Naoki Toshima, Hiroyuki Asanuma( Role: Joint author)

    VHC Publishers  1992 

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    Responsible for pages:147   Language:English

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MISC 21

  1. DNA-assisted swarm control in a biomolecular motor system

    Jakia Jannat Keya, Ryuhei Suzuki, Arif Md. Rashedul Kabir, Daisuke Inoue, Hiroyuki Asanuma, Kazuki Sada, Henry Hess, Akinori Kuzuya, Akira Kakugo

    Nature Communications   Vol. 9 ( 1 ) page: 453   2018.12

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    Language:English   Publishing type:Rapid communication, short report, research note, etc. (scientific journal)   Publisher:Nature Publishing Group  

    In nature, swarming behavior has evolved repeatedly among motile organisms because it confers a variety of beneficial emergent properties. These include improved information gathering, protection from predators, and resource utilization. Some organisms, e.g., locusts, switch between solitary and swarm behavior in response to external stimuli. Aspects of swarming behavior have been demonstrated for motile supramolecular systems composed of biomolecular motors and cytoskeletal filaments, where cross-linkers induce large scale organization. The capabilities of such supramolecular systems may be further extended if the swarming behavior can be programmed and controlled. Here, we demonstrate that the swarming of DNA-functionalized microtubules (MTs) propelled by surface-adhered kinesin motors can be programmed and reversibly regulated by DNA signals. Emergent swarm behavior, such as translational and circular motion, can be selected by tuning the MT stiffness. Photoresponsive DNA containing azobenzene groups enables switching between solitary and swarm behavior in response to stimulation with visible or ultraviolet light.

    DOI: 10.1038/s41467-017-02778-5

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  2. Development of Visible-Light-Responsive RNA Scissors Based on a 10–23 DNAzyme

    Yukiko Kamiya, Yu Arimura, Hideaki Ooi, Kenjiro Kato, Xing-Guo Liang, Hiroyuki Asanuma

    ChemBioChem   Vol. 19 ( 12 ) page: 1305 - 1311   2018.6

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    Language:English   Publishing type:Rapid communication, short report, research note, etc. (scientific journal)   Publisher:Wiley-VCH Verlag  

    The 10–23 DNAzyme is an artificially developed functional oligonucleotide that can cleave RNA in a sequence-specific manner. In this study, we designed a new photo-driven DNAzyme incorporating a photoresponsive DNA overhang complementary to the catalytic core region. The photoresponsive overhang region of the DNAzyme included either azobenzene components (Azos) or 2,6-dimethyl-4-(methylthio)azobenzene units (SDM-Azos) each attached to a d-threoninol linker. When the Azos or SDM-Azos were in the trans form, the photoresponsive DNA overhang hybridized with the DNAzyme, and the RNA cleavage activity was suppressed. cis Isomerization of Azos or SDM-Azos, induced by 365 or 400 nm light, respectively, destabilized the duplex between the photoresponsive overhang and the catalytic core, and the DNAzyme recovered RNA cleavage activity. Reversible photoswitching of the DNAzyme activity was achieved by use of specific light irradiation. Further, light-dependent photoswitching of protein expression in the presence of the DNAzyme was demonstrated. Thus, this photo-driven DNAzyme has potential for application as a photocontrolled gene silencing system and a photoactivatable gene expression system.

    DOI: 10.1002/cbic.201800020

    Scopus

    PubMed

  3. DNA Microcapsule for Photo-Triggered Drug Release Systems

    Yukiko Kamiya, Yoshinobu Yamada, Takahiro Muro, Kazunori Matsuura, Hiroyuki Asanuma

    CHEMMEDCHEM   Vol. 12 ( 24 ) page: 2016 - 2021   2017.12

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    Language:English   Publishing type:Rapid communication, short report, research note, etc. (scientific journal)   Publisher:WILEY-V C H VERLAG GMBH  

    In this study we constructed spherical photo-responsive microcapsules composed of three photo-switchable DNA strands. These strands first formed a three-way junction (TWJ) motif that further self-assembled to form microspheres through hybridization of the sticky-end regions of each branch. To serve as the photo-switch, multiple unmodified azobenzene (Azo) or 2,6-dimethyl-4-(methylthio)azobenzene (SDM-Azo) were introduced into the sticky-end regions via a d-threoninol linker. The DNA capsule structure deformed upon trans-to-cis isomerization of Azo or SDM-Azo induced by specific light irradiation. In addition, photo-triggered release of encapsulated small molecules from the DNA microcapsule was successfully achieved. Moreover, we demonstrated that photo-triggered release of doxorubicin caused cytotoxicity to cultured cells. This biocompatible photo-responsive microcapsule has potential application as a photo-controlled drug-release system.

    DOI: 10.1002/cmdc.201700512

    Web of Science

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    PubMed

  4. Introduction of 2,6-Diaminopurines into Serinol Nucleic Acid Improves Anti-miRNA Performance

    Yukiko Kamiya, Yuka Donoshita, Hiroshi Kamimoto, Keiji Murayama, Jumpei Ariyoshi, Hiroyuki Asanuma

    CHEMBIOCHEM   Vol. 18 ( 19 ) page: 1917 - 1922   2017.10

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    Language:English   Publishing type:Rapid communication, short report, research note, etc. (scientific journal)   Publisher:WILEY-V C H VERLAG GMBH  

    MicroRNAs (miRNAs) are endogenous small RNAs that regulate gene expression at the post-transcriptional level by sequence-specific hybridisation. Anti-miRNA oligonucleotides (AMOs) are inhibitors of miRNA activity. Chemical modification of AMOs is required to increase binding affinity and stability in serum and cells. In this study, we synthesised AMOs with our original acyclic nucleic acid, serinol nucleic acid (SNA), backbone and with the artificial nucleobase 2,6-diaminopurine. The AMO composed of only SNA had strong nuclease resistance and blocked endogenous miRNA activity. A significant improvement in anti-miRNA activity of the AMO was achieved by introduction of a 2,6-diaminopurine residues into the SNA backbone. In addition, we found that the enhancement in AMO activity depended on the position of the 2,6-diaminopurine residue in the sequence. The high potency of the SNA-AMOs suggests that these oligomers will be useful as therapeutic reagents for control of miRNA function in patients and as tools for investigating the roles of microRNAs in cells.

    DOI: 10.1002/cbic.201700272

    Web of Science

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  5. Chaperone-Polymer-Assisted, Photodriven DNA Strand Displacement

    Cheng Bohao, Kashida Hiromu, Shimada Naohiko, Maruyama Atsushi, Asanuma Hiroyuki

    CHEMBIOCHEM   Vol. 18 ( 16 ) page: 1568-1572 - 1572   2017.8

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    DOI: 10.1002/cbic.201700202

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  6. D-aTNA Circuit Orthogonal to DNA Can Be Operated by RNA Input via SNA

    Keiji Murayama, Ryuya Nagao, Hiroyuki Asanuma

    CHEMISTRYSELECT   Vol. 2 ( 20 ) page: 5624 - 5627   2017.7

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    Language:English   Publishing type:Rapid communication, short report, research note, etc. (scientific journal)   Publisher:WILEY-V C H VERLAG GMBH  

    For a signal amplification system that is orthogonal to DNA, we designed a simplified seesaw gate composed of only D-aTNA. This new system performed signal amplification by toehold exchange reaction just as the DNA circuit did. Moreover, the D-aTNA circuit was not affected by natural nucleic acids carrying sequences complementary to the D-aTNA. In the presence of an SNA interface, however, an RNA signal was converted to D-aTNA signal, resulting in successful activation of D-aTNA circuit. This system can be used to design signal-amplification circuits that are not influenced by contaminating DNA and RNA.

    DOI: 10.1002/slct.201701126

    Web of Science

    Scopus

  7. Orientation-dependent FRET system reveals differences in structures and flexibilities of nicked and gapped DNA duplexes

    Hiromu Kashida, Ayako Kurihara, Hayato Kawai, Hiroyuki Asanuma

    NUCLEIC ACIDS RESEARCH   Vol. 45 ( 11 ) page: e105   2017.6

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    Language:English   Publishing type:Rapid communication, short report, research note, etc. (scientific journal)   Publisher:OXFORD UNIV PRESS  

    Differences in structures and flexibilities of DNA duplexes play important roles on recognition by DNA-binding proteins. We herein describe a novel method for structural analyses of DNA duplexes by using orientation dependence of Forster resonance energy transfer (FRET). We first analyzed canonical B-form duplex and correct structural parameters were obtained. The experimental FRET efficiencies were in excellent agreement with values theoretically calculated by using determined parameters. We then investigated DNA duplexes with nick and gaps, which are key intermediates in DNA repair systems. Effects of gap size on structures and flexibilities were successfully revealed. Since our method is facile and sensitive, it could be widely used to analyze DNA structures containing damages and non-natural molecules.

    DOI: 10.1093/nar/gkx200

    Web of Science

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  8. Design of photofunctional oligonucleotides by copolymerization of natural nucleobases with base surrogates prepared from acyclic scaffolds Invited Reviewed

    Hiroyuki Asanuma, Keiji Murayama, Yukiko Kamiya, Hiromu Kashida

    Polymer Journal   Vol. 49 ( 3 ) page: 279 - 289   2017.3

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    Language:English   Publishing type:Article, review, commentary, editorial, etc. (scientific journal)   Publisher:Nature Publishing Group  

    Further development of DNA nanotechnology requires new functional oligonucleotides composed of nucleobases beyond the native four. In this review, we demonstrate new methodology for DNA and RNA functionalization using a base surrogate prepared from d-threoninol (2-amino-1,3-butanediol). Using this nucleobase surrogate, we can introduce functional molecules at any position of the sequence. Our methodology is conceptually similar to the copolymerization of multiple monomers: phosphoramidite monomers corresponding to the base surrogate and natural nucleotides are copolymerized on a solid support to prepare the functional oligonucleotides. Copolymerization allows for stable functional motifs, including wedges, interstrand-wedges, dimers and clusters. By selecting suitable functional molecules and motifs, we can design photofunctional oligonucleotides, such as: (1) photoresponsive DNA that enables reversible formation and dissociation of the duplex by photoirradiation
    (2) [2+2] photocycloaddition of stilbene derivatives
    (3) orientation-dependent FRET (fluorescence (Förster) resonance energy transfer) systems
    (4) sequence-specific fluorescent probe for the detection of DNA and RNA
    and (5) functional siRNA for fluorescent labeling of mature RISC (RNA-induced silencing complex).

    DOI: 10.1038/pj.2016.120

    Scopus

  9. Effect of Methyl Group on Acyclic Serinol Scaffold for Tethering Dyes on the DNA Duplex Stability

    Keiji Murayama, Hiroyuki Asanuma

    CHEMBIOCHEM   Vol. 18 ( 1 ) page: 142 - 149   2017.1

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    Language:English   Publishing type:Rapid communication, short report, research note, etc. (scientific journal)   Publisher:WILEY-V C H VERLAG GMBH  

    Acyclic serinol derivatives are useful scaffolds for tethering dyes within DNA duplexes. Here we synthesised an inverse L-threoninol (il-threoninol) scaffold and compared its effect on DNA duplex stability to other acyclic artificial nucleic acid scaffolds that are based on D-threoninol, L-threoninol, and serinol. When planar trans-azobenzene was incorporated into the DNA duplex through a single bulge-like motif (the wedge), the il-threoninol scaffold stabilised the duplex most efficiently. When scaffolds were incorporated in complementary positions (dimer motif) or in three adjacent positions (cluster motif), D-threoninol was the most stabilising. CD spectra indicated that the effect of scaffold on the duplex stability was closely related to the winding induced by each scaffold. When trans-azobenzene was photo-isomerised to non-planar cis-azobenzene, il-threoninol destabilised the duplex most strongly, irrespective of the number of artificial residues incorporated. The properties of the il-threoninol scaffold make it a useful tether for dyes or other functionalities.

    DOI: 10.1002/cbic.201600558

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  10. Antisense oligonucleotide modified with serinol nucleic acid (SNA) induces exon skipping in mdx myotubes Reviewed

    Bao T. Le, Keiji Murayama, Fazel Shabanpoor, Hiroyuki Asanuma, Rakesh N. Veedu

    RSC ADVANCES   Vol. 7 ( 54 ) page: 34049 - 34052   2017

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    Language:English   Publishing type:Rapid communication, short report, research note, etc. (scientific journal)   Publisher:ROYAL SOC CHEMISTRY  

    Serinol nucleic acid (SNA) is a novel nucleic acid analogue that can form highly stable heteroduplexes with complementary DNA and RNA sequences. Structurally, SNA is a close mimic to peptide nucleic acid (PNA) which is widely used in diagnostic and therapeutic applications. SNA chemistry is relatively new, and so far the scope of SNA has only been explored in improving the efficacy of small interfering RNA and for developing a highly sensitive molecular beacon for diagnostic applications. In this study, we investigated the potential of SNA-modified antisense oligonucleotide (AO) in parallel to PNA-oligo for splicemodulation in an in vitro cellular model of Duchenne muscular dystrophy (DMD). We synthesized a 20mer SNA and PNA antisense oligonucleotide (AO) designed to induce exon-23 skipping in the mouse dystrophin gene transcript. Our results demonstrated that the SNA AO induced exon-23 skipping at all tested concentrations, whereas the corresponding PNA AO failed to induce any exon-23 skipping upon 24 hours of transfection using Lipofectin transfection reagent. Our results further expands the potential of SNA oligonucleotides in therapeutic applications.

    DOI: 10.1039/c7ra06091b

    Web of Science

  11. Antisense oligonucleotide modified with serinol nucleic acid (SNA) induces exon skipping in mdx myotubes

    Bao T. Le, Keiji Murayama, Fazel Shabanpoor, Hiroyuki Asanuma, Rakesh N. Veedu

    RSC ADVANCES   Vol. 7 ( 54 ) page: 34049 - 34052   2017

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    Language:English   Publishing type:Rapid communication, short report, research note, etc. (scientific journal)   Publisher:ROYAL SOC CHEMISTRY  

    Serinol nucleic acid (SNA) is a novel nucleic acid analogue that can form highly stable heteroduplexes with complementary DNA and RNA sequences. Structurally, SNA is a close mimic to peptide nucleic acid (PNA) which is widely used in diagnostic and therapeutic applications. SNA chemistry is relatively new, and so far the scope of SNA has only been explored in improving the efficacy of small interfering RNA and for developing a highly sensitive molecular beacon for diagnostic applications. In this study, we investigated the potential of SNA-modified antisense oligonucleotide (AO) in parallel to PNA-oligo for splicemodulation in an in vitro cellular model of Duchenne muscular dystrophy (DMD). We synthesized a 20mer SNA and PNA antisense oligonucleotide (AO) designed to induce exon-23 skipping in the mouse dystrophin gene transcript. Our results demonstrated that the SNA AO induced exon-23 skipping at all tested concentrations, whereas the corresponding PNA AO failed to induce any exon-23 skipping upon 24 hours of transfection using Lipofectin transfection reagent. Our results further expands the potential of SNA oligonucleotides in therapeutic applications.

    DOI: 10.1039/c7ra06091b

    Web of Science

  12. Hetero-Selective DNA-Like Duplex Stabilized by Donor-Acceptor Interactions Reviewed

    Tetsuya Doi, Takumi Sakakibara, Hiromu Kashida, Yasuyuki Araki, Takehiko Wada, Hiroyuki Asanuma

    CHEMISTRY-A EUROPEAN JOURNAL   Vol. 21 ( 45 ) page: 15974 - +   2015.11

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    Language:English   Publishing type:Rapid communication, short report, research note, etc. (scientific journal)   Publisher:WILEY-V C H VERLAG GMBH  

    We report on the characterization of a novel hetero-selective DNA-like duplex of pyrene and anthraquinone pseudo base pairs. The pyrene/anthraquinone pairs showed excellent selectivity in hetero-recognition and even trimers were found to form a hetero-duplex. Pyrene and anthraquinone moieties were tethered on acyclic D-threoninol linkers and linked to adjacent residues by using standard phosphoramidite chemistry. When pyrene and anthraquinone were incorporated at pairing positions in complementary strands of natural DNA oligonucleotides, the duplex was stabilized significantly. Moreover, a pyrene hexamer and an anthraquinone hexamer formed a stable artificial hetero-duplex without the assistance of natural base pairs. The pyrene/anthraquinone pair was so stable that even trimers formed a hetero-duplex under conditions in which natural DNA strands of three residues do not.

    DOI: 10.1002/chem.201502653

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  13. Ultrasensitive Molecular Beacon Designed with Totally Serinol Nucleic Acid (SNA) for Monitoring mRNA in Cells Invited Reviewed

    Keiji Murayama, Yukiko Kamiya, Hiromu Kashida, Hiroyuki Asanuma

    CHEMBIOCHEM   Vol. 16 ( 9 ) page: 1298 - 1301   2015.6

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    Language:English   Publishing type:Rapid communication, short report, research note, etc. (scientific journal)   Publisher:WILEY-V C H VERLAG GMBH  

    An artificial nucleic acid based on acyclic serinol building blocks and termed serinol nucleic acid (SNA) was used to construct a fluorescent probe for RNA visualization in cells. The molecular beacon (MB) composed of only SNA with a fluorophore at one terminus and a quencher at the other was resistant to enzymatic digestion, due to its unnatural acyclic scaffold. The SNA-MB could detect its complementary RNA with extremely high sensitivity; the signal-to-background (S/B) ratio was as high as 930 when perylene and anthraquinone were used as the fluorophore and quencher pair. A high S/B ratio was also achieved with SNA-MB tethering the conventional Cy3 fluorophore, and this probe enabled selective visualization of target mRNA in fixed cells. Thus, SNA-MB has potential for use as a biological tool capable of visualizing RNA in living cells.

    DOI: 10.1002/cbic.201500167

    Web of Science

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    PubMed

  14. Evaluation of intrinsic spectroscopic properties of chromophore assemblies by shielding with cyclohexyl base pairs within a DNA duplex Reviewed

    Hiromu Kashida, Naofumi Higashiyama, Tomohiro Kato, Hiroyuki Asanuma

    BIOORGANIC & MEDICINAL CHEMISTRY   Vol. 21 ( 20 ) page: 6191 - 6197   2013.10

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    Language:English   Publishing type:Rapid communication, short report, research note, etc. (scientific journal)   Publisher:PERGAMON-ELSEVIER SCIENCE LTD  

    Here, we investigated spectroscopic behaviors of tetramethylrhodamine (TMR) homo- and hetero-dimers within DNA duplex. In order to shield the chromophores from natural base pairs, we used cyclohexyl base pairs as 'insulators'; these pairs were inserted between the chromophores and nucleobases. When a single TMR moiety was sandwiched between cyclohexyl base pairs, the emission intensity increased by fivefold relative to a TMR between natural base pairs, because electron transfer from nucleobases was suppressed. Next, we inserted two TMRs between the cyclohexyl base pairs and found that they facilitated H-dimer formation of TMR; a distinct hypsochromic shift was induced only when cyclohexyl base pairs were inserted. We further examined quenching behavior of a TMR paired with a quencher dye between cyclohexyl base pairs. Interestingly, fluorescence from TMR was quenched by nitro methyl red more efficiently in the presence of cyclohexyl base pairs than in their absence. This suggests that neighboring natural base pairs disturbed electron or hole transfer between the fluorophore and the quencher. The cyclohexyl base pairs shielded the chromophore pair from the natural base pairs and allowed intrinsic electron transfer. (C) 2013 Elsevier Ltd. All rights reserved.

    DOI: 10.1016/j.bmc.2013.04.032

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    PubMed

  15. Highly stable duplex formation by artificial nucleic acids aTNA and SNA with acyclic scaffolds Reviewed

    Murayama, K, Tanaka, Y, Toda, T, Kashida, H, Asanuma, H

    Chem. Eur. J.   Vol. 19 ( 42 ) page: 14151 - 14158   2013

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    Language:English   Publishing type:Rapid communication, short report, research note, etc. (scientific journal)  

    DOI: 10.1002/chem.201301578

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    PubMed

  16. Selective labeling of mature RISC using a siRNA carrying fluorophore-quencher pair Reviewed

    Yukiko Kamiya, Anna Ito, Hiroshi Ito, Masaaki Urushihara, Junya Takai, Taiga Fujii, Xingguo Liang, Hiromu Kashida, Hiroyuki Asanuma

    CHEMICAL SCIENCE   Vol. 4 ( 10 ) page: 4016 - 4021   2013

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    Language:English   Publishing type:Rapid communication, short report, research note, etc. (scientific journal)   Publisher:ROYAL SOC CHEMISTRY  

    RNA interference (RNAi) is an endogenous gene silencing system that has been harnessed to inhibit expression of specific genes through the introduction of short double-stranded RNAs, called small interfering RNAs (siRNAs) into cells. After entry into a cell, an siRNA is assembled into the RNA-induced silencing complex (RISC) and suppresses the target gene translation through interaction between the antisense (guide) strand of the siRNA and the target mRNA. To evaluate the intracellular fate of siRNAs, we performed imaging analyses using siRNAs labeled with newly designed fluorophore-quencher clusters introduced through the base surrogate with D-threoninol as a scaffold. Fluorescence microscopy analyses indicated that mature RISC containing fluorescently labeled antisense strand was localized within P-bodies. Thus, the antisense strand uptake into the RISC machinery was successfully visualized.

    DOI: 10.1039/c3sc51197a

    Web of Science

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  17. Ultrafast photoisomerization and its single-shot pump pulse efficiency of trans-azobenzene derivative: Compound for photosensitive DNA Reviewed

    Tao Chen, Atsushi Yamaguchi, Kazumasa Igarashi, Naoya Nakagawa, Hidenori Nishioka, Hiroyuki Asanuma, Mikio Yamashita

    OPTICS COMMUNICATIONS   Vol. 285 ( 6 ) page: 1206 - 1211   2012.3

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    Language:English   Publishing type:Rapid communication, short report, research note, etc. (scientific journal)   Publisher:ELSEVIER SCIENCE BV  

    The femtosecond photoisomerization processes of trans (T) 4-carboxy-2',6'-dimethylazobenzen, which has been employed recently as an efficient photoregulator of DNA hybridization, were clarified by the rate equation analysis of measured transient absorbance changes with (350 nm) and without (380 nm) ground-state absorption of both the reactant (T) and photoproduct (cis: C) isomers under S-2(T)-band excitation (360 nm, 150 fs pump): after excitation to the S-2(T) state with a 450-fs lifetime, similar to 1.5% of the 1-molecules in the S-2(T) state are isomerized to the c-form within similar to 6 ps through the intermediate state (so called bottleneck state), but most of those return back to the T ground-state S-2(T) via the internal conversion processes with an ultrafast kinetic rate of 2.2 x 10(12) s(-1). Moreover, the rate equation analysis enables us to determine the T-to-C photoisomerization rate eta(T,C) per pump pulse to be 0.0011 at the pump energy of 80 nJ from the amplitude A(3,350) of the offset component in the 350-nm probe signal, and to obtain the photoisomerization quantum yield Phi(T,C) = 0.094. The latter value is slightly lower than that of T-azobenzene, and well agrees with that (Phi(T,C) = 0.097) measured by the conventional CW irradiation method using a photostationary state. (C) 2011 Elsevier B.V. All rights reserved.

    DOI: 10.1016/j.optcom.2011.10.032

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  18. Nick Sealing by T4 DNA Ligase on a Modified DNA Template Tethering a Functional Molecule on D-Threoninol Reviewed

    Liang Xingguo, Kenta Fujioka, Hiroyuki Asanuma

    Chem. Eur. J.   Vol. 17   page: 10388-10396   2011

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  19. Photon-fueled DNA nanodevice carrying two different photoswitches Reviewed

    Hidenori Nishioka, Xingguo Liang, Tomohiro Kato, Hiroyuki Asanuma

    Angew. Chem. Int. Ed.     page: ***-***   2011

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  20. DNAを切断するはさみ

    西岡英則, 浅沼浩之

    化学   Vol. 64   page: 70-71   2009

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    Language:Japanese   Publishing type:Article, review, commentary, editorial, etc. (scientific journal)  

    遺伝子工学(遺伝子組み換え技術)は、1)遺伝子であるDNAの特定の位置での“裁断”、2)得られたDNA断片の、ベクターと呼ばれる遺伝子の“運び屋”への“縫製”、そして3)ベクターの細胞内への導入(形質転換)、という3つの基本技術に基づいている。この中でも1)のDNAを“裁断”する “はさみ”=制限酵素 の発見が、現在の遺伝子工学を可能にしたと言っても過言ではない。この天然由来の“はさみ”に相当する制限酵素には様々な種類が存在し、その多くは4~6塩基程度の塩基配列を認識してDNAを切断する。したがって数千塩基程度の短い遺伝子ならば、天然の制限酵素を用いることで特定の1~2箇所を切断することが可能である。しかしながら、高等生物のような巨大なゲノムDNAに対して利用すると非常に多くの断片が生じてしまう。例えば、30億塩基を持つヒトゲノムに対して6塩基しか認識しない制限酵素を利用すると、おおよそ73万 (= 30億÷46)もの断片が生じてし

  21. Unexpected efficient ab initio DNA synthesis at low temperature by using thermophilic DNA

    Xingguo Liang, Tomohiro Kato, Hiroyuki Asanuma

    Nucleic Acids Symp. Ser.   Vol. 51   page: 351-352   2007.11

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    Language:English   Publishing type:Research paper, summary (national, other academic conference)  

    DNA was synthesized in the absence of DNA or RNA as template (or primer) from dNTPs at relatively low temperatures (25~50oC) by thermophilic Vent DNA polymerase whose proper reaction temperature for primer extension is 70~80oC. Unexpectedly, the ab initio DNA synthesis was even more efficient at 50oC as compared with that at 70oC. Interestingly, the ab initio DNA synthesis by Vent (exo-), a mutant version of Vent DNA polymerase lacking of 3&amp;cent;&amp;reg;5&amp;cent; exonuclease activity, became much less efficient, and it could only carry out ab intio DNA synthesis after a long incubation time. This remarkable difference between Vent and Vent (exo-) indicates that the exonuclease activity domain of Vent may play an important role at the initiation step of ab initio DNA synthesis.

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Presentations 98

  1. RNAより前に、XNAの世界は存在したか? Invited

    浅沼浩之

    生命の起原および進化学会 シンポジウム w/ABC早稲田サテライト  2021.3.11  生命の起原および進化学会

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    Event date: 2021.3

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Venue:On-line   Country:Japan  

  2. 非環状型人工核酸SNAとその類縁体の医療展開 Invited

    浅沼浩之

    令和2年度東海シンポジウム  2021.1.15  高分子学会東海支部

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    Event date: 2021.1

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Venue:On-line   Country:Japan  

  3. How far can we escape from DNA? Invited International conference

    Hiroyuki Asanuma

    Program Conference CLiC digital summer school  

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    Event date: 2020.8

    Language:English   Presentation type:Oral presentation (invited, special)  

    Venue:Fraukfurt on line   Country:Japan  

  4. Photoresponsive XNAs for the photo-switching of bio- and nano-functions International conference

    Hiroyuki Asanuma

    China-Japan Joint Interdisciplinary Symposium on Molecular Magnetic Materials 

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    Event date: 2019.12

    Language:English   Presentation type:Oral presentation (invited, special)  

    Venue:Guangzhou   Country:China  

  5. Acyclic XNAs of controlled orthogonality towards DNA and RNA Invited

    Hiroyuki Asanuma

    The Fourth A3 Roundtable Meeting on Asia Chemical Probe Research Hub  

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    Event date: 2019.11

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  6. Acyclic SNA and aTNA as a new class of XNA for bio- and nanotechnology Invited

    Hiroyuki Asanuma

    ISNAC 2019  

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    Event date: 2019.10

    Language:English   Presentation type:Oral presentation (invited, special)  

    Venue:Koganei Civic Center   Country:Japan  

  7. DNA nanocapsule for photo-triggered drug release Invited International conference

    Hiroyuki Asanuma

    2019 International Research Forum on Biology and Medical Science (IRFBMS 2019)  

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    Event date: 2019.8

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Taiwan, Province of China  

  8. DNA and XNA nanomachines powered by light irradiation Invited

    Hiroyuki Asanuma

    10th NTTH Joint Symposium  

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    Event date: 2019.7

    Language:English   Presentation type:Oral presentation (invited, special)  

    Venue:Hotel Hokke Club Hakodate   Country:Japan  

  9. Design of functional oligonucleotide with acyclic scaffold Invited International conference

    Hiroyuki Asanuma

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    Event date: 2019.6

    Language:English   Presentation type:Oral presentation (invited, special)  

    Venue:Shenyang Pharmaceutical University   Country:China  

  10. 非環状型人工核酸が拓く新たなバイオテクノロジー Invited

    浅沼 浩之

    ワークショップ「核酸化学の開く未来」 

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    Event date: 2019.6

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  11. Azobenzene-tethered DNA for photo-triggered nanocapsule for drug release Invited International conference

    Hiroyuki Asanuma

    World Chemistry Conference and Exhibition 2019 (WCCE-2019) 

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    Event date: 2019.6

    Language:English   Presentation type:Oral presentation (invited, special)  

    Venue:Brussels, Belgium   Country:Belgium  

  12. Totally acyclic XNAs for medical applications Invited International conference

    Hiroyuki Asanuma

    Functional Nucleic Acids: From Laboratory to Targeted Molecular Therapy(FNA Perth 2018) 

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    Event date: 2018.11

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Australia  

  13. DNA二重鎖のナノフォトニクスへの応用 Invited

    浅沼 浩之

    第22回 VBLシンポジウム  

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    Event date: 2018.11

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  14. Azobenzene-Tethered DNA for Photo-Driven Nanomachine Invited International conference

    Hiroyuki Asanuma

    XIX NOST-Organic Chemistry Conference (XIX-NOST-OCC) 

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    Event date: 2018.9

    Language:English   Presentation type:Oral presentation (invited, special)  

    Venue:Hotel Grand Hyatt, Goa, India   Country:India  

  15. Light-triggered DNA nanomachine Invited

    Hiroyuki Asanuma

    FISNA2018 

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    Event date: 2018.7

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  16. 医療応用を目指した核酸の機能的再インストール Invited

    浅沼浩之

    第29回万有仙台シンポジウム―未来を指向した有機化学 

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    Event date: 2018.6

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Venue:仙台   Country:Japan  

  17. 非環状型人工核酸による分子演算の拡張と核酸医薬への展開 Invited

    浅沼浩之

    情報計算化学生物学会(CBI学会) 

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    Event date: 2018.5

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Venue:グランフロント大阪 ナレッジキャピタル   Country:Japan  

  18. DNA nanomachine and nanoarchitecture powered by light-irradiation Invited International conference

    Hiroyuki Asanuma

    The International Conference of Layers, Films and Membranes for Green, Environmental and Biomedical Sciences (LFM2018) 

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    Event date: 2018.5

    Language:English   Presentation type:Oral presentation (keynote)  

    Venue: National Taiwan University of Science and Technology, Taipei (Tiwan)   Country:Taiwan, Province of China  

  19. Creation of functional oligonucleotide with nucleotide-analogues designed from acyclic scaffold Invited

    Hiroyuki Asanuma

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    Event date: 2018.3

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  20. Azobenzene-tethered DNA for the photo-regulation of DNA functions Invited International conference

    Hiroyuki Asanuma

    INTERNATIONAL CONGRESS ON PURE & APPLIED CHEMISTRY 2018 (ICPAC2018) 

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    Event date: 2018.3

    Language:English   Presentation type:Oral presentation (invited, special)  

    Venue:Siem Reap, Cambodia   Country:Cambodia  

  21. Light-driven DNA nanomachine with an azobenzene-tethered DNA as photon-engine International conference

    Hiroyuki Asanuma

    the Pure and Applied Chemistry International Conference 2018 (PACCON 2018) 

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    Event date: 2018.2

    Language:English   Presentation type:Oral presentation (invited, special)  

    Venue: Hat Yai, Songkhla (Thailand)   Country:Thailand  

  22. Light-driven molecular machines with azobenzene-tethered DNA Invited International conference

    Hiroyuki Asanuma

    International Conference on Natural and Artificial Molecular Machines (NAMM2018) 

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    Event date: 2017.12

    Language:English   Presentation type:Oral presentation (invited, special)  

    Venue:IIT Bombay (India)   Country:India  

  23. "Design of totally acyclic XNAs for medical applications Invited

    Hiroyuki Asanuma

    The Second International Symposium on Biofunctional Chemistry (ISBC2017) 

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    Event date: 2017.12

    Language:English   Presentation type:Oral presentation (invited, special)  

    Venue:Kyoto Univ. (Kyoto)   Country:Japan  

  24. SNA and iL-aTNA for nucleic acid medicine Invited

    Hiroyuki Asanuma

    1st Minisymposium on Material Biology  

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    Event date: 2017.10

    Language:English   Presentation type:Oral presentation (invited, special)  

    Venue:Tokyo institute of Technology   Country:Japan  

  25. Orientation-dependent FRET in DNA duplex Invited

    Hiroyuki Asanuma

    FISNA2017 

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    Event date: 2017.7

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  26. Orientation-Dependent FRET in DNA Duplex for Structural Analysis of Secondary Structure in Solution Invited International conference

    Hiroyuki Asanuma

    NTTH symposium 

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    Event date: 2017.7

    Language:English   Presentation type:Oral presentation (invited, special)  

    Venue:Takayama, Gifu   Country:Japan  

  27. Programmable Artificial Nucleic Acids for Bio-application Invited

    Hiroyuki Asanuma

    The 20th ISIR International Symposium  

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    Event date: 2016.12

    Language:English   Presentation type:Oral presentation (invited, special)  

    Venue:Osaka, Japan   Country:Japan  

  28. D-L-aTNA and SNA as a new class of acyclic XNA Invited International conference

    Hiroyuki Asanuma

    Beilstein Organic Chemistry Symposium 2016 Nucleic Acid Chemistry  

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    Event date: 2016.10

    Language:English   Presentation type:Oral presentation (invited, special)  

    Venue: Prien (Chiemsee), Germany   Country:Germany  

  29. Physics in DNA(4); [2+2] photodimerization of stilbene derivatives within the DNA duplex Invited International conference

    Hiroyuki Asanuma, Tetsuya Doi, Hiromu Kashida

    The First Roundtable Meeting on Chemical Probe Research Hub 

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    Event date: 2016.9

    Language:English   Presentation type:Oral presentation (invited, special)  

    Venue: Fukuoka, Japan   Country:Japan  

  30. Orientation-dependent FRET in DNA duplex International conference

    Hiroyuki Asanuma

    3rd Fluorescent Biomolecules and Their Building Blocks-Design and Applications (FB3) 

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    Event date: 2016.7

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:China  

  31. Tracing the Fate of siRNA

    Hiroyuki Asanuma

    FIBER International Summit for Nucleic Acids 2016 (FISNA2016) 

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    Event date: 2016.7

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  32. 非環状型人工核酸による光機能性ナノマテリアルの創製

    浅沼浩之

    第65回高分子学会年次大会 

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    Event date: 2016.5

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Venue:神戸国際会議場・展示場 神戸   Country:Japan  

  33. Stemless linear probe for the detection of RNA in living cell International conference

    H. Asanuma, M. Akahane, R. Niwa, Y. Kamiya, H. Kashida

    Pacifichem2015  

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    Event date: 2015.12

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:United States  

  34. Stemless linear probe for detecting mRNA in living cell International conference

    Hiroyuki Asanuma, Mariko Akahane, Yukiko Kamiya, Hiromu Kashida

    BIT's 6th World Gene Convention-2015 

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    Event date: 2015.11

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:China  

  35. RNA detection in living cell with super-sensitive linear probe International conference

    Hiroyuki Asanuma

    International Conference on Small Science 2015 (ICSS-2015) 

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    Event date: 2015.11

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Thailand  

  36. Tracing the "fate" of siRNA International conference

    Yukiko Kamiya, Anna Ito, and Hiroyuki Asanuma

    The 3rd China-Japan Symposium on Nanomedicine 

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    Event date: 2015.6

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:China  

  37. Stemless linear probe with multiple fluorophores on D-threoninols for thefluorescent imaging of m-RNA in cell. International conference

    Hiroyuki Asanuma, Mariko Akahane, Hiromu Kashida, Yukiko Kamiya

    1st International Caparica Conference on Chromogenic and Emissive Materials 

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    Event date: 2014.9

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Portugal  

  38. de novo Design of functional oligonucleotide with acyclic scaffold International conference

    Hiroyuki Asanuma

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    Event date: 2014.7

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:United Kingdom  

  39. Orientation-dependent FRET between the intercalated donor and acceptor fluorophores International conference

    Hiromu Kashida, Ayako Kurihara, Tomohiro Kato, and Hiroyuki Asanuma

    XVIth Symposium on Chemistry of Nucleic Acid Components 

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    Event date: 2014.6

    Language:English   Presentation type:Oral presentation (general)  

    Country:Czech Republic  

  40. Design of highly sensitive fluorescent probe prepared from acyclic threoninol International conference

    Hiroyuki Asanuma, Yukiko Kamiya Hiromu Kashida, Xingguo Liang

    2014 China-Japan-Korea and Southeast Asia Joint Symposium on ADVANCED PROCESSING TECHNOLOGY and SAFETY CONTROL of AQUATIC PRODUCTS 

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    Event date: 2014.5

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:China  

  41. Functional siRNA for RNAi activation, improvement of strand selection, and fluorescence tracing of RISC International conference

    Hiroyuki Asanuma

    RNA-Methods Workshop 

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    Event date: 2013.12

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Germany  

  42. Azobenzene as a molecular engine for driving DNA-based nanomachine with light International conference

    Hiroyuki Asanuma

    Selective Regulation in Nanoscaled systems 

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    Event date: 2013.12

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Germany  

  43. Orientation-dependent FRET between the fluorophores within DNA duplex International conference

    Hiroyuki Asanuma

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    Event date: 2013.11

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Korea, Republic of  

  44. Functional siRNA for fluorescent monitoring of RISC with improved activity and strand selectivity

    Hiroyuki Asanuma, Anna Ito, Junya Takai, Masaaki Urushihara, Hiroshi Ito, Taiga Fujii, Xingguo Liang, and Yukiko Kamiya

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    Event date: 2013.11

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  45. Physics in DNA International conference

    Hiroyuki Asanuma

    A3RONA 2013 in Kobe 

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    Event date: 2013.8 - 2013.9

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  46. DNA nano-engineering for the construction of photon-fuelled molecular-machine with azobenzenes as molecular engine International conference

    Hiroyuki Asanuma

    French-Japanese Seminar on Bioinspired Methods and Applications 

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    Event date: 2013.2

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  47. DNA nano-engineering for the construction of photon-fuelled molecular-machine.

    H. Asanuma, H. Nishioka, X.G. Liang, Y. Kamiya

    5th NTTH symposium 

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    Event date: 2012.12

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  48. Control of emission property by assembling dyes for designing intelligent probe International conference

    Hiroyuki Asanuma

    2012 Telluride Workshop on Nucleic Acid Chemistry 

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    Event date: 2012.7 - 2012.8

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:United States  

  49. Photon-fuelled DNA nanomachine carrying azobenzene as molecular engine International conference

    Hiroyuki Asanuma

    CIMTECH2012 

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    Event date: 2012.6

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Italy  

  50. Highly Sensitive Fluorescent Probe designed with Threoninol-Nucleotides International conference

    Hiroyuki Asanuma

    A3RONA 2012 

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    Event date: 2012.5

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Korea, Republic of  

  51. New Artificial Nucleic Acids from Acyclic Scaffolds

    K. Murayama, T. Toda, H. Kashida, and H. Asanuma

    BMMP-12 

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    Event date: 2012.1

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  52. Artificial nucleotides for therapy-siRNA activation and probing-

    Hiroyuki Asanuma

    GCOE satellite sympoium  

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    Event date: 2011.11

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  53. Photon-fuelled nanomachine carrying azobenzene as molecular engine International conference

    Hiroyuki Asanuma

    A3RONA2011 

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    Event date: 2011.10

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:China  

  54. OLD BUT NEW ARTIFICIAL NUCLEIC ACIDS FROM ACYCLIC THREONINOL (aTNA) AND SERINOL (SNA) International conference

    Hiromu Kashida, Keiji Murayama, Takasuke Toda, Xingguo Liang, and Hiroyuki Asanuma

    XVth Symposium on Chemistry of Nucleic Acid Components 

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    Event date: 2011.6

    Language:English   Presentation type:Oral presentation (keynote)  

    Country:Czech Republic  

  55. Light-up of DNA with artificial nucleotides

    H. Kashida, K. Sekiguchi, H. Asanuma

    BMMP11 

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    Event date: 2011.1

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  56. 次世代核酸医薬を目指した人工核酸の設計

    浅沼浩之

    名古屋大学予防早期医療創成センター 第4回研究会 

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    Event date: 2010.11

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  57. Light-up of DNA with Threoninol-Nucleotides International conference

    A3RONA 2010 JAPAN 

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    Event date: 2010.10

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  58. 人工DNAを活用した簡便かつ高感度検出が可能なプローブ設計

    浅沼浩之

    生体分子計測のボトムアップテクノロジー 

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    Event date: 2010.10

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  59. AZOBENZENE-TETHERED DNA FOR THE PHOTOREGULATION OF DNA FUNCTIONS

    IRT 2010 - XIX International Round Table on Nucleosides, Nucleotides and Nucleic Acids 

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    Event date: 2010.8

    Language:English   Presentation type:Oral presentation (invited, special)  

  60. カートリッジ型人工核酸によるDNAの光機能化

    国際バイオEXPO 

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    Event date: 2010.6

    Language:Japanese   Presentation type:Oral presentation (general)  

    Country:Japan  

  61. RATIONAL DESIGN OF PHOTORESPONSIVE DNA WITH CARTRIDGE-TYPE NUCLEOTIDE International conference

    The 4th International Symposium on Polymer Chemistry (PC2010) 

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    Event date: 2010.6

    Language:English   Presentation type:Oral presentation (invited, special)  

  62. Design of in-stem molecular beacon (ISMB) with "threoninol nucleotide" for the discrimination of polymorphisms International conference

    Gene-2009 

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    Event date: 2009.12

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  63. 遺伝子発現の光制御を目指した光応答性DNAの開発

    第30回日本レーザー医学会総会 

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    Event date: 2009.12

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  64. Threoninol-nucleotidesによるDNAの再インストール

    浅沼浩之

    第58回高分子討論会 

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    Event date: 2009.9

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  65. Rational design of functional DNA with threoninol-nucleotides International conference

    Vielberth-Symposium on Functional Nucleic Acids 

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    Event date: 2009.9

    Language:English   Presentation type:Oral presentation (invited, special)  

  66. Photo-driven DNA Nanomachine with New Duplex Motif Composed of Threoninol International conference

    International Conference on Materials for Advanced Technologies 

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    Event date: 2009.7

    Language:English   Presentation type:Oral presentation (invited, special)  

    In the present paper, we demonstrate photoresponsive DNA tweezers as a nanomachine fuelled with photons by using azobenzene-modified DNA. The tweezers are opened by UV light irradiation (330-350 nm) and closed by visible light irradiation (440-460 nm) without adding oligonucleotides as the fuel.

  67. 光機能性インテリジェントDNAの設計と応用

    平成21年度第三回PST-net 例会 

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    Event date: 2009.4

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

    光機能性DNAを用いた機能性材料の設計と応用について講演する。

  68. 光が導くバイオテクノロジー

    「光科学技術と応用」シンポジウム 

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    Event date: 2009.2

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

    光応答性DNAを用いた遺伝子発現の光制御に関する今後の展望について講演する。

  69. DNAを利用した光機能マテリアルの開発

    平成20年度東海シンポジウム 

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    Event date: 2009.1

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

    我々は、非環状リンカーのD-Threoninolを活用した機能分子の導入法が上記の目的に合うことを見出した。D-ThreoninolをScaffoldに用いて機能分子(インターカレーター)を導入した“人工塩基=Threoninol nucleotide”は、任意の配列に任意の数DNA中に導入することが可能であり、しかも二重鎖の不安定化や基質特異性を損なわずに二重鎖内にインターカレートする。

  70. Photoregulation of Gene Expression with Azobenzene-tethered Promoter International conference

    Ninth International Symposium on biomimetic Materials Processing (BMMP-9) 

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    Event date: 2009.1

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

    In the present paper, we propose another strategy for the photoregulation of gene expression with the azobenzene-tethered DNA. Azobenzene is introduced into the promoter region (T7-promoter) of RNA polymerase (RNAP) and transcription reaction by RNAP is photoregulated by trans-cis isomerization of the incorporated azobenzenes.

  71. 非環状リンカーによるDNAの再インストール

    日本学術振興会第174委員会第27回研究会 

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    Event date: 2008.12

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

    本講演でリボースに代わる新たなScaffoldとして非環状リンカーのD-Threoninol(Fig.1a参照)を活用した“DNAの再インストール”と、その応用展開について解説する。

  72. PHOTOREGULATION OF DNA FUNCTIONS BY AZOBENZENE-TETHERED OLIGONUCLEOTIDES International conference

    NU-UM Joint Symposium 

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    Event date: 2008.11

    Language:English   Presentation type:Oral presentation (invited, special)  

    Here, efficient photo-switching of hybridization with this modified DNA and its application to the bio-reaction are introduced.

  73. 配列の差異を検出するインテリジェントDNAプローブの開発

    第39回中部化学関係学協会支部連合秋季大会 

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    Event date: 2008.11

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

    本講演では、このthreoninol-nucleotideを活用した、SNPsやIndelsを検出可能なインテリジェントDNAプローブについて解説する。

  74. AZOBENZENE-TETHERED PROMOTER TOWARDS THE PHOTO-REGULATION OF GENE EXPRESSION International conference

    Japan-Korea Polymer Young Scientists Symposium 

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    Event date: 2008.10

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

    A simple and effective approach for introducing azobenzene moieties tethered on D-threoninol to long duplex DNA (gene) was developed. By PCR and enzymatic ligation, the chemically modified part was introduced to the exact position we expected. By using the constructed photoresponsive gene, the GFP expression could be simply switched on and off by light-irradiation. As the photoswitch was equipped in the promoter, this strategy is promising to photoregulate the expression of any gene or functiona

  75. DNAの再インストールによる光デバイス化

    高分子エレクトロニクス研究会 

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    Event date: 2008.6

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

    我々はリボースに頼らない非天然機能分子の導入法の一つとしてD-threoninolが非常に有効であることを見出し、これをScaffoldに用いたDNAの“再インストール”を行っている。本講演では、アゾベンゼン導入D-threoninolを使用した光デバイスとしてのDNAの再インストールについて紹介する。

  76. Interstrand Clustering of Dyes in the DNA Duplex with Threoninol International conference

    Hiroyuki Asanuma, Taiga Fujii, Hiromu Kashida

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    Event date: 2008.1

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  77. リボースに頼らないDNAの光機能化

    浅沼浩之

    機能性分子シンポジウム 

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    Event date: 2008.1

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

    本発表では、D-threoninolをScaffoldに使用したDNAの再インストールについて、紹介する。

  78. 情報を持った繊維:DNAファイバーの光機能化

    浅沼浩之

    繊維学会夏季セミナー 

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    Event date: 2007.9

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

    筆者らは、核酸が関与する酵素反応や分子マシンの光制御を目的とした光機能化DNAファイバーの開発を目指した。光刺激は数ある外部刺激の中でも1)反応系を汚染しない、2)分子設計により励起波長の制御が可能、3)レンズによる集光やレーザー光の利用で局所的な刺激ができる、といった長所を持つ。また近年パルスレーザーの進歩に伴って多光子励起が可能になり、より長波長の光による色素分子の励起も容易になりつつある。ここでは筆者らが近年開発した可逆的な応答を示す光機能化DNAファイバーについて解説する。

  79. DNAの再構築 -リボースを使用しないオリゴヌクレオチドの機能化-

    浅沼浩之

    FIBERシンポジウム 

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    Event date: 2007.6

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

    我々は、リボースに頼らない非天然分子の導入法の一つとしてD-threoninolを提案してきた。ScaffoldとしてD-threoninolを用いると、DNA二重鎖の安定性を損なうことなくインターカレーターを多数導入することが出来る。またD-threoninolに導入した機能分子を“擬似塩基”として天然のオリゴヌクレオチド中に導入することも可能である。本講演では、D-threoninolをScaffoldに用いたDNAの機能化について解説する。

  80. 超分子デバイスとしての機能性DNA

    浅沼浩之

    第10回VBLシンポジウム 

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    Event date: 2006.10

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

    本発表では、筆者らが近年開発した可逆的な応答を示す光デバイス化DNAについて解説する。

  81. Azobenzene-Tethered DNA as a Photo-Switching Biodevice International conference

    11th International Symposium on Colloidal and Molecular Electro-Optics (ELOPTO-2006) 

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    Event date: 2006.5

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

    DNA has not only a biological role of storing genetic information but also various physical and chemical functions. These role and functions are mainly based on the spontaneous hybridization of two strands that are complementary each other. If the formation and dissociation of the DNA duplex can be photo-regulated as schematically illustrated in Fig.1, we can get a new effective photo-switching biodevice and scope of the application should be extended, such as artificial regulation of gene exp

  82. 色素とのコンジュゲーションによるDNAの光機能化

    浅沼浩之

    表面技術協会 第113講演大会 

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    Event date: 2006.3

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

    色素分子は、発光・吸収などの光学特性や、特定波長の光照射による可逆的な構造異性化など特異的な性質を有しており、DNAとのコンジュゲーションによって光応答性などDNAに新たな機能の付与が期待できる。逆にDNAの超分子性を活用することで色素分子のクラスター化が容易となり、単量体では実現不可能な光学物性の発現が期待できる。本講演では、互いの特性を生かした色素とDNAの新たなコンジュゲートについて、筆者らの最近の成果を紹介する。

  83. PHOTOREGULATION OF DNA FUNCTIONS BY AZOBENZENE-TETHERED OLIGONUCLEOTIDES International conference

    Sixth International Symposium on Biomimetic Materials Processing (BMMP-6) 

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    Event date: 2006.1

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

    We have synthesized modified DNA tethering azobenzenes, and hybridization with its complementary strand has been successfully photo-regulated. Here, efficient photo-switching of hybridization with this modified DNA and its application to the bio-reaction are introduced.

  84. 生体機能の光制御を目指したアゾベンゼン導入DNAの設計

    浅沼浩之

    第16回MRSシンポジウム 

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    Event date: 2005.12

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  85. 機能分子との交互コンジュゲーションが広げるDNAの可能性

    浅沼浩之

    SORST ジョイントシンポジウム (4)  ― クロスオーバーする生命と化学 ― 

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    Event date: 2005.11

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

    機能分子の核酸への導入は、天然に無い性能をDNAやRNAに付与する上で有効な手段である。しかし化学修飾は多くの場合二重鎖の不安定化や配列特異性の低下を伴うため、5’末端への機能分子の導入が一般的である。もちろん精緻にデザインした化学修飾ヌクレオシドを合成してDNA鎖の内部に導入した例も多数報告されているが、合成や分子設計に煩雑さを伴う場合もある。従ってDNA二重鎖の安定性や配列特異性を損なわず簡便に機能分子を多数導入できる一般的な手法が開発されれば、応用の可能性が大きく広がると期待できる。我々はアゾベンゼン

  86. New Artificial Nucleic Acids from Acyclic Scaffolds International conference

    K. Murayama, T. Toda, H. Kashida, H. Asanuma

    BMMP-12  2012.1.24 

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    Language:English   Presentation type:Oral presentation (invited, special)  

  87. 非環状型人工核酸が拓く新たなバイオテクノロジー Invited International conference

    浅沼 浩之

    ワークショップ「核酸化学の開く未来」  2019.6.19  埼玉大学先端産業国際ラボラトリー

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    Language:Japanese   Presentation type:Oral presentation (invited, special)  

  88. 医療応用を目指した核酸の機能的再インストール Invited International conference

    浅沼浩之

    第29回万有仙台シンポジウム―未来を指向した有機化学  2018.6.8  万有財団

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    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Venue:仙台  

  89. Tracing the "fate" of siRNA

    Yukiko Kamiya, Anna Ito, Hiroyuki Asanuma

    The 3rd China-Japan Symposium on Nanomedicine  2015.6.19 

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    Language:English   Presentation type:Oral presentation (invited, special)  

  90. Totally acyclic XNAs for medical applications Invited

    Hiroyuki Asanuma

    Functional Nucleic Acids: From Laboratory to Targeted Molecular Therapy(FNA Perth 2018)  2018.11.22 

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    Language:English   Presentation type:Oral presentation (invited, special)  

  91. Physics in DNA(4); [2+2] photodimerization of stilbene derivatives within the DNA duplex Invited

    Hiroyuki Asanuma, Tetsuya Doi, Hiromu Kashida

    The First Roundtable Meeting on Chemical Probe Research Hub  2016.9.22 

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    Language:English   Presentation type:Oral presentation (invited, special)  

    Venue:Fukuoka, Japan  

  92. Physics in DNA

    Hiroyuki Asanuma

    A3RONA 2013 in Kobe  2013.8.30 

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    Language:English   Presentation type:Oral presentation (invited, special)  

  93. Photoresponsive XNAs for the photo-switching of bio- and nano-functions

    Hiroyuki Asanuma

    China-Japan Joint Interdisciplinary Symposium on Molecular Magnetic Materials  2019.12.27 

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    Language:English   Presentation type:Oral presentation (invited, special)  

    Venue:Guangzhou  

  94. Photon-fuelled nanomachine carrying azobenzene as molecular engine

    Hiroyuki Asanuma

    A3RONA2011  2011.10.14 

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    Language:English   Presentation type:Oral presentation (invited, special)  

  95. Orientation-Dependent FRET in DNA Duplex for Structural Analysis of Secondary Structure in Solution Invited

    Hiroyuki Asanuma

    NTTH symposium  2017.7.14 

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    Language:English   Presentation type:Oral presentation (invited, special)  

    Venue:Takayama, Gifu  

  96. Orientation-dependent FRET between the intercalated donor and acceptor fluorophores

    Hiromu Kashida, Ayako Kurihara, Tomohiro Kato, Hiroyuki Asanuma

    XVIth Symposium on Chemistry of Nucleic Acid Components  2014.6.8 

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    Language:English   Presentation type:Oral presentation (general)  

  97. Orientation-dependent FRET between the fluorophores within DNA duplex

    Hiroyuki Asanuma

    2013.11.24 

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    Language:English   Presentation type:Oral presentation (invited, special)  

  98. OLD BUT NEW ARTIFICIAL NUCLEIC ACIDS FROM ACYCLIC THREONINOL (aTNA) AND SERINOL (SNA)

    Hiromu Kashida, Keiji Murayama, Takasuke Toda, Xingguo Liang, Hiroyuki Asanuma

    XVth Symposium on Chemistry of Nucleic Acid Components  2011.6.5 

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    Language:English   Presentation type:Oral presentation (keynote)  

▼display all

Research Project for Joint Research, Competitive Funding, etc. 3

  1. 非環状型機能性人工核酸の開発

    Grant number:AS2915131U  2017.10 - 2020.3

    研究成果展開事業 研究成果最適展開支援プログラムA-STEP 

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    Authorship:Principal investigator  Grant type:Competitive

    Grant amount:\51350000 ( Direct Cost: \39500000 、 Indirect Cost:\11850000 )

  2. DNAハイブリダイゼーションの高効率可逆光スイッチング技術の開発と,そのバイオテクノロジーへの応用

    2005.10 - 2011.3

      More details

    Grant type:Competitive

  3. 生体反応の光制御を目指した人工核酸デバイスの創製

    2002.11 - 2006.3

    科学技術振興機構PRESTO 

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    Grant type:Competitive

KAKENHI (Grants-in-Aid for Scientific Research) 26

  1. Creation of artificial genetic system with acyclic artificial nucleic acids and application to evolutionary molecular engineering

    Grant number:21H05025  2021.7 - 2026.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (S)

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    Authorship:Principal investigator  Grant type:Competitive

    Grant amount:\190450000 ( Direct Cost: \146500000 、 Indirect Cost:\43950000 )

  2. 核酸医薬への応用を目指した非環状型人工核酸の開発

    2019.9

    国立研究開発法人日本医療研究開発機構  先端的バイオ創薬等基盤技術開発事業 

    浅沼浩之

      More details

    Authorship:Principal investigator  Grant type:Competitive

    Grant amount:\146900000 ( Direct Cost: \113000000 、 Indirect Cost:\33900000 )

  3. Design of robust and error-free signal-amplification circuit with orthogonal artificial nucleic acids

    Grant number:18H03933  2018.4 - 2021.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (A)

    Asanuma Hiroyuki

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    Authorship:Principal investigator  Grant type:Competitive

    Grant amount:\44980000 ( Direct Cost: \34600000 、 Indirect Cost:\10380000 )

    We have previously developed our original artificial nucleic acid, D-aTNA, which cross-pairs with neither natural D-DNA nor D-RNA. In contrast to D-aTNA, our SNA can cross-pair with D-aTNA, D-DNA, and D-RNA. With these artificial nucleic acids, a new signal amplification system was designed by combining D-aTNA amplification circuit with SNA interface. The D-aTNA amplification circuit can be triggered by natural D-RNA that is orthogonal to D-aTNA because interface SNA can convert input D-RNA into D-aTNA output. By using this system, we have successfully developed robust signal amplification system that can detect small amount of microRNA (miR21) in the presence of contaminating DNA and RNA.

  4. 非環状型機能性人工核酸の開発

    Grant number:AS2915131U  2017.10 - 2020.3

    国立研究開発法人科学技術振興機構  研究成果最適展開支援プログラム(A-STEP) 

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    Authorship:Principal investigator  Grant type:Competitive

    Grant amount:\51350000 ( Direct Cost: \39500000 、 Indirect Cost:\11850000 )

  5. Design of cross-talking amplification circuit with orthogonal nucleic acid

    Grant number:16K12522  2016.4 - 2018.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Challenging Exploratory Research

    Asanuma Hiroyuki

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    Authorship:Principal investigator  Grant type:Competitive

    Grant amount:\3510000 ( Direct Cost: \2700000 、 Indirect Cost:\810000 )

    Orthogonality is a key concept that has been broadly interpreted to mean that components or elements do not affect each other or behave independently. Previously, we have developed three artificial nucleic acids, D-aTNA, L-aTNA, SNA, composed of acyclic serinol derivatives as scaffolds. All of them can form remarkably stable homo-duplexes. While D-aTNA cross-pairs neither natural DNA (D-DNA) nor RNA (D-RNA), SNA with achiral scaffold can cross-pair with D-, L-aTNA, D-DNA, and D-RNA. In the present study, we designed a logic gate with D-aTNA that is orthogonal to D-RNA, which can be activated by D-RNA input via SNA as an interface: A seesaw gate with D-aTNA and interface SNA targeting miR21 was designed. Fluorescence could successfully be amplified by D-RNA (miR21) input that triggered D-aTNA seesaw gate via SNA.

  6. Development of highly sensitive linear probe without stem structure

    Grant number:25248037  2013.4 - 2016.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (A)

    Asanuma Hiroyuki, KAMIYA Yukiko, KASHIDA Hiromu

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    Authorship:Principal investigator  Grant type:Competitive

    Grant amount:\47450000 ( Direct Cost: \36500000 、 Indirect Cost:\10950000 )

    We have designed new fluorescent probe termed linear probe that does not involve stem structure. In this project, we have successfully developed extremely sensitive linear probe involving both perylenes and anthraquinones as fluorophores and quenchers, respectively; signal-to-back ground ratio became as high as 1600. Due to the remarkable nuclease resistivity, newly designed linear probe could fluorescently detect mRNA in cell. We have further developed strand-invader by combining linear probe and PNA. For this purpose, we multiply introduced ethynylperylenes and anthraquinones into DNA for stable complexation with DNA and suppressed complexation with PNA. When linear probe was incubated double-stranded DNA involving target site in the presence of complementary PNA, we could observe fluorescent increase due to the strand invasion. Even PCR product could be fluorescently labelled in a strand-invading manner.

  7. Development of highly sensitive linear probe that does not require stem structure

    2013.4 - 2015.3

    Grant-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research(A)

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    Authorship:Principal investigator  Grant type:Competitive

    Grant amount:\47450000 ( Direct Cost: \36500000 、 Indirect Cost:\10950000 )

  8. Motion generation based on cooperation of structured gel and chemical reaction field

    Grant number:24104005  2012.6 - 2017.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

    Hagiya Masami, KAWAMATA Ibuki, HAMADA Shogo

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    Authorship:Coinvestigator(s)  Grant type:Competitive

    In the study of slime type robot, we aimed "expansion of scale" of molecular robot. Specifically, using a polymer gel as a reaction field, a heterogeneous reaction space of order of millimeter is generated, and various molecular devices are operated on it. This concept ultimately aims at realization of macroscopic functions such as taxis. The results obtained in the project include a method of controlling reaction/diffusion behavior of molecular devices based on quantitative measurement in a gel, development of various new gel actuators, a method of controlling sol-gel phase transition, and a theoretical framework called “gel automaton” for programming the discrete reaction fields defined on the cell space of the gel.

  9. Development of a new strand-invader with artificial nucleotides

    Grant number:23651128  2011 - 2012

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Challenging Exploratory Research

    ASANUMA Hiroyuki

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    Authorship:Principal investigator  Grant type:Competitive

    Grant amount:\4030000 ( Direct Cost: \3100000 、 Indirect Cost:\930000 )

    In this project, we aimed at developing a new strand-invader by combining unmodified peptide nucleic acid (PNA) and modified DNA (TN -DNA) involving new base-surrogate=Threoninol-Nucleotide (TN) that tethers a functional molecule such as intercalator on D-threoninol. As a possible strand-invader, the duplex stability should be in the following order; DNA/PNA, TN-DNA/DNA > DNA/DNA > TN-DNA/PNA. First, we searched a functional molecule and optimum way of introducing TN into DNA that satisfies above requisites. We found that planar molecule (intercalator) with electron-withdrawing group could significantly stabilize the DNA duplex. Furthermore, introduction of TN at every two nucleotides into DNA remarkably facilitated the duplex formation with DNA and retarded hybridization with PNA. On the basis of these results, we combined unmodified PNA and TN-DNA involving anthraquinone as a strand-invader, which was successfully invaded into the target DNA duplex.

  10. Development of a photo-driven molecular machine with photo-responsive DNA

    Grant number:21241031  2009 - 2012

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (A)

    ASANUMA Hiroyuki, LIANG Xingguo

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    Authorship:Principal investigator  Grant type:Competitive

    Grant amount:\46800000 ( Direct Cost: \36000000 、 Indirect Cost:\10800000 )

    In this project, we aimed at creating new photo-driven DNA machines with photo-responsive DNA involving azobenzenes. First, we designed a newly modified azobenzene that enables efficient photo-regulation of DNA hybridization. We found that modification of a distal benzene ring at two ortho-positions was effective for the improvement of both photoregulatory efficiency and thermal stability of cis-form. Furthermore, we also clarified that the modified duplex of alternating base-pair and azobenzene residues allowed complete photo-regulation of DNA hybridization only by light-irradiation. Based on these results, we successfully constructed 1) photo-driven DNA machine that can reversibly digest target RNA, 2) photo-degradable DNA nano-capsule, and 3) DNA machine that can move like seesaw by the combination with visible light-responsive azobenzene.

  11. Gene Manipulation of Huge DNA by Super Artificial Restriction Enzyme

    Grant number:18001001  2006 - 2009

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Specially Promoted Research

    KOMIYAMA Makoto, , ASANUMA Hiroyuki, SUMAOKA Jun

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    Authorship:Coinvestigator(s)  Grant type:Competitive

    We developed man-made tools (super artificial restriction enzyme) which cut double-stranded DNA at desired site with desired site-specificity. Even huge genomic DNA (e.g., the genome of human beings composed of 3x10^9 base-pairs) was selectively hydrolyzed at one target site. The scission fragments were connected with foreign DNA using DNA ligase, and the recombinant DNA was successfully expressed in mammalian cells. Furthermore, the site-selective scissions by the super artificial restriction enzyme were satisfactorily recognized by the repair system in human cells and promoted the desired homologous recombination. High potential of the super artificial restriction enzyme for future applications has been indicated.

  12. 新規人工核酸"グライコ核酸"の創製

    Grant number:18655069  2006 - 2007

    科学研究費助成事業  萌芽研究

    浅沼 浩之

      More details

    Authorship:Principal investigator  Grant type:Competitive

    Grant amount:\3600000 ( Direct Cost: \3600000 )

    本研究ではペプチド核酸に糖鎖を導入したグライコ核酸を設計・創製する。そして1)糖鎖導入で従来のPNAに両親媒性を付与することで20mer以上の長鎖DNAに対する二重鎖形成能を飛躍的に高める、2)糖鎖の持っ親水性を活用して疎水性の高いインターカレーターの導入を可能にする、ことを目標とする。
    18年度の研究成果において本研究の目標に掲げた親水性の付与を実現したので、19年度は得られたグライコ核酸のタンパク質との特異的相互作用について検討した。まず18年度に確立したグライコ核酸の"ヌクレオシド"モノマーの合成法に従い、アミノ酸リンカーにD-およびL-Lysを用いて機能分子としてマンノースを導入したカートリッジモノマーを設計・合成した。さらにFmoc固相合成法によりマンノースユニットを持った"グライコ核酸"を合成し、マンノースに特異的なレクチンであるConcanavalin A(ConA)を使用して、グライコ核酸との相互作用を蛍光強度の変化で評価した。その結果、PNA中にマンノースユニットを1つ導入したグライコ核酸のConA認識能力は単糖と同程度であったが、二つ導入した系では糖のクラスター効果に由来する高い認識力が認められた。このように、任意の場所に任意の数の糖モノマーを導入できる本研究のグライコ核酸の特徴を活かすことで、高いタンパク質認識能を付与可能なことも明らかとなった。本研究者はアゾベンゼンのような疎水性の高いインターカレーターをPNA中に導入する方法も併せて確立したので、本申請研究のグライコ核酸と組み合わせることで更なる高機能化が期待できる。

  13. Construction of artificial DNA device for the photo-switching of molecular nano machine

    Grant number:17310066  2005 - 2007

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

    ASANUMA Hroyuki

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    Authorship:Principal investigator  Grant type:Competitive

    Grant amount:\15530000 ( Direct Cost: \14900000 、 Indirect Cost:\630000 )

    In the present study, we developed 1)photo-responsive DNAs(=artificial DNA devices) that are applicable to the photo-switching of nano-machine,2)photo-fueled molecular tweezers.
    Photo-responsive DNA that corresponds to the "engine" of a molecular machine was successfully synthesized on the basis of precise molecular design. The photo-regulatory efficiency of the obtained azobenzene-tethered DNA was three-fold higher than that of our previously reported one : the duplex was largely stabilized in transform and was further destabilized in cis-form with the newly synthesized photo-responsive DNA. Furthermore, we have successfully designed new photo-responsive DNA with reversed switching mode : the duplex was stabilized in cis-form whereas destabilized in trans-form.
    By utilizing one of the photo-responsive DNAs synthesized as above, photo-driven molecular machine -molecular tweezers- was developed. In contrast with the previous DNA nano-tweezers that used oligonucleotides as the fuel, our new nano-tweezers mount photo-responsive DNA as a "photo-engine". In other words, our nano-tweezers are "solar-driven" nano-machine. As exactly designed, the photo-driven nano-tweezers could be opened by irradiating UV light and closed by irradiating visible light.
    For the previous DNA nano-tweezers, oligonucleotides were used as the fuel : the mechanical motion was carried out by the hybridization of one DNA fuel to target sequences followed by removing it with another DNA that is completely or partially complementary to the first one. As a result, a duplex. DNA was produced as a waste product in every working cycle. Thus, the operating efficiency decreased gradually with the accumulation of "wastes". In our system, opening and closing are carried out by successive photo-irradiation to the solution involving photoresponsive DNA with UV and visible light that is environmental-friendly and never contaminate the system. For every cycle, almost all the tweezers were closed after visible light irradiation, and the tweezers were open after UV light irradiation. The cycling efficiency did not decrease after open and close of the tweezers for ten times, because no extra oligonucleotides were added. Thus, this molecular machine can be operated semipermanently as long as the DNAs involved are not destroyed.

  14. 形態変化する分子を用いた並行計算と分散計算

    Grant number:14085202  2002 - 2006

    科学研究費助成事業  特定領域研究

    萩谷 昌己, 横山 茂之, 陶山 明, 浅沼 浩之, 藤井 輝夫, JOHN Rose, 村田 智, 岩崎 裕, 吉信 達夫

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    Authorship:Coinvestigator(s)  Grant type:Competitive

    形態変化するDNA分子の設計方法:萩谷は、連続ヘアピンからなる分子マシンに関して、ヘアピンの配列を変化させたときに、3連続ヘアピンから成る分子マシンの挙動がどのように変化するかを調べた。分子マシンの光制御を目指した光機能性超分子の構築:浅沼は、これまでとは逆に「cis-体で二重鎖形成、trans-体で解離」というスイッチングが可能な光応答性DNAの設計と実現に成功した。ヘアピンとバルジによる並行計算:萩谷は、Whiplash PCRの熱力学的な解析と、状態遷移の効率化(Displacement WPCR)を行った。レトロウィルスによる並行計算:陶山は、二つの正帰還と一つの負帰還反応から構成されたオシレータをRTRACの基本反応を用いて構築した。シミュレーションにより発振可能な条件が存在することを確かめた後、実装を進めた。翻訳系による並行計算:横山は、翻訳システムを利用した「オートマトン」を動物細胞(培養細胞)内でも構築することを目標に、非天然型アミノ酸が細胞に与えられた場合にのみ活性化され、サプレッサーtRNAにアミノ酸を結合するような酵素(アミノアシルtRNA合成酵素)を用いることにより、サプレションを制御する機構を構築した。DNA Walker:萩谷は、DNA Walkerの構築に向けて、温度、pH、光の三種類の入力によって駆動する分子マシンに関する予備実験を行った。特に、これらの三種類の入力の独立性について調べた。マイクロチップのための微量液体制御機構の開発:藤井は、液滴操作に必要な周辺技術等の整備を進め、オンデマンド式で液滴の生成・合一の操作が可能にした。また、本技術を用いてDNAとPNAのハイブリダイゼーション反応と電気泳動による反応産物の分離操作をデバイス上で実現した

  15. Artificial Restriction Enzymes for Future Nucleic Acids Chemistry

    Grant number:13132204  2001 - 2004

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research on Priority Areas

    KOMIYAMA Makoto, ASANUMA Hiroyuki, SUMAOKA Jun

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    Authorship:Coinvestigator(s)  Grant type:Competitive

    We have achieved the sequence selective scissions of both DNA and RNA by using our artificial systems.
    1. DNA cleavage
    We found that the phosphodiester linkages in gap sites were preferentially hydrolyzed by a Ce(IV)/EDTA complex. Even though the complex was not covalently bound to any sequence-recognizing moiety, the DNA scission selectively occurs at the gap sites, since the linkages therein is more susceptible to catalysis by the Ce(IV) complex than are those in double-stranded portions. Furthermore, this gap-selective DNA hydrolysis was greatly promoted by introducing monophosphate groups at the gap sites and recruiting the Ce(IV) complex to the gap site.
    By combining Ce(IV)/EDTA with, two pseudocomplementary peptide nucleic acids (pcPNAs), both strands in double-stranded DNA were selectively hydrolyzed at the target site. When two pcPNAs invaded into the double-stranded DNA, only the designated portion in each of the two strands was single-stranded like structure. On the treatment of this invasion complex with Ce(IV)/EDTA, both of the single-stranded portions are selectively hydrolyzed. With the use of two pcPNAs bearing either aminocarboxylates or phosphates, the DNA scission at target site was greatly promoted. Furthermore, the hydrolytic scission products were successfully connected with foreign double-stranded DNA by using T4 ligase.
    2. RNA cleavage,
    When oligonucleotides bearing two acridine groups form heteroduplexes with substrate RNA, the two phosphodiester linkages in front of the acridines were selectively activated and preferentially hydrolyzed by lanthanide ion. By using these systems, RNA fragments of predetermined length were obtained from long RNA substrates and analyzed by MALDI-TOF MS. Single nucleotide polymorphisms in homozygous and heterozygous samples were accurately and easily detected in terms of difference in mass number.

  16. 光応答性DNAによる酵素反応の光制御

    Grant number:13878116  2001

    科学研究費助成事業  萌芽的研究

    浅沼 浩之, 小宮山 真

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    Authorship:Principal investigator  Grant type:Competitive

    Grant amount:\2100000 ( Direct Cost: \2100000 )

    本研究では、アゾベンゼンをT7プロモーターに導入し、アゾベンゼンのtrans-cis異性化によるT7-RNAPのプロモーター部位への結合を制御することで、転写反応の光制御を目指した。アゾベンゼンはT7プロモーターのnon-template鎖に導入したところ、プロモーターの上流-10と-11位の間にアゾベンゼンを導入した場合に最も効果的な光制御が実現できた。
    アゾベンゼンの無い天然のプロモーターを用いた場合は、UV照射下でも未照射下とほぼ同じ速度で転写反応が進行した。しかしアゾベンゼン導入プロモーターを用いると、暗条件下では転写産物がほとんど得られなかったのに対し、UV照射下では天然のプロモーターとほぼ同量のm-RNAが得られた。すなわちアゾベンゼンがtrans-体の場合は転写反応が著しく抑制されるのに対し(転写off)、cis-体では転写が天然のプロモーターと同程度進行すると(転写on)が明らかとなった。この光応答性プロモーターを用いれば、転写反応を光照射のみでon-off制御することが可能となった。すなわち、暗条件下では"スイッチ"はoffであったが、UV照射によってスイッチがonになり、m-RNAが生成した。この後、更に可視光照射によって再びスイッチをoffに切り替えることが出来た。この様に、光応答性プロモーターを用いることで転写反応のon-off制御を実現した。

  17. 化学修飾DNAを用いた遺伝子発現の光制御

    Grant number:11167216  2000

    科学研究費助成事業  特定領域研究(A)

    浅沼 浩之, 小宮山 真

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    Authorship:Principal investigator  Grant type:Competitive

    Grant amount:\3500000 ( Direct Cost: \3500000 )

    本申請では、遺伝子発現の光制御を目指している。前年度我々は、トリメチレンリンカーの中心の炭素にアゾベンゼンを導入した修飾DNAを合成し、アゾベンゼンの光異性化によって二重鎖の形成と解離を光のみで制御できることを明らかにしている。本年度はその機構を明らかにするため、アゾベンゼンを含むDNAの二重鎖の構造を2D NMRによって解析した。その結果、1)trans-アゾベンゼンが隣接する塩基対間にインターカレートしている、2)trans-アゾベンゼンがインターカレートすることでメジャーグルーブ側に傾いている、ことが判明した。一方cis-体は非平面分子であるため、スタッキングによる安定化が得られずむしろ立体障害で不安定化し、結果としてtrans→cis異性化によって二重鎖形成能が大きく変化することが明らかとなった。また、NOESYの詳細な解析から、極性の高い成分はRのコンフィギュレーションであることも明らかにした。
    更に光応答性DNAを、T7-DNAポリメラーゼによるDNAの伸長反応に応用し、目論見どおりアゾベンゼンの光異性化で、伸長反応をON-OFF制御できることを明らかにした。更に詳細な解析から、モジュレーターが5'末端付近から徐々に剥がれるような機構で光制御が実現できていることを見出した。
    光応答性DNAを酵素反応の制御に応用するためには、天然の構造からの差異は小さいほうが良い。そこでリボースの2'Oにアゾベンゼンを導入したウリジンを合成し、DNA内に組み込んだ。この系は配列依存性が大きいが、trans-cis異性化でTmが変化することを見出した。また、アゾベンゼンと並んで代表的な光異性化分子であるスピロピラン導入DNAも合成に成功した。

  18. モレキュラーインプリント法でシクロデキストリンの配向を制御したレセプターの構築

    Grant number:11750734  1999 - 2000

    科学研究費助成事業  奨励研究(A)

    浅沼 浩之

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    Authorship:Principal investigator  Grant type:Competitive

    Grant amount:\2200000 ( Direct Cost: \2200000 )

    我々はすでに、β-シクロデキストリン(β-CyD)の配向の制御にモレキュラーインプリント法を適用することで、コレステロールを強く認識する架橋シクロデキストリン高分子の合成に成功している。更にMALDI-TOFMSを用いた分析から、コレステロールが鋳型として存在することで、CyDの二量化が促進されることを見出した。また、CyDのビニルモノマーを用いることで水中での鋳型重合を実現し、ジペプチドや抗生物質を選択的に認識する人工レセプターの合成にも成功している。本年度はこの手法の液体高速クロマトグラフィー(HPLC)の担体への応用を目指した。
    バッチテストでインプリント効果が確認されているコレステロールを鋳型として合成した高分子を適当な大きさに粉砕し、ステンレススチールカラムに充填してHPLCとしてのゲスト保持能を検討した。その結果、鋳型分子であるコレステロールに対して高い保持能を示した。一方鋳型分子以外の分子に対する保持能は、わずかしか向上せず、インプリント効果により、鋳型分子に特異的な認識部位が形成されていることが明らかとなった。
    また、メチレンビスアクリルアミドを架橋剤に用いてCyDのビニルモノマーとの共重合により水中で合成した架橋シクロデキストリン高分子は、力学的強度が小さく、耐圧性に乏しかった。そこで、十分な強度を持つシリカゲル上にインプリント高分子を固定化することで耐圧性を向上させることに成功した。このようにして得られたHPLC担体は、水を溶離液として使用しても鋳型分子に対して高い保持能を示すことが明らかとなった。以上の様に、本研究のインプリント高分子は、HPLC担体としても応用可能なことが明らかとなった。

  19. 水系で水素結合により分子認識するハイブリッドポリマーの構築

    Grant number:10126209  1998

    科学研究費助成事業  特定領域研究(A)

    浅沼 浩之

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    Authorship:Principal investigator  Grant type:Competitive

    Grant amount:\2000000 ( Direct Cost: \2000000 )

    天然の抗体と同様に水溶液中で基質を正確に認識する人工レセプターの合成は、ホスト・ゲスト化学に携わる研究者にとって究極の目標である。本年度は(1)高分子効果による水溶液中での水素結合形成の促進、ならびに(2)モレキュラーインプリント法によるホスト分子相互の分子配向の制御、を追究した。
    (1) 高分子効果による水溶液中での水素結合形成の促進
    本研究者は、既にポリ(2-ビニル-4,6-ジアミノ-1,3,5-トリアジン)(PVDAT)が水溶液中で、相補的な水素結合によりチミンとウラシルを選択的に認識することを見出している。しかしPVDATは水に不溶の高分子であり、固-液界面という特殊な環境が水中での水素結合に寄与していることも予想された。そこで2-ビニル-4,6-ジアミノ-1,3,5-トリアジン(VDAT)をアクリルアミドと共重合させて水に可溶化し、高分子場が均一水溶液中でも相補的な水素結合形成に有効に機能するか検討した。その結果、上記共重合体は、均一水溶液においても相補的な水素結合を形成してチミンを選択的に認識することが判明した。以上より、高分子場が均一水溶液中でも水素結合形成に有効なことが明らかとなった。
    (2) モレキュラーインプリント法によるホスト分子相互の分子配向の制御
    本研究者は、シクロデキストリン(CyD)を鋳型分子存在下でDMSO中でジイソシアナート架橋することで、水中で基質を選択的に認識する人工レセプターが合成であることを明らかにしている。本年度は、この方法で形成される認識部位の構造を物理化学的な手段を用いて詳細に分析した。その結果、コレステロールを鋳型分子に用いた場合、2分子のβ-CyDがジイソシアナートで架橋された構造を持つ認識部位が高分子内に形成されていることを明らかにした。

  20. 水系で水素結合により分子認識する人工高分子レセプターの開発

    Grant number:09750964  1998

    科学研究費助成事業  奨励研究(A)

    浅沼 浩之

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    Authorship:Principal investigator  Grant type:Competitive

    Grant amount:\1800000 ( Direct Cost: \1800000 )

    本研究者は、水に不溶のポリ(2-ビニル-4,6-ジアミノ-1,3,5-トリアジン)(PVDAT)が水溶液からチミンとウラシルを選択的に認識・分離することを見出し、これがジアミノトリアジン残基との相補的水素結合の形成に基づくことを分光学的な手法で明らかにした。高分子場が形成する疎水場は水溶液中だけでなくアルコール中でも有効であり、メタノール中でも相補的水素結合形成によってチミンとウラシルを認識・分離した。またメタノール中ではスタッキング相互作用など疎水相互作用が強く働かないため、相補的水素結合の数に基づく基質選択性は水中よりも高かった。
    さらに高分子場が上記のような不均一系ではなく、均一水溶液系でも有効に疎水場を形成して基質との相補的水素結合が可能となるか検討した。ジアミノトリアジン残基を持つ水溶性高分子は、2-ビニル-4,6-ジアミノ-1,3,5-トリアジンをアクリルアミドと共重合させることで得られた。上記共重合体は、均一水溶中でもチミンを選択的に認識することが、限外ろ過膜を使用した透析実験より判明した。またH-NMR測定より、チミンのイミドプロトンのみが共重合体の存在下で低磁場シフトしたことから、チミンの認識が相補的水素結合に基づいていることを明らかにした。一方対応するモノマーでは、チミンとの相補的水素結合の形成は全く認められなかった。以上より、高分子場が均一水溶液中でも水素結合形成に有効なことが明らかとなった。

  21. 水溶液中で水素結合を形成し、基質を分子認識するハイブリッドポリマーの構築

    Grant number:09232213  1997

    科学研究費助成事業  重点領域研究

    小宮山 真, 浅沼 浩之

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    Authorship:Coinvestigator(s)  Grant type:Competitive

    これまでに合成されている水素結合部位で分子認識する人工レセプターは、水溶液中では、水分子が水素結合サイトに対して競争阻害を起こすために十分に機能しない。我々は、これらの問題の解決を目指して、高分子効果の活用を検討した。その結果、ジアミノトリアジンを側鎖に持つポリ2-ビニル4,6-ジアミノトリアジン(PVDT)が、水の中でも、相補的な水素結合を効率的に形成し、基質を高選択的に認識することを見出した。すなわち、一連の核酸塩基の中で、ジアミノトリアジンと3本の相補的水素結合を形成するウラシルおよびチミンのみがPVDTにより強く吸着される。それに対して、水素結合サイトが2箇所であるシトシンの吸着はわずかであり、水素結合サイトが1箇所であるピリミジンは吸着されない。このように、PVDTの複合体形成能は、ゲストとの相補的水素結合サイトの数と良好に対応している。PVDTとウラシルとの結合定数をLangmuirプロットにより見積もったところ、93M^<-1>と十分に大きな値であった。それに対して、PVDTの単量体モデルおよび2量体モデルは、ウラシルと水素結合を形成しない。こうして、(1)PVDTが、水溶液中で、水素結合によりゲスト化合物を効率的かつ選択的に分子認識すること、および(2)水中での水素結合形成には高分子場か必須であること が明らかとなった。さらに我々は、目的とするゲスト化合物に対応した人工レセプターを自在に構築する手法の開発を目指して、ゲスト化合物の存在下にシクロデキストリン(CyD)を架橋し、CyD柏互の分子配向を制御した。今年度に主たる認識対象としたのはコレステロールであり、鋳型分子としてのコレステロール存在下でβ‐CyDをDMSO中でジイソシアネート架橋することで、水溶液中でコレステロールを強く認識する人エレセプターの合成にも成功した。

  22. 細胞内微量miRNAの検出を目指した人工核酸によるシグナル増幅回路の開発

    2016.4 - 2021.3

    公益財団法人 旭硝子財団  ステップアップ助成 

    浅沼浩之

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    Authorship:Principal investigator  Grant type:Competitive

    Grant amount:\12000000 ( Direct Cost: \12000000 )

  23. 構造化ゲルと化学反応場の協働による運動創発

    2012.10 - 2017.3

    科学研究費補助金  研究領域提案型(計画研究)

    浅沼浩之

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    Authorship:Coinvestigator(s)  Grant type:Competitive

    Grant amount:\52000000 ( Direct Cost: \40000000 、 Indirect Cost:\12000000 )

  24. 医療応用を目指した人工核酸の創成

    2012.4 - 2015.3

    キャノン財団  研究助成プログラム「産業基盤の創生」 

    浅沼浩之

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    Authorship:Principal investigator  Grant type:Competitive

    Grant amount:\20000000 ( Direct Cost: \20000000 )

  25. スーパー制限酵素による巨大DNAの遺伝子操作

    2006.10 - 2011.3

    科学研究費補助金 

    小宮山真

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    Authorship:Coinvestigator(s) 

  26. 新規人工核酸“グライコ核酸”の創製

    2006

    科学研究費補助金  萌芽研究,課題番号:18655069

    浅沼 浩之

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    Authorship:Principal investigator 

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Industrial property rights 14

  1. 人工核酸を含むオリゴヌクレオチド

    浅沼浩之、樫田啓、村山恵司

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    Application no:特願2015-003424  Date applied:2015.1

    Country of applicant:Domestic  

  2. 人工核酸を含むオリゴヌクレオチド

    浅沼浩之, 樫田啓, 村山恵司

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    Application no:特願2015-003424  Date applied:2015.1

  3. 蛍光標識オリゴヌクレオチド誘導体及びその利用

    浅沼浩之 樫田啓 近藤展代 大澤卓矢 赤羽真理子

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    Applicant:名古屋大

    Application no:特願2011―221332号  Date applied:2011.10

    Country of applicant:Domestic  

  4. オリゴヌクレオチドプローブ及びその利用

    浅沼浩之、丸山厚、嶋田直彦、梁興国、樫田啓、藤井大雅、大澤卓矢、吉田安子、丹羽孝介

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    Applicant:日本碍子株式会社

    Application no:特願2011-33986  Date applied:2011.2

    Country of applicant:Domestic  

  5. イン・ステムビーコン型プローブ用のハイブリダイゼーション剤及びその利用

    丸山厚,嶋田直彦,浅沼浩之,梁興国,樫田啓,藤井大雅,大澤卓矢,吉田安子,丹羽孝介

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    Applicant:日本碍子株式会社

    Application no:特願2011―033986号  Date applied:2011

    Country of applicant:Domestic  

  6. オリゴヌクレオチド及びその利用

    浅沼 浩之、 樫田 啓、 関口 康司、近藤 展代

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    Application no:特願2010-206043  Date applied:2010.9

    Country of applicant:Domestic  

  7. オリゴヌクレオチドおよびその利用

    浅沼 浩之、 梁 興国、 樫田 啓、 西岡 英則、藤井 大雅、石川 顕慎

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    Application no:特願2010-194942  Date applied:2010.8

    Country of applicant:Domestic  

  8. インスレーター及びその利用

    樫田啓、浅沼浩之、関口康司

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    Applicant:法人名大

    Application no:特願2010-042632  Date applied:2010.2

    Country of applicant:Domestic  

  9. 標的核酸の検出方法

    浅沼浩之、梁興国、樫田啓、吉田安子、吉良茂樹、丹羽孝介

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    Applicant:法人名大、日本ガイシ(株)

    Application no:特願2009-298170  Date applied:2009.12

    Country of applicant:Domestic  

  10. オリゴヌクレオチドプローブ及びその利用

    浅沼浩之、梁興国、樫田啓、原雄一、吉田安子、吉良茂樹

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    Applicant:法人名大、日本ガイシ(株)

    Application no:特願2009-298160  Date applied:2009.12

    Country of applicant:Domestic  

  11. オリゴヌクレオチドプローブ及びその利用

    浅沼浩之、梁興国、樫田啓、吉田安子、高瀬智和、丹羽孝介

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    Applicant:法人名大、日本ガイシ(株)

    Application no:PCT/JP2009/061980  Date applied:2009.6

    Country of applicant:Domestic  

  12. ターゲットDNAの特異増幅方法の開発

    梁興国、浅沼浩之、鈴木昌友、加藤智博

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    Application no:特願2009-145741  Date applied:2009.6

    Country of applicant:Domestic  

  13. オリゴヌクレオチドプローブ及びその利用

    浅沼 浩之、梁 興国、樫田 啓、吉田 安子、高瀬 智和、丹羽 孝介

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    Application no:特願2008-172526  Date applied:2008.7

    Country of applicant:Domestic  

  14. DNAエンザイムおよびその活性制御方法

    浅沼浩之、小宮山 真、松永 大次郎、倉持 壮

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    Applicant:独立行政法人科学技術振興機構

    Application no:特願2004-55086  Date applied:2005.2

    Announcement no:PCT/JP/2005/003052 

    Country of applicant:Foreign country  

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Teaching Experience (Off-campus) 2

  1. 光スイッチングデバイスとしての光応答性DNAの開発と、その応用

    2007.4 - 2008.3 名古屋市立大学 大学院薬学研究科)

  2. 生命分子工学特論

    2005.4 - 2006.3 東京大学大学院工学系研究科化学生命工学専攻)