Faculty Profiles - MURAYAMA Keiji

Papers - MURAYAMA Keiji

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Nonenzymatic polymerase-like template-directed synthesis of acyclic l-threoninol nucleic acid Reviewed Open Access

Murayama Keiji, Okita Hikari, Kuriki Takumi, Asanuma Hiroyuki

NATURE COMMUNICATIONS Vol. 12 ( 1 ) 2021.2

Omega Nucleic Acids (ΩNA), Ultimate Nucleic Acids for Future Technology Reviewed Open Access

Hamada, S; Murayama, K; Takezawa, Y; Toyoda, R; Kuzuya, A

MOLECULES Vol. 31 ( 3 ) 2026.2

Membrane-Penetrating Molecular Device Based on a Triplex Containing Acyclic L-Threoninol Nucleic Acid Functionalized with Cholesterol Reviewed Open Access

Liu, KF; Asanuma, H; Murayama, K

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 2025.11

Reversible photocycloaddition of 8-pyrenylvinylguanine for photoreactive serinol nucleic acid (SNA) Reviewed

Murayama, K; Ikeda, A; Sato, F; Asanuma, H

ORGANIC & BIOMOLECULAR CHEMISTRY 2025.7

Highly Effective Chemical Ligation of DNA and l-aTNA. Reviewed International journal

Hikari Okita, Keiji Murayama, Hiroyuki Asanuma

Current protocols Vol. 5 ( 5 ) page： e70140 2025.5

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

Chemical ligation of nucleic acids is a significant strategy for the establishment of a variety of functional biological tools and other applications. However, the conventional methodology has been suffering from low reaction efficiency or generation of unnatural structures at the ligation site. This article describes an effective chemical ligation method that connects the hydroxyl group and the monophosphate group at the nick site on the template, generating a natural phosphodiester bond. The method uses only N-cyanoimidazole (CNIm) and divalent metal cations to achieve chemical ligation in a template-directed manner, which can be applied to the ligations of not only DNA but also artificial nucleic acids such as acyclic l-threoninol nucleic acid (l-aTNA). Quantitative ligation is available within 10 min for l-aTNA fragments on an l-aTNA template, and within 2 hr for DNA fragments on a DNA template under optimized conditions. The effective chemical ligation system reported here will enable the development of biotechnology and nanotechnology, including exploration of l-aTNA aptamer via in vitro selection, chemical synthesis of genome-sized DNA and l-aTNA, functionalization of nanostructure, and creation of an l-aTNA-based artificial life in the future. © 2025 Wiley Periodicals LLC. Basic Protocol 1: Chemical ligation using CNIm and divalent metal cation Basic Protocol 2: Imaging analysis of ligation reaction Basic Protocol 3: Mass spectrometry of ligation products Support Protocol: Kinetic analysis.

DOI： 10.1002/cpz1.70140

Web of Science

PubMed

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Chirality-Promoted Chemical Ligation and Reverse Transcription of Acyclic Threoninol Nucleic Acid. Reviewed International journal

Hikari Okita, Keiji Murayama, Hiroyuki Asanuma

Journal of the American Chemical Society Vol. 147 ( 21 ) page： 17967 - 17974 2025.4

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

The building blocks of current life on Earth are chiral compounds, such as 2'-deoxy-D-ribose of DNA and L-amino acids with homochirality, which play an important role in various biological reactions. We investigated the effect of chirality on the template-directed chemical synthesis of nucleic acids as a model for primitive replication of genetic materials in the absence of enzymes. The efficiency of the template-directed chemical ligation of two acyclic nucleic acids, achiral serinol nucleic acid (SNA) and chiral acyclic l-threoninol nucleic acid (L-aTNA), induced by N-cyanoimidazole and a divalent metal cation, was evaluated. The chemical ligation of SNA fragments on an SNA template was much slower than the ligation of L-aTNA fragments on an L-aTNA template. Examination of L-aTNA and SNA heteroligation and the effects of chimeric template strands revealed the crucial importance of L-aTNA chirality, which induces helical propagation and fixes the local conformation of the reactive phosphate group for effective chemical ligation. DNA and RNA templates also enhanced the ligation of SNA and L-aTNA fragments. "Reverse transcription" from template RNA to L-aTNA was also demonstrated. Our findings show that scaffold chirality is crucial for chemical replication and reverse transcription in XNA-based systems. Furthermore, the reverse transcription from RNA to L-aTNA will find applications in XNA-based in vitro selection, the creation of artificial life, and nanotechnologies.

DOI： 10.1021/jacs.5c03128

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Reversible Optical Control of Receptor Tyrosine Kinase Activity and ERK Dynamics Using Azobenzene-Carrying DNA Aptamer Agonist

Masahiro Wakano, Masaya Tsunoda, Keiji Murayama, Jumpei Morimoto, Ryosuke Ueki, Saeko Aoyama-Ishiwatari, Yusuke Hirabayashi, Hiroyuki Asanuma, Shinsuke Sando

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Vol. 147 ( 13 ) page： 11477 - 11484 2025.3

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

Receptor tyrosine kinases (RTKs) play a pivotal role in cell signaling through their activation via dimerization. Recent studies have demonstrated the importance of the temporal dynamics of RTK activity and downstream signals, such as ERK, in determining the cell fate. To better understand these dynamics, it is essential to develop methods capable of controlling the RTK activity with high temporal resolution. However, techniques for precisely modulating the activity of endogenous RTKs without requiring genetic modification remain insufficiently established. In this study, we developed a DNA aptamer agonist, Met-azo-aptamer, which enables reversible optical control of the activity of the c-Met receptor, a member of the RTK family. This was achieved by incorporating azobenzene, a photoisomerizable molecule, into a DNA aptamer that binds to c-Met. This design allows light-induced switching between the active and inactive structures of the aptamer. When the aptamer was applied to HeLa cells and exposed to ultraviolet or blue light, phosphorylation signals within the cells were activated in response to the light patterns. Furthermore, by variation of the light patterns, the Met-azo-aptamer successfully controlled the timing, amplitude, and duration of downstream ERK activation. The Met-azo-aptamer developed in this study offers a high-resolution method for investigating the relationship between RTK activation patterns and cell function or fate.

DOI： 10.1021/jacs.5c01559

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A Light-Powered Single-Stranded DNA Molecular Motor with Colour-Selective Single-Step Control Reviewed International coauthorship Open Access

Anderson, T; Wu, W; Sirbu, O; Tong, KS; Siti, W; Liu, XR; Kou, B; Murayama, K; Asanuma, H; Wang, ZS

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION Vol. 63 ( 32 ) 2024.8

DNA Reaction System That Acquires Classical Conditioning Reviewed International coauthorship

Nakakuki, T; Toyonari, M; Aso, K; Murayama, K; Asanuma, H; de Greef, TFA

ACS SYNTHETIC BIOLOGY Vol. 13 ( 2 ) page： 521 - 529 2024.1

Highly Functional Acyclic Xeno Nucleic Acids Invited Reviewed

Murayama, K; Okita, H; Asanuma, H

BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN Vol. 96 ( 10 ) page： 1179 - 1187 2023.10

Rapid Chemical Ligation of DNA and Acyclic Threoninol Nucleic Acid (aTNA) for Effective Nonenzymatic Primer Extension Reviewed Open Access

Hikari Okita, Shuto Kondo, Keiji Murayama, Hiroyuki Asanuma

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Vol. 145 ( 32 ) page： 17872 - 17880 2023.7

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

Previously, nonenzymatic primer extension reaction of acyclic l-threoninol nucleic acid (L-aTNA) wasachieved in the presence of N-cyanoimidazole (CNIm)and Mn2+; however, the reaction conditions were not optimizedand a mechanistic insight was not sufficient. Herein, we report investigationof the kinetics and reaction mechanism of the chemical ligation ofL-aTNA to L-aTNA and of DNA to DNA.We found that Cd2+, Ni2+, and Co2+ accelerated ligation of both L-aTNA and DNA and that the rate-determining step was activationof the phosphate group. The activation was enhanced by duplex formationbetween a phosphorylated L-aTNA fragment and template,resulting in unexpectedly more effective L-aTNA ligationthan DNA ligation. Under optimized conditions, an 8-mer L-aTNA primer could be elongated by ligation to L-aTNA trimers to produce a 29-mer full-length oligomer with60% yield within 2 h at 4 & DEG;C. This highly effective chemicalligation system will allow construction of artificial genomes, robustDNA nanostructures, and xeno nucleic acids for use in selection methods.Our findings also shed light on the possible pre-RNA world.

DOI： 10.1021/jacs.3c04979

Open Access

Web of Science

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Functionalization of acyclic xenonucleic acid with modified nucleobases Invited Reviewed Open Access

Keiji Murayama, Yuuhei Yamano, Hiroyuki Asanuma

Polymer Journal Vol. 55 ( 7 ) page： 743 - 752 2023.7

Authorship：Lead author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：Springer Science and Business Media LLC

DOI： 10.1038/s41428-023-00776-7

Open Access

Web of Science

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Other Link： https://www.nature.com/articles/s41428-023-00776-7

Kinesin motors driven microtubule swarming triggered by UV light Reviewed

Ishii Satsuki, Akter Mousumi, Murayama Keiji, Kabir Arif Md Rashedul, Asanuma Hiroyuki, Sada Kazuki, Kakugo Akira

POLYMER JOURNAL Vol. 54 ( 12 ) page： 1501 - 1507 2022.12

DNA Concentration Regulator That can be Driven for a Long Time Reviewed Open Access

Nakakuki Takashi, Murayama Keiji, Asanuma Hiroyuki

NEW GENERATION COMPUTING Vol. 40 ( 2 ) page： 681 - 702 2022.7

Orthogonal Amplification Circuits Composed of Acyclic NucleicAcids Enable RNA Detection br Reviewed Open Access

Chen Yanglingzhi, Nagao Ryuya, Murayama Keiji, Asanuma Hiroyuki

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Vol. 144 ( 13 ) page： 5887 - 5892 2022.4

Methyl group configuration on acyclic threoninol nucleic acids (aTNAs) impacts supramolecular properties Reviewed

Murayama Keiji, Kashida Hiromu, Asanuma Hiroyuki

ORGANIC & BIOMOLECULAR CHEMISTRY 2022.3

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

Ishii Satsuki, Murayama Keiji, Sada Kazuki, Asanuma Hiroyuki, Kakugo Akira

CHEMISTRY LETTERS Vol. 51 ( 3 ) page： 292 - 295 2022.3

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

Chen Yanglingzhi, Murayama Keiji, Asanuma Hiroyuki

CHEMISTRY LETTERS Vol. 51 ( 3 ) page： 330 - 333 2022.3

Renewable DNA Proportional-Integral Controller with Photoresponsive Molecules Open Access

Tamba Masaaki, Murayama Keiji, Asanuma Hiroyuki, Nakakuki Takashi

MICROMACHINES Vol. 13 ( 2 ) 2022.2

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

Asanuma Hiroyuki, Kamiya Yukiko, Kashida Hiromu, Murayama Keiji

CHEMICAL COMMUNICATIONS 2022.1

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

Kashida Hiromu, Nishikawa Keiji, Ito Yuka, Murayama Keiji, Hayashi Ichiyo, Kakuta Takahiro, Ogoshi Tomoki, Asanuma Hiroyuki

CHEMISTRY-A EUROPEAN JOURNAL Vol. 27 ( 59 ) page： 14582 - 14585 2021.10

RNA以前に非環状型XNAがPre-RNAとして存在したか? Invited

浅沼浩之, 沖田ひかり, 村山恵司

Vol. 49 page： 9 2021.9

Design and Hybridization Properties of Acyclic Xeno Nucleic Acid Oligomers Reviewed

Murayama Keiji, Asanuma Hiroyuki

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

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

Yamano Yuuhei, Murayama Keiji, Asanuma Hiroyuki

Dual Crosslinking Photo-Switches for Orthogonal Photo-Control of Hybridization Between Serinol Nucleic Acid and RNA Vol. 27 ( 14 ) page： 4599 - 4604 2021.3

Light-Regulated Liquid-Liquid Phase Separation for Spatiotemporal Protein Recruitment and Cell Aggregation Reviewed

Light-Regulated Liquid-Liquid Phase Separation for Spatiotemporal Protein Recruitment and Cell Aggregation

Light-Regulated Liquid-Liquid Phase Separation for Spatiotemporal Protein Recruitment and Cell Aggregation Vol. 13 ( 4 ) page： 5652 - 5659 2021.2

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

Kamiya Yukiko, Satoh Tadashi, Kodama Atsuji, Suzuki Tatsuya, Murayama Keiji, Kashida Hiromu, Uchiyama Susumu, Kato Koichi, Asanuma Hiroyuki

COMMUNICATIONS CHEMISTRY Vol. 3 ( 1 ) 2020.11

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

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

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

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

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

cis-On/trans-Off of DNA Hybridization with Alkylthio-azobenzene on L-Threoninol Responding to Visible Light

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

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

Orthogonally Photocontrolled Non-Autonomous DNA Walker

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

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

The Use of Serinol Nucleic Acids as Ultrasensitive Molecular Beacons

Murayama Keiji, Kashida Hiromu, Asanuma Hiroyuki

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

The DNA duplex as an aqueous one-dimensional soft crystal scaffold for photochemistry. Invited Reviewed Open Access

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

Bull. Chem. Soc. Jpn. Vol. 91 page： 1739-1748 2018.12

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

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

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

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

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

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

RSC ADVANCES Vol. 7 ( 54 ) page： 34049-34052 2017.7

Design of photofunctional oligonucleotides by copolymerization of natural nucleobases with base surrogates prepared from acyclic scaffolds

Asanuma Hiroyuki, Murayama Keiji, Kamiya Yukiko, Kashida Hiromu

POLYMER JOURNAL Vol. 49 ( 3 ) page： 279 - 289 2017.3

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

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

村山恵司, 浅沼浩之

化学 Vol. 71 ( 3 ) page： 66-67 2016.3

Acyclic artificial nucleic acids with phosphodiester bonds exhibit unique functions Reviewed Open Access

H. Kashida; K. Murayama; H. Asanuma

Polymer J. Vol. 48 page： 781-786 2016

Strand-invading linear probe combined with unmodified PNA Reviewed

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

Bioorg. Med. Chem. Vol. 24 page： 4129-4137 2016

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. Vol. 22 page： 267-273 2016

新規人工核酸SNAを用いたRNAイメージング

樫田啓, 村山恵司, 浅沼浩之

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

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

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

Chem. Eur. J. page： 6500-6503 2015

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

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

Chem. Commun. page： 6500-6503 2015

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

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

ChemBioChem page： 1298-1301 2015

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

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

Chem. Eur. J. page： 15974-15980 2015

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

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

ChemBioChem page： 2549-2555 2014

The sugar-deficient G-quadruplex: incorporation of aTNA in quadruplex 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

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 page： 14151-14158 2013

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

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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Papers - MURAYAMA Keiji