Faculty Profiles - ABE Hiroshi

Papers - ABE Hiroshi

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In vitro selection of a photoresponsive RNA aptamer to hemin Reviewed

Mingzhe Liu, Hiroshi Jinmei, Hiroshi Abe, Yoshihiro Ito

BIOORGANIC & MEDICINAL CHEMISTRY LETTERS Vol. 20 ( 9 ) page： 2964 - 2967 2010.5

Language：English Publishing type：Research paper (scientific journal) Publisher：PERGAMON-ELSEVIER SCIENCE LTD

A photoresponsive RNA aptamer to hemin was selected in vitro from a random sequence library of RNAs with azobenzene residues. The aptamer bound to hemin under visible light irradiation and was released by ultraviolet light. (C) 2010 Elsevier Ltd. All rights reserved.

DOI： 10.1016/j.bmcl.2010.02.109

New fluorogenic probe for detection of glutathione s-transferase activity in living cells

Ito Mika, Abe Hiroshi, Shibata Aya, Shimizu Shigeru, Alander Johan, Morgenstern Ralf, Ito Yoshihiro

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY Vol. 239 2010.3

Design and synthesis of indole derivatives of adenophostin A. A entry into subtype-selective IP<inf>3</inf> receptor ligands Reviewed

Tetsuya Mochizuki, Akihiko Tanimura, Akihiro Nezu, Mika Ito, Hiroshi Abe, Yoshihiro Ito, Mitsuhiro Arisawa, Satoshi Shuto

Tetrahedron Letters Vol. 51 ( 6 ) page： 977 - 979 2010.2

Publishing type：Research paper (scientific journal)

Indole derivatives 3a and 3b of adenophostin A (2) in which the adenine of 2 was replaced with indole or 4-fluoroindole was designed as potential inositol trisphosphate receptor ligands. These target compounds were successfully synthesized from the key disaccharide unit 6. Biological evaluation showed that 3b selectively activates IP3R1, a subtype of IP3 receptors. © 2009 Elsevier Ltd. All rights reserved.

DOI： 10.1016/j.tetlet.2009.12.045

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Synthesis and structural and pharmacological properties of cyclopropane-based conformationally restricted analogs of 4-methylhistamine as histamine H<inf>3</inf>/H<inf>4</inf> receptor ligands Reviewed

Takaaki Kobayashi, Mizuki Watanabe, Akira Yoshida, Shizuo Yamada, Mika Ito, Hiroshi Abe, Yoshihiro Ito, Mituhiro Arisawa, Satoshi Shuto

Bioorganic and Medicinal Chemistry Vol. 18 ( 3 ) page： 1076 - 1082 2010.2

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

On the basis of the previous results on a histamine H4 receptor agonist 4-methylhistamine and a cyclopropane-based conformationally restricted analog CEIC (3) with potent H3/H4 receptor antagonistic effect, 4-methylhistamine analogs 4 and 5 of CEIC were designed and synthesized. Compound 4 showed strong affinity (Ki = 38.7 nM) for the H3 receptor, which was more potent than a well-known H3 antagonist thioperamide. Stable tautomer and conformation of 3 and 4, which can affect the pharmacological activity, were analyzed by ab initio calculations. © 2009 Elsevier Ltd. All rights reserved.

DOI： 10.1016/j.bmc.2009.12.046

Hemin-Binding Aptamers and Aptazymes Reviewed

Mingzhe Liu, Hiroshi Abe, Yoshihiro Ito

GREEN POLYMER CHEMISTRY: BIOCATALYSIS AND BIOMATERIALS Vol. 1043 page： 111 - 123 2010

Language：English Publishing type：Research paper (international conference proceedings) Publisher：AMER CHEMICAL SOC

Aptamers are oligonucleotides that have been engineered through repeated rounds of in vitro selection or by the process of Systematic Evolution of Ligands by EXponential enrichment (SELEX) to bind to various molecular targets such as small molecules, proteins, nucleic acids, and even cells and tissues. Aptamers offer similar molecular recognition properties to the more commonly used antibodies. In addition to their ability to discriminate their target, aptamers offer some advantages over antibodies. For example, aptamers can be engineered completely in a test tube and are readily produced using chemical processes. On the other hand, some aptamers that have been developed exhibit enzyme activity after binding to their target molecule, and function as 'aptazymes'. Numerous aptamers and aptazymes have been used in biotechnology, diagnostics and therapy. In this study, we demonstrate that natural DNA/RNA aptamers produced by selection in vitro, not only bind to hemin, but also show peroxidase activity when in such complexes (i.e., they function as aptazymes).

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Photoactivatable fluorescein derivatives with azidomethyl caging groups for tracing oligonucleotides in living human cells Reviewed

Kazuhiro Furukawa, Hiroshi Abe, Satoshi Tsuneda, Yoshihiro Ito

ORGANIC & BIOMOLECULAR CHEMISTRY Vol. 8 ( 10 ) page： 2309 - 2311 2010

Hemin-Binding Aptamers and Aptazymes

Mingahe Liu, Horoshi Abe, Yoshihiro Ito

ACS Symposium Series 1043(Green Polymer Chemistry) page： 111-123 2010

Hemin-Binding Aptamers and Aptazymes

Liu Mingzhe, Abe Hiroshi, Ito Yoshihiro

GREEN POLYMER CHEMISTRY: BIOCATALYSIS AND BIOMATERIALS Vol. 1043 page： 111 - 123 2010

Establishment of a deformable aorta model based on patient's chest CT data

Tokuyasu T., Shuto T., Yufu K., Abe H., Marui A., Kanao S., Komeda M.

2009 4th International Conference on Innovative Computing, Information and Control, ICICIC 2009 page： 1339 - 1342 2009.12

Publisher：2009 4th International Conference on Innovative Computing, Information and Control, ICICIC 2009

For arch aorta surgery, cardiac surgeons approach to the diseased area with median incision and stemotomy according to the operation plan based on patient's medical images. Even using latest medical diagnosis instruments, however, it is impossible to estimate the shape of aneurysm, so that operation planning plan based on medical images is hard to be perfect. As the mentioned above, cardiac surgeons can not recognize the statement of patient's aneurysm before operation. Because of difficulty to completely recognize the statement of aneurysm from patient's medical images, operation plan often has to be changed during the operation. Therefore the coauthor cardiac surgeons highly expect a diagnosis support system that enables them to observe the shape of aneurysm from any angle and to virtually palpate it in order to make more safety operation plan. Then this study aims to develop of a diagnosis assistant system by using virtual reality and haptic interface under considering realtime interaction between them. © 2009 IEEE.

DOI： 10.1109/ICICIC.2009.194

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Reduction-Triggered Fluorescence Probe for Peptide-Templated Reactions Reviewed

Aya Shibata, Hiroshi Abe, Kazuhiro Furukawa, Satoshi Tsuneda, Yoshihiro Ito

CHEMICAL & PHARMACEUTICAL BULLETIN Vol. 57 ( 11 ) page： 1223 - 1226 2009.11

Language：English Publishing type：Research paper (scientific journal) Publisher：PHARMACEUTICAL SOC JAPAN

We developed a new nucleic acid-based fluorescence probe for protein detection. The method is based on the scission of an aptamer into two probes, which are then attached with a chemically reactive fluorogenic compound. The protein-dependent association of the two probes accelerates a reduction-triggered fluorogenic reaction and indicates the presence of the target protein. which is detected using a fluorescence readout. The fluorescence signal is generated via the deprotection of the azidomethyl group of fluorescein. The arginine-rich motif peptide of the human immunodeficiency virus-1 Rev protein was targeted by this type of probe. Emission was detected at 522 nm and was enhanced by about 19.4-fold in the presence of the target peptide. An oligonucleotide-based reduction-1 triggered fluorescence probe was successfully applied to the defection of the Rev peptide ill solution.

DOI： 10.1248/cpb.57.1223

Characterization of a new fluorogenic substrate for microsomal glutathione transferase 1 Reviewed

Johan Alander, Katarina Johansson, Vanina Dahlstrom Heuser, Henny Farebo, Julia Jarvliden, Hiroshi Abe, Aya Shibata, Mika Ito, Yoshihiro Ito, Ralf Morgenstern

ANALYTICAL BIOCHEMISTRY Vol. 390 ( 1 ) page： 52 - 56 2009.7

Language：English Publishing type：Research paper (scientific journal) Publisher：ACADEMIC PRESS INC ELSEVIER SCIENCE

A new thiol-reactive electrophilic, disubstituted rhodamine-based fluorogenic probe (bis-2,4-dinitrobenzenesulfonyl rhodamine [BDR]) with very high quantum yield was synthesized and described recently [A. Shibata et al., Bioorg. Med. Chem. Lett. 18 (2008) 2246-2249]. Because hydrophobic electrophiles are often conjugated by glutathione transferases, the BDR or monosubstituted rhodamine derivatives (2,4-dinitrobenzenesulfonyl rhodamine [DR]) were tested with microsomal glutathione transferase 1 (MGST1) and shown to function as substrates. The kinetic parameters for purified enzyme and DR were k(cat) = 0.075 +/- 0.005 s(-1) and K(m) = 21 +/- 3 mu M (k(cat)/K(m) = 3.6 x 10(3) +/- 5.6 x 10(2) M(-1) s(-1)), giving a rate enhancement of 10(6) compared with the nonenzymatic reaction. In cells overexpressing MGST1, the addition of BDR Caused a time-dependent increase of fluorescence compared with control cells. Preincubating the cells with a thiol reagent (N-ethylmaleimide) abolished the fluorescent signal. By using DR, we Could determine the MGST1 activity in whole cell extracts with high sensitivity. In addition, the activity could be increased by thiol reagents (a hallmark of MGST1). Thus, we have identified a new fluorogenic substrate for MGST1 that will be a useful tool in the study of this enzyme and related enzymes. (C) 2009 Elsevier Inc. All rights reserved.

DOI： 10.1016/j.ab.2009.03.046

Reduction-Triggered Fluorescent Amplification Probe for the Detection of Endogenous RNAs in Living Human Cells Reviewed

Kazuhiro Furukawa, Hiroshi Abe, Kayo Hibino, Yasushi Sako, Satoshi Tsuneda, Yoshihiro Ito

BIOCONJUGATE CHEMISTRY Vol. 20 ( 5 ) page： 1026 - 1036 2009.5

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

Oligonucleotide-templated reactions are attracting attention as a method for RNA detection in living cells. Previously, a reduction-triggered fluorescence probe has been reported that is based on azide reduction to switch fluorescence on. In this article, we report a more advanced probe, a reduction-triggered fluorescent amplification probe that is capable of amplifying a target signal. Azidomethyl fluorescein was newly synthesized and introduced into a probe. Azido-masked fluorescein on the probe showed a strong turn-on fluorescence signal upon oligonucleotide-templated Staudinger reduction. The catalytic reaction of the probe offered a turnover number of 50 as fluorescence readout within 4 h. Finally, probes were introduced into human leukemia HL-60 cells by use of streptolysin O pore-forming peptide. We successfully detected and quantitated the 28S rRNA and P-Actin mRNA signal above the background by flow cytometry. In addition, the same RNA targets were imaged by fluorescence microscopy. The data suggest that a reduction-triggered amplification probe may be a powerful tool in analyzing the localization, transcription, or processing of RNA species in living eukaryotic cells.

DOI： 10.1021/bc900040t

In vitro selection of hemin-binding catalytic RNA Reviewed

Mingzhe Liu, Takuma Kagahara, Hiroshi Abe, Yoshihiro Ito

BIOORGANIC & MEDICINAL CHEMISTRY LETTERS Vol. 19 ( 5 ) page： 1484 - 1487 2009.3

Language：English Publishing type：Research paper (scientific journal) Publisher：PERGAMON-ELSEVIER SCIENCE LTD

Catalytic RNAs with peroxidase activity were obtained by the in vitro selection of RNA aptamer-binding hemin. One of the RNA aptamers selected showed binding affinity to hemin with a dissociation constant of 0.8 mu M and exhibited high peroxidase activity by forming a complex with hemin. The catalytic efficiency of the RNA-hemin complex was 10-fold higher than that of hemin alone. (C) 2009 Elsevier Ltd. All rights reserved.

DOI： 10.1016/j.bmcl.2009.01.016

細胞機能制御高分子と再生医療高分子

伊藤嘉浩、北嶋隆、阿部洋

細胞機能制御高分子と再生医療高分子 Vol. 58 ( 3月 ) page：全 2009.3

Direct In Vitro Selection of Hemin-Binding DNA Aptamer with Peroxidase Activity Reviewed

Mingzhe Liu, Takuma Kagahara, Hiroshi Abe, Yoshihiro Ito

BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN Vol. 82 ( 1 ) page： 99 - 104 2009.1

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

A novel hemin-binding DNA was synthesized using in vitro selection (SELEX) method. The selected DNA not only bound to the hemin. but also had peroxidase activity when complexed with hemin. A pool of 104-nt single-stranded DNA (ssDNA) molecules containing a randomized sequence of 60nt was synthesized. The DNA pool having random sequences was incubated with a hemin-immobilized affinity column. Bound DNAs were eluted with hemin solution and amplified by PCR with biotin-labeled primers. ssDNAs were isolated from the biotin-labeled double-stranded DNA (dsDNA) molecules after each selection process. After four rounds of selection process, the selected DNAs were cloned and sequenced. Four DNA aptamers were chemically synthesized from the sequenced clones. Two aptamers exhibited binding, affinity to hermin and peroxidase activity. A 21-nt oligonucleotide was designed from the aptamer sequence that formed a complex with hermin and exhibited high peroxidase activity.

DOI： 10.1246/bcsj.82.99

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Protein detection using oligonucleotide probes Reviewed

Aya Shibata, Hiroshi Abe, Kazuhiro Furukawa, Satoshi Tsuneda, Yoshihiro Ito

Nucleic Acids Symposium Series Vol. 53 page： 157 - 158 2009

DNA templated nucleophilic aromatic substitution reactions for fluorogenic sensing of oligonucleotides Reviewed

Aya Shibata, Hiroshi Abe, Mika Ito, Yuko Kondo, Shigeru Shimizu, Kyoko Aikawa, Yoshihiro Ito

CHEMICAL COMMUNICATIONS Vol. 43 ( 43 ) page： 6586 - 6588 2009

Reduction-triggered red fluorescent probes for dual-color detection of oligonucleotide sequences Reviewed

Kazuhiro Furukawa, Hiroshi Abe, Jin Wang, Miwako Uda, Hiroyuki Koshino, Satoshi Tsuneda, Yoshihiro Ito

ORGANIC & BIOMOLECULAR CHEMISTRY Vol. 7 ( 4 ) page： 671 - 677 2009

Language：English Publishing type：Research paper (scientific journal) Publisher：ROYAL SOC CHEMISTRY

We have developed a new red fluorogenic compound derived from naphthorhodamine for a reduction-triggered fluorescence probe to sense oligonucleotides. The fluorogenic reaction between naphthorhodamine azide derivatives and reducing reagents such as triphenylphosphine (TPP) on the DNA target does not use any enzyme or reagent, and fluoresces at 650 nm. The probes were used for dual color detection of a single nucleotide difference on the leukemia-related bcr/abl gene.

DOI： 10.1039/b817228e

Synthetic nanocircular RNA for controlling of gene expression Reviewed

Hiroshi Abe, Naoko Abe, Miwako Uda, Satoshi Tsuneda, Yoshihiro Ito

Nucleic Acids Symposium Series Vol. 53 page： 65 - 66 2009

Synthetic nanocircular RNA for controlling of gene expression. Reviewed

Abe H, Abe N, Uda M, Tsuneda S, Ito Y

Nucleic acids symposium series (2004) ( 53 ) page： 65 - 6 2009

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Papers - ABE Hiroshi