Faculty Profiles - ABE Hiroshi

Papers - ABE Hiroshi

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Protein detection using oligonucleotide probes. Reviewed

Shibata A, Abe H, Furukawa K, Tsuneda S, Ito Y

Nucleic acids symposium series (2004) ( 53 ) page： 157 - 8 2009

In vitro selection of RNA aptamer to hemin.

Liu M., Kagahara T., Abe H., Ito Y.

Nucleic acids symposium series (2004) ( 52 ) page： 513 - 514 2008.12

Publisher：Nucleic acids symposium series (2004)

A new RNA aptamer-binding hemin was synthesized by the in vitro selection (SELEX) method. A pool of 103 bases single strand DNAs containing a randomized sequence of 59 bases was synthesized. The pool was incubated with hemin on hemin-immobilized affinity column. Bound RNAs were eluted off with hemin solution and amplified by PCR. After 3 rounds of selection process, the selected RNAs were cloned and sequenced. Some RNA aptamers, which have affinity to hemin, was selected.

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Nanocircular RNAs for RNA interference.

Abe H., Abe N., Harada M., Tsuneda S., Ito Y.

Nucleic acids symposium series (2004) ( 52 ) page： 505 - 506 2008.12

Publisher：Nucleic acids symposium series (2004)

We designed and synthesized dumbbell-shaped nanocircular RNAs for RNA interference applications, which consist of a stem and two loops(1). RNA dumbbells are specifically recognized and cleaved by the human Dicer enzyme, and are thus transformed into double-stranded RNA in cells, although this RNA is resistant to degradation in serum. The structure was optimized to maximize its RNAi activity. The most potent activity was achieved when the stem length was 23 base pairs. The RNAi activity is prolonged by the shape of the molecule, an endless structure, compared with that of normal siRNA.

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Fluorogenic probe triggered by reduction for nucleic acids sensing.

Furukawa K., Abe H., Wang J., Oki K., Uda M., Tsuneda S., Ito Y.

Nucleic acids symposium series (2004) ( 52 ) page： 353 - 354 2008.12

Publisher：Nucleic acids symposium series (2004)

A reduction-triggered fluorescence probe with a new fluorogenic compound derivatized from rhodamine 110 was developed for sensing oligonucleotides. The chemistry to activate the compound involves the reaction between the azide group of rhodamine derivatives and reducing reagents, with the fluorescence signal appearing after reduction of the azide group. The reaction proceeds under biological conditions to produce fluorescence signal within 10-20 min in the presence of target DNA or RNA. The probes were successfully applied to the detection of oligonucleotides in solution and endogenous RNA in bacterial cells.

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Fluorescence generation from tandem repeats of a malachite green RNA aptamer using rolling circle transcription Reviewed

Kazuhiro Furukawa, Hiroshi Abe, Naoko Abe, Mitsuru Harada, Satoshi Tsuneda, Yoshihiro Ito

BIOORGANIC & MEDICINAL CHEMISTRY LETTERS Vol. 18 ( 16 ) page： 4562 - 4565 2008.8

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

We demonstrate a generation of tandem repeats of a malachite green (MG) RNA aptamer using rolling circle transcription. To keep the higher-order structure of each aptamer on long RNA, we designed a sequence of circular DNA with a 14-base linker. T7 RNA polymerase was superior to Escherichia coli RNA polymerase in the specific transcription of the MG RNA aptamer. Finally. the generation of the fluorescence signal was confirmed from aptamer repeats with MG. (c) 2008 Elsevier Ltd. All rights reserved.

DOI： 10.1016/j.bmcl.2008.07.040

A reduction-triggered fluorescence probe for sensing nucleic acids Reviewed

Hiroshi Abe, Jin Wang, Kazuhiro Furukawa, Kazuma Oki, Miwako Uda, Satoshi Tsuneda, Yoshihiro Ito

BIOCONJUGATE CHEMISTRY Vol. 19 ( 6 ) page： 1219 - 1226 2008.6

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

We have developed a reduction-triggered fluorescence probe with a new fluorogenic compound derivatized from Rhodamine for sensing oligonucleotides. The chemistry to activate the compound involves the reaction between the azide group of rhodamine derivatives and the reducing reagents, with the fluorescence signal appearing after reduction of the azide group. The signal/background ratio of this fluorogenic compound reached 2100-fold enhancement in fluorescence intensity. Dithio-1,4-threitol or triphenylphosphine as reducing reagents were successfully utilized for this chemistry to be introduced into the DNA probe. The genetic detection requires that two strands of DNA bind onto target oligonticleotides, one probe carrying a reducible fluorogenic compound while the other carries the reducing reagents. The reaction proceeds automatically without any enzymes or reagents under biological conditions to produce a fluorescence signal within 10-20 min in the presence of target DNA or RNA. In addition, the probe was very stable tinder biological conditions, even such extreme conditions as pH 5 solution, pH 10 solution, or high temperature (90 degrees C) with no undesirable background signal. The probes were successfully applied to the detection of oligonucleotides at the single nucleotide level in solution and endogenous RNA in bacterial cells.

DOI： 10.1021/bc800014d

MEDI 134-Multiple chemical ligation under thermal cycle

Kondo Yuko, Abe Hiroshi, Jinmei Hiroshi, Abe Naoko, Aikawa Kyoko, Matsumoto Isamu, Ito Yoshihiro

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY Vol. 235 2008.4

Rhodamine-based fluorogenic probe for imaging biological thiol Reviewed

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

BIOORGANIC & MEDICINAL CHEMISTRY LETTERS Vol. 18 ( 7 ) page： 2246 - 2249 2008.4

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

We have developed a new fluorescent probe for biological thiol. The probe was synthesized by the modi. cation of the 2,4-dinitrobenzenesulfonyl group with rhodamine 110. The selective detection of thiol species such as cysteine or glutathione was achieved in biological conditions. Moreover, the probe was successfully applied to the imaging of thiol species in living human cells. (C) 2008 Elsevier Ltd. All rights reserved.

DOI： 10.1016/j.bmcl.2008.03.014

Synthesis of (+/-)-9-[c-4, t-5-bis(hydroxymethyl)cyclopent-2-en-r-1-yl]-9H-adenine (BCA) derivatives branched at the 4 '-position based on intramolecular SH2 ' cyclization Reviewed

Hiroki Kumamoto, Nonoko Takahashi, Tomomi Shimamura, Hiromichi Tanaka, Kazuo T. Nakamura, Takayuki Hamasaki, Masanori Baba, Hiroshi Abe, Masahiko Yano, Nobuyuki Kato

TETRAHEDRON Vol. 64 ( 7 ) page： 1494 - 1505 2008.2

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

Synthesis of W-branched BCA analogues (5) was carried out. Stereospecific construction of the cis-disposed 4'-carbon-substituents and 5'-hydroxymethyl group was secured by employing the bicyclo[3.3.0]lactone 16 as a key intermediate, which was prepared by radical-mediated intramolecular S(H)2' cyclization of the phenylselenomethyl ester 15. After manipulation of the double bond of 16, bis(Boc)adenine was introduced based on the Mitsunobu reaction of the allyl alcohol 24. Transformation of the lactone function of 27 allowed preparation of the 4'-hydroxymethyl (31). the 4'-vinyl (32), the 4'-cyano (34), and the 4'-ethynyl (35) derivatives. Anti-HIV and anti-HCV activities of the free nucleosides 36-38 were also examined. (c) 2007 Elsevier Ltd. All rights reserved.

DOI： 10.1016/j.tet.2007.11.038

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Chemical aminoacylation of RNA by an intermolecular adenosine transfer reaction Reviewed

Mingzhe Liu, Hiroshi Jinmei, Hiroshi Abe, Yoshihiro Ito

CHEMISTRY LETTERS Vol. 37 ( 1 ) page： 102 - 103 2008.1

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

RNA aminoacylation, based on an adenosine transfer mechanism, was achieved by the intermolecular transfer of phenylalaninyl adenosine from a donor probe to an acceptor RNA. This method can be applied to a wide variety of unnatural amino acids for tRNA aminoacylation.

DOI： 10.1246/cl.2008.102

Web of Science

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Stereoselective glycosylation based on the conformational restriction of pyranoses Reviewed

Satoshi Shuto, Satoshi Ichikawa, Hiroshi Abe, Akira Matsuda

JOURNAL OF SYNTHETIC ORGANIC CHEMISTRY JAPAN Vol. 66 ( 1 ) page： 50 - 60 2008.1

Language：Japanese Publisher：SOC SYNTHETIC ORGANIC CHEM JPN

Despite considerable progress and extensive effort, a general method for highly stereoselective glycosylation particularly for the 1,2-cis-glycosylation has not yet been developed and therefore is required. The alpha/beta-stereo selectivity in glycosylation can be affected by the steric and stereoelectronic (anomeric) effects around the anomeric center, which depend on the conformation of the glycosyl donor substrates. Therefore, we hypothesized that highly alpha- and beta-selective glycosylation can be realized by employing conformationally restricted substrates. We showed that the alpha/beta-stereoselectivity was significantly increased by the conformational restriction and was completely inverted by changing the substrate conformation from the C-4(1)-form into the C-1(4)-form in radical and nucleophilic C-glycosylation reactions as well as in O-glycosylation reactions. The conformational restriction of substrates also effectively facilitates the alpha- and beta-selective radical cyclization reaction at the anomeric position. Using the method, C-glucoside trisphosphates designed as Ca2+-mobilizing agents were successfully,synthesized.

DOI： 10.5059/yukigoseikyokaishi.66.50

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Rapid DNA chemical ligation for amplification of RNA and DNA signal Reviewed

Hiroshi Abe, Yuko Kondo, Hiroshi Jinmei, Naoko Abe, Kazuhiro Furukawa, Atsushi Uchiyama, Satoshi Tsuneda, Kyoko Aikawa, Isamu Matsumoto, Yoshihiro Ito

BIOCONJUGATE CHEMISTRY Vol. 19 ( 1 ) page： 327 - 333 2008.1

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

Enzymatic ligation methods are useful in the diagnostic detection of DNA sequences. Here, we describe the investigation of nonenzymatic phosphorothioate-iodoacetyl DNA chemical ligation as a method for the detection and identification of RNA and DNA. The specificity of ligation on the DNA target is shown to allow the discrimination of a single point mutation with a drop in the ligation yield of up to 16.1-fold. Although enzymatic ligation has very low activity for RNA targets, this reaction is very efficient for RNA targets. The speed of the chemical ligation with an RNA target achieves a 70% yield in 5 s, which is equal to or better than that of ligase-enzyme-mediated ligation with a DNA target. The reaction also exhibits a significant level of signal amplification under thermal cycling in periods as short as 100-120 min, with the RNA or DNA target acting in a catalytic way to ligate multiple pairs of probes.

DOI： 10.1021/bc700244s

In vitro selection of RNA aptamer to hemin. Reviewed

Mingze Liu, Takuma Kagahara, Hiroshi Abe, Yoshihiro Ito

Nucleic Acids Symposium Series Vol. 52 page： 513 - 514 2008

Fluorogenic probe triggered by reduction for nucleic acids sensing. Reviewed

Furukawa K, Abe H, Wang J, Oki K, Uda M, Tsuneda S, Ito Y

Nucleic acids symposium series (2004) ( 52 ) page： 353-4 2008