研究者詳細 - 阿部　洋

論文 - 阿部　洋

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Protein detection using oligonucleotide probes. 査読有り

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

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

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Nucleic acids symposium series (2004)

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 chemical reaction and indicates the presence of the target protein, which is detected using a fluorescence readout. The arginine-rich motif peptide was targeted by this type of probe. In presence of the peptide, the fluorescence signal at 450 nm increased, and no significant increase in fluorescence was observed in the absence of the peptide. An oligonucleotide-based fluorescence probe was successfully applied to the detection of the ARM peptide in solution.

DOI： 10.1093/nass/nrp079

Scopus

PubMed

In vitro selection of RNA aptamer to hemin.

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

Nucleic acids symposium series (2004) ( 52 ) 頁： 513 - 514 2008年12月

出版者・発行元：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.

Scopus

Nanocircular RNAs for RNA interference.

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

Nucleic acids symposium series (2004) ( 52 ) 頁： 505 - 506 2008年12月

出版者・発行元：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.

Scopus

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 ) 頁： 353 - 354 2008年12月

出版者・発行元：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.

Scopus

Fluorescence generation from tandem repeats of a malachite green RNA aptamer using rolling circle transcription 査読有り

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

BIOORGANIC & MEDICINAL CHEMISTRY LETTERS 18 巻 ( 16 ) 頁： 4562 - 4565 2008年8月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Bioorganic and Medicinal Chemistry Letters

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. © 2008 Elsevier Ltd. All rights reserved.

DOI： 10.1016/j.bmcl.2008.07.040

A reduction-triggered fluorescence probe for sensing nucleic acids 査読有り

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

BIOCONJUGATE CHEMISTRY 19 巻 ( 6 ) 頁： 1219 - 1226 2008年6月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Bioconjugate Chemistry

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 oligonucleotides, 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 under biological conditions, even such extreme conditions as pH 5 solution, pH 10 solution, or high temperature (90°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. © 2008 American Chemical Society.

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 235 巻 2008年4月

Rhodamine-based fluorogenic probe for imaging biological thiol 査読有り

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

BIOORGANIC & MEDICINAL CHEMISTRY LETTERS 18 巻 ( 7 ) 頁： 2246 - 2249 2008年4月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Bioorganic and Medicinal Chemistry Letters

We have developed a new fluorescent probe for biological thiol. The probe was synthesized by the modification 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. © 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 査読有り

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

TETRAHEDRON 64 巻 ( 7 ) 頁： 1494 - 1505 2008年2月

Chemical aminoacylation of RNA by an intermolecular adenosine transfer reaction 査読有り

Liu Mingzhe, Jinmei Hiroshi, Abe Hiroshi, Ito Yoshihiro

CHEMISTRY LETTERS 37 巻 ( 1 ) 頁： 102 - 103 2008年1月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Chemistry Letters

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. Copyright © 2008 The Chemical Society of Japan.

DOI： 10.1246/cl.2008.102

Web of Science

Scopus

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Stereoselective glycosylation based on the conformational restriction of pyranoses 査読有り

Satoshi Shuto, Satoshi Ichikawa, Hiroshi Abe, Akira Matsuda

JOURNAL OF SYNTHETIC ORGANIC CHEMISTRY JAPAN 66 巻 ( 1 ) 頁： 50 - 60 2008年1月

記述言語：日本語出版者・発行元：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

Web of Science

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Rapid DNA chemical ligation for amplification of RNA and DNA signal 査読有り

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

BIOCONJUGATE CHEMISTRY 19 巻 ( 1 ) 頁： 327 - 333 2008年1月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Bioconjugate Chemistry

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. © 2008 American Chemical Society.

DOI： 10.1021/bc700244s

In vitro selection of RNA aptamer to hemin. 査読有り

Mingze Liu, Takuma Kagahara, Hiroshi Abe, Yoshihiro Ito

Nucleic Acids Symposium Series 52 巻頁： 513 - 514 2008年

Fluorogenic probe triggered by reduction for nucleic acids sensing. 査読有り

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

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