Publications

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Articles, Protocols and Reviews

【2022】

  1. "Eukaryotic artificial ON-riboswitches that respond efficiently to mid-sized short peptides"
    Hajime Takahashi, Ryo Okubo, Atsushi Ogawa*
    Bioorg. Med. Chem. Lett. 2022, 71, 128839. [link]

【2021】

  1. "Coupled in vitro transcription/translation based on wheat germ extract for efficient expression from PCR-generated templates in short-time batch reactions"
    Hajime Takahashi and Atsushi Ogawa*
    Bioorg. Med. Chem. Lett. 2021, 52, 128412. [link]

  2. "A Detailed Protocol for Preparing Millimeter-Sized Supergiant Liposomes That Permit Efficient Eukaryotic Cell-Free Translation in the Interior" [Protocol]
    Hajime Takahashi and Atsushi Ogawa*
    Bio-protocol 2021, 11, e4054. [link]
    #selected as the outside front cover

  3. "Molecular detection using aptamer-modified gold nanoparticles with an immobilized DNA brush for the prevention of non-specific aggregation"
    Yuki Yano-Ozawa, Nadine Lobsiger, Yu Muto, Takahiro Mori, Ken Yoshimura, Yuki Yano, Wendelin Jan Stark, Mizuo Maeda, Tsuyoshi Asahi, Atsushi Ogawa, Tamotsu Zako*
    RSC Adv. 2021, 11, 11984-11991. [link]

  4. "Suppressor tRNA-based Biosensors for Detecting Analytes" [Review]
    Atsushi Ogawa*
    Anal. Sci. 2021, 37, 407-414. [link]

【2020】

  1. "In Vitro Selection of RNA Aptamers Binding to Nanosized DNA for Constructing Artificial Riboswitches"
    Atsushi Ogawa* and Yu Itoh
    ACS Synth. Biol. 2020, 9, 2648-2655. [link]

  2. "Development of human CBF1-targeting single-stranded DNA aptamers with anti-angiogenic activity in vitro"
    Mari Tezuka-Kagajo(#), Masashi Maekawa(#),* Atsushi Ogawa(#),* Yoshiko Hatta, Eiichi Ishii, Mariko Eguchi, Shigeki Higashiyama*
    Nucleic Acid Ther. 2020, 30, 365-378. [link]
    (#)These authors equally contributed to this work.

  3. "Preparation of a Millimeter-Sized Supergiant Liposome That Allows for Efficient, Eukaryotic Cell-Free Translation in the Interior by Spontaneous Emulsion Transfer"
    Hajime Takahashi and Atsushi Ogawa*
    ACS Synth. Biol. 2020, 9, 1608-1614. [link]

【2019】

  1. "Mutation of the start codon to enhance Cripavirus internal ribosome entry site-mediated translation in a wheat germ extract"
    Atsushi Ogawa* and Masashi Takamatsu
    Bioorg. Med. Chem. Lett. 2019, 29, 126729. [link]

  2. "In vitro selection of a 3’ terminal short protector that stabilizes transcripts to improve the translation efficiency in a wheat germ extract"
    Atsushi Ogawa,* Akane Kutsuna, Masashi Takamatsu, Tatsuya Okuzono
    Bioorg. Med. Chem. Lett. 2019, 29, 2141-2144. [link]

  3. "Detection of Gold Nanoparticles Aggregation using Light Scattering for Molecular Sensing"
    Yuki Yano, Masamichi Nisougi, Yuki Yano-Ozawa, Tsuyoshi Ohguni, Atsushi Ogawa, Mizuo Maeda, Tsuyoshi Asahi, Tamotsu Zako*
    Anal. Sci. 2019, 35, 685-690. [link]
    #selected as a hot article

  4. "Modification of carbon metabolism in Synechococcus elongatus PCC 7942 by cyanophage-derived sigma factors for bioproduction improvement"
    Naruhiko Sawa, Tsuneyuki Tatsuke, Atsushi Ogawa, Yasutaka Hirokawa, Takashi Osanai, Taizo Hanai*
    J. Biosci. Bioeng. 2019, 127, 256-264. [link]

【2018】

  1. "Canonical translation-modulating OFF-riboswitches with a single aptamer binding to a small molecule that function in a higher eukaryotic cell-free expression system"
    Atsushi Ogawa,* Yuta Murashige, Hajime Takahashi
    Bioorg. Med. Chem. Lett. 2018, 28, 2353-2357. [link]

  2. "Rational Design of Artificial Riboswitches" [Review]
    Atsushi Ogawa*
    Applied RNA Bioscience 2018, 79-93. [link]

【2017】

  1. "Artificial OFF-Riboswitches That Downregulate Internal Ribosome Entry without Hybridization Switches in a Eukaryotic Cell-Free Translation System"
    Atsushi Ogawa,* Hiroki Masuoka, Tsubasa Ota
    ACS Synth. Biol. 2017, 6, 1656-1662. [link]

  2. "Ligand-responsive upregulation of 3' CITE-mediated translation in a wheat germ cell-free expression system"
    Atsushi Ogawa,* Yuta Murashige, Junichiro Tabuchi, Taiki Omatsu
    Mol. BioSyst. 2017, 13, 314-319. [link]

【2016】

  1. "Biofunction-assisted DNA detection through RNase H-enhanced 3' processing of a premature tRNA probe in a wheat germ extract"
    Atsushi Ogawa,* Junichiro Tabuchi, Yasunori Doi, Masashi Takamatsu
    Bioorg. Med. Chem. Lett. 2016, 26, 3658-3661. [link]

  2. "Rational optimization of amber suppressor tRNAs toward efficient incorporation of a non-natural amino acid into protein in a eukaryotic wheat germ extract"
    Atsushi Ogawa,* Yuki Namba, Mai Gakumasawa
    Org. Biomol. Chem. 2016, 14, 2671-2678. [link]

【2015】

  1. "Biofunction-assisted aptasensors based on ligand-dependent 3’ processing of a suppressor tRNA in a wheat germ extract"
    Atsushi Ogawa* and Junichiro Tabuchi
    Org. Biomol. Chem. 2015, 13, 6681-6685. [link]
    #selected as a hot article
    #selected as the inside front cover
    (Correction: Org. Biomol. Chem. 2015, 13, 8365. [link])

  2. "Engineering of Ribosomal Shunt-Modulating Eukaryotic ON Riboswitches by Using a Cell-Free Translation System" [Protocol]
    Atsushi Ogawa*
    Methods Enzymol. 2015, 550, 109-128. [link]

  3. "Investigation of end processing and degradation of premature tRNAs and their application to stabilization of in vitro transcripts in wheat germ extract"
    Atsushi Ogawa* and Yasunori Doi
    Org. Biomol. Chem. 2015, 13, 1008-1012. [link]

【2014】

  1. "Thermodynamics-based Rational Design of DNA Block Copolymers for Quantitative Detection of Single-Nucleotide Polymorphisms by Affinity Capillary Electrophoresis"
    Ayumi Kimura, Naoki Kanayama, Atsushi Ogawa, Hideaki Shibata, Hideo Nakashita, Tohru Takarada,* Mizuo Maeda
    Anal. Chem. 2014, 86, 11425-11433. [link]

  2. "Identification of short untranslated regions that sufficiently enhance translation in high-quality wheat germ extract"
    Atsushi Ogawa,* Junichiro Tabuchi, Yasunori Doi
    Bioorg. Med. Chem. Lett. 2014, 24, 3724-3727. [link]

  3. "Rational Design of Artificial ON-Riboswitches" [Protocol]
    Atsushi Ogawa*
    Methods Mol. Biol. 2014, 1111, 165-181. [link]

【2013】

  1. "Theophylline-dependent Riboswitch as a Novel Genetic Tool for Strict Regulation of Protein Expression in Cyanobacterium Synechococcus elongatus PCC 7942"
    Yoichi Nakahira, Atsushi Ogawa, Hiroyuki Asano, Tokitaka Oyama, Yuzuru Tozawa*
    Plant Cell Physiol. 2013, 54, 1724-1735. [link]

  2. "Ligand-Dependent Upregulation of Ribosomal Shunting"
    Atsushi Ogawa*
    ChemBioChem 2013, 14, 1539-1543. [link]
    #selected as a very important paper (VIP)
    #selected as the outside front cover

  3. "Dumbbell-Shaped DNA Analytes Amplified by Polymerase Chain Reaction for Robust Single-Nucleotide Polymorphism Genotyping by Affinity Capillary Electrophoresis"
    Hideaki Shibata, Atsushi Ogawa, Naoki Kanayama, Tohru Takarada,* Mizuo Maeda
    Anal. Chem. 2013, 85, 5347-5352. [link]

  4. "Multiple-input and visible-output logic gates using signal-converting DNA machines and gold nanoparticle aggregation"
    Atsushi Ogawa* and Yukiko Susaki
    Org. Biomol. Chem. 2013, 11, 3272-3276. [link]
    #selected as the outside front cover

【2012】

  1. "A Concept for Selection of Codon-Suppressor tRNAs Based on Read-Through Ribosome Display in an In Vitro Compartmentalized Cell-Free Translation System"
    Atsushi Ogawa,* Masayoshi Hayami, Shinsuke Sando,* Yasuhiro Aoyama
    J. Nucleic Acids 2012, Article ID 538129, 1-7. [link]

  2. "Rational construction of eukaryotic OFF-riboswitches that downregulate internal ribosome entry site-mediated translation in response to their ligands"
    Atsushi Ogawa*
    Bioorg. Med. Chem. Lett. 2012, 22, 1639-1642. [link]

【2011】

  1. "Improvement of in vitro-transcribed amber suppressor tRNAs toward higher suppression efficiency in wheat germ extract"
    Atsushi Ogawa,* Yasunori Doi, Nobuto Matsushita
    Org. Biomol. Chem. 2011, 9, 8495-8503. [link]

  2. "Multiple-Catalytic Sensing of Nucleic Acid Sequences by Utilising a DNA-RNA-DNA Chimeric Antisense Probe and RNase H with a Eukaryotic Cell-Free Translation System"
    Atsushi Ogawa*
    ChemBioChem 2011, 12, 881-885. [link]

  3. "Rational Design of Artificial Riboswitches Based on Ligand-Dependent Modulation of Internal Ribosome Entry in Wheat Germ Extract and Their Applications as Label-Free Biosensors"
    Atsushi Ogawa*
    RNA 2011, 17, 478-488. [link]

  4. "RNA aptazyme-tethered large gold nanoparticles for on-the-spot sensing of the aptazyme ligand"
    Atsushi Ogawa*
    Bioorg. Med. Chem. Lett. 2011, 21, 155-159. [link]

【2010】

  1. "Isothermal Sensitive Detection of MicroRNA Using an Autonomous DNA Machine Recycling Output as Input"
    Atsushi Ogawa*
    Bioorg. Med. Chem. Lett. 2010, 20, 6056-6060. [link]

【2009】

  1. "Biofunction-Assisted Sensors Based on a New Method for Converting Aptazyme Activity into Reporter Protein Expression with High Efficiency in Wheat Germ Extract"
    Atsushi Ogawa*
    ChemBioChem 2009, 10, 2465-2468. [link]

  2. "Easy design of logic gates based on aptazymes and noncrosslinking gold nanoparticle aggregation"
    Atsushi Ogawa* and Mizuo Maeda*
    Chem. Commun. 2009, 4666-4668. [link]
    #highlighted in the magazine "Highlights in Chemical Science"

  3. "Detector-free and Multiple Sensing of Various Molecules Using Gold Nanoparticles and Aptazymes"
    Atsushi Ogawa* and Mizuo Maeda*
    Chem. Lett. 2009, 38, 848-849. [link]

【2008】

  1. "A Novel Label-Free Biosensor Using an Aptazyme-Suppressor-tRNA Conjugate and an Amber-Mutated Reporter Gene"
    Atsushi Ogawa* and Mizuo Maeda
    ChemBioChem 2008, 9, 2204-2208. [link]

  2. "Simple and Rapid Colorimetric Detection of Cofactors of Aptazymes Using Noncrosslinking Gold Nanoparticle Aggregation"
    Atsushi Ogawa* and Mizuo Maeda*
    Bioorg. Med. Chem. Lett. 2008, 18, 6517-6520. [link]

  3. "An Artificial Aptazyme-Based Riboswitch and its Cascading System in E. Coli"
    Atsushi Ogawa* and Mizuo Maeda
    ChemBioChem 2008, 9, 206-209. [link]
    # Most Cited Articles among those published in ChemBioChem in 2007 or 2008 (Top 25)

【2007】

  1. "Aptazyme-Based Riboswitches as Label-Free and Detector-Free Sensors for Cofactors"
    Atsushi Ogawa* and Mizuo Maeda
    Bioorg. Med. Chem. Lett. 2007, 17, 3156-3160. [link]

Others

  1. "30歳単身から始めた地方での研究室運営十数年"
    小川 敦司
    日本化学会 生体機能関連化学部会NEWS LETTER 2020, 35, 34-35. [link]

  2. "Methods in Molecular Biology: Artificial Riboswitches"
    Atsushi Ogawa (Editor)
    Springer 2014. [link]

  3. Book Review on "Methods in Molecular Biology: Riboswitches"
    Atsushi Ogawa
    ChemBioChem (Wiley) 2009, 10, 2802-2803. [link]

  4. "金テクノロジー −その基礎と応用−:第23章「金ナノ粒子を用いるバイオセンシング」"
    小川 敦司、前田 瑞夫
    シーエムシー出版 2009, 294-308. [link]

  5. "機能性核酸を用いたターゲット分子簡易検出システムの開発"
    小川 敦司、前田 瑞夫
    日本化学会 生体機能関連化学部会NEWS LETTER 2008, 23, 6-9. [link]

 

"Making the simple complicated is commonplace; making the complicated simple, awesomely simple, that's creativity"
- Charles Mingus