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Organization for Promotion of Research and Industry-Academic Regional Collaboration Institute for Tenure Track Promotion |
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Title |
Associate Professor |
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FUKUNAGA Keisuke
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Degree 【 display / non-display 】
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Ph.D. in Engineering ( 2014.3 The University of Electro-Communications )
Research Interests 【 display / non-display 】
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Directed evolution
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Biotechnology
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Synthetic Biology
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RNA aptamer
Research Areas 【 display / non-display 】
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Manufacturing Technology (Mechanical Engineering, Electrical and Electronic Engineering, Chemical Engineering) / Biofunction and bioprocess engineering
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Nanotechnology/Materials / Bio chemistry
Professional Memberships 【 display / non-display 】
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「細胞を創る」研究会
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日本化学会・生体機能関連化学部会
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日本生物工学会
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日本核酸化学会
Papers 【 display / non-display 】
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In vitro evolution of adenosine A2A receptor based on an antagonist binding using ribosome display
Genki Fukasawa, Yuma Matsuoka, Duy Phuoc Tran, Keisuke Fukunaga, Haruka Nishigaki, Tomohiro Doura, Naohiro Terasaka, Ako Kagawa, Takeshi Murata, Akio Kitao, Shigeki Kiyonaka, Tomoaki Matsuura
ChemRxiv 2025.7
Language：English Publishing type：Research paper (scientific journal)
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Structural insights into lab-coevolved RNA–RBP pairs and applications of synthetic riboswitches in cell-free system Reviewed International journal
Keisuke Fukunaga, Takamasa Teramoto, Momoka Nakashima, Toshitaka Ohtani, Riku Katsuki, Tomoaki Matsuura, Yohei Yokobayashi, Yoshimitsu Kakuta
Nucleic Acids Research 53 ( 6 ) 2025.3
Authorship：Lead author, Corresponding author Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1093/nar/gkaf212
DOI： 10.1093/nar/gkaf212
Other Link： https://doi.org/10.1093/nar/gkaf212
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Switchable and orthogonal gene expression control inside artificial cells by synthetic riboswitches Reviewed International coauthorship International journal
Yuta Ishii, Keisuke Fukunaga, Aileen Cooney, Yohei Yokobayashi, Tomoaki Matsuura
Chemical Communications 60 ( 46 ) 5972 - 5975 2024.5
Authorship：Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：Chemical Communications
Here we report two novel synthetic riboswitches that respond to ASP2905 and theophylline and function in reconstituted cell-free protein synthesis (CFPS) system. We encapsulated the CFPS system as well as DNA-templated encoding reporter genes regulated by these orthogonal riboswitches inside liposomes, and achieved switchable and orthogonal control over gene expression by external stimulation with the cognate ligands.
DOI： 10.1039/d4cc00965g
DOI： 10.1039/d4cc00965g
Other Link： https://t2r2.star.titech.ac.jp/cgi-bin/publicationinfo.cgi?q_publication_content_number=CTT100928039
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Small-Molecule Aptamer for Regulating RNA Functions in Mammalian Cells and Animals Reviewed International journal
Fukunaga K., Dhamodharan V., Miyahira N., Nomura Y., Mustafina K., Oosumi Y., Takayama K., Kanai A., Yokobayashi Y.
Journal of the American Chemical Society 145 ( 14 ) 7820 - 7828 2023.4
Authorship：Lead author Language：English Publishing type：Research paper (scientific journal) Publisher：Journal of the American Chemical Society
Synthetic riboswitches that can regulate gene expression by a small molecule recognized by an RNA aptamer in mammalian cells have various potential applications in biotechnology and medicine. However, the variety of small molecules and their cognate aptamers that have been demonstrated to function in mammalian cells is limited. The currently available aptamer-ligand pairs also require high small molecule concentrations to enable gene regulation, making them less desirable for industrial and biomedical applications. We conducted in vitro selection of RNA aptamers against a small molecule ASP7967 whose structure is closely related to ASP2905, a known inhibitor of potassium voltage-gated channel sub-family H member 3 (KCNH3). One of the aptamers selected (AC17-4) was found to be functional in HEK293 cells, and it was used to design aptazyme-based riboswitches that can activate gene expression (>10-fold) in the presence of ASP2905 or ASP7967 at as low as 5 μM in the culture medium. An aptazyme-based riboswitch was successfully used to regulate human erythropoietin expression in mice injected with an adeno-associated virus (AAV8) vector using orally administered ASP7967. Furthermore, by combining aptazyme-based and exon-skipping riboswitch mechanisms, an ON/OFF ratio approaching 300 was achieved with a low basal expression level in cultured cells.
DOI： 10.1021/jacs.2c12332
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Directed evolution of orthogonal RNA–RBP pairs through library-vs-library in vitro selection Reviewed International journal
Keisuke Fukunaga, Yohei Yokobayashi
50 ( 2 ) 601 - 616 2022.1
Authorship：Lead author Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1093/nar/gkab527
Books 【 display / non-display 】
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若手研究者からのメッセージ
福永 圭佑（ Role： Sole author）
日本化学会 バイオテクノロジー部会 ニュースレター 2022
Language：Japanese
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PD-SELEX法を用いた直交性RNA-RBPペアの指向性進化
福永 圭佑（ Role： Sole author）
日本化学会 生体機能関連化学部会 ニュースレター 2021
Language：Japanese
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Site-specific N-terminal Fluorescent Labeling of Unprotected Peptides
Keisuke Fukunaga, Takayoshi Watanabe, and Takahiro Hohsaka（ Role： Joint author）
Peptide Science 2015 2016
Language：English
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An Artificial Molecule-Peptide Hybrid Discovered via the 10BASEd-T Binds to the Substrate-Binding Site of Glutathione S-Transferase
Keisuke Fukunaga, Takaaki Hatanaka, Yuji Ito, and Masumi Taki（ Role： Joint author）
Peptide Science 2013 2014
Language：English
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Construction of a Peptide Expression Vector Library for Phenotypic Screening of Bioactive Peptides in Yeast
Keisuke Fukunaga and Masumi Taki（ Role： Joint author）
Peptide Science 2013 2014
Language：English
Presentations 【 display / non-display 】
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Exploration of RNA Aptamers Against Photoreceptor Protein DrBphP Through SELEX Method International conference
Zimu Zhang, Keisuke Fukunaga, Tomoaki Matsuura
13th ELSI International Symposium 2025
Event date： 2025.1
Language：English Presentation type：Poster presentation
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Searching for proper fatty acids for the construction of growing vesicles International conference
Ayumi Koyama, Takayoshi Watanabe, Kaito Seo, Keisuke Fukunaga, Tomoaki Matsuura
13th ELSI International Symposium 2025
Event date： 2025.1
Language：English Presentation type：Poster presentation
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Orthogonal gene regulation using RBP-based riboswitches inside artificial cells International conference
Toshitaka Ohtani, Keisuke Fukunaga, Yoshikazu Tanaka, Tomoaki Matsuura
13th ELSI International Symposium 2025
Event date： 2025.1
Language：English Presentation type：Poster presentation
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Investigating RNA-Phospholipid Interactions: Insights into the Mechanisms of Protocellular Assembly International conference
Arshjot Mann, Keisuke Fukunaga, Tomoaki Matsuura
13th ELSI International Symposium 2025
Event date： 2025.1
Language：English Presentation type：Poster presentation
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Molecular Threads: Unravelling the RNA-Lipid interactions in Early Cell Assembly
Arshjot Mann, Keisuke Fukunaga, Tomoaki Matsuura
Astrobiology Graduate Conference Japan (AbGradJ) 2024.12
Event date： 2024.12
Language：English Presentation type：Poster presentation
Works 【 display / non-display 】
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Crystal structure of the L7Ae derivative protein LS12 in RNA-free state
Takamasa Teramoto, Momoka Nakshima, Keisuke Fukunaga, Yohei Yokobayashi, Yoshimitsu Kakuta
2025.4.2
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Crystal structure of the L7Ae derivative protein LS12 in complex with its co-evolved target CS2 RNA
Takamasa Teramoto, Momoka Nakshima, Keisuke Fukunaga, Yohei Yokobayashi, Yoshimitsu Kakuta
2025.4.2
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Crystal structure of the L7Ae derivative protein LS4 in complex with its co-evolved target CS1 RNA
Takamasa Teramoto, Momoka Nakshima, Keisuke Fukunaga, Yohei Yokobayashi, Yoshimitsu Kakuta
2025.4.2
Awards 【 display / non-display 】
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第13回新化学技術研究奨励賞
2024.6 公益社団法人新化学技術推進協会（JACI）
本人
Award type：Award from publisher, newspaper, foundation, etc.
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支部長賞
2023.7 日本生物工学会東日本支部
本人
Award type：Award from Japanese society, conference, symposium, etc.
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部会講演賞
2021.9 第15回バイオ関連化学シンポジウム
本人
Award type：Award from Japanese society, conference, symposium, etc.
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FIBER核酸化学 若手講演賞
2021.8 FIBER日本核酸化学会若手フォーラム
本人
Award type：Award from Japanese society, conference, symposium, etc.
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若手口頭発表優秀賞
2013.11 第4回 アジア−太平洋国際ペプチドシンポジウム
本人
Award type：Award from international society, conference, symposium, etc.