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Pseudo-natural RNA structures as promising modules to construct functional RNA nanostructures with geometrical shapes

Research Project

Project/Area Number 15K05561
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Bio-related chemistry
Research InstitutionUniversity of Toyama

Principal Investigator

Yoshiya Ikawa  富山大学, 大学院理工学研究部(理学), 教授 (70281087)

Co-Investigator(Renkei-kenkyūsha) FURUTA HIROYUKI  九州大学, 大学院工学研究院, 教授 (40244157)
Project Period (FY) 2015-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
Fiscal Year 2017: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Fiscal Year 2016: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Fiscal Year 2015: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
KeywordsRNAナノテクノロジー / リボザイム / RNA構造 / ナノ集積構造 / RNA / RNAナノ構造 / ナノテクノロジー / RNA工学
Outline of Final Research Achievements

RNA is a biopolymer that is attractive for constructing nanoscale objects with complex structures. The 3D structure of a group I (GI) ribozyme has a modular architecture, which can be separated into an activator module and a catalytic module. The fully active ribozyme can be reconstructed by assembling the two separately prepared modules through specific assembly between the two modules. Such non-covalent assembly of the two modules allows the design of 1D-array and polygonal RNA nanostructures. Through rational redesign of the parent GI ribozyme, we constructed variant GI ribozymes as unit RNAs for 1D-arry oligomers and polygonal-shaped oligomers with catalytic activity. Programmed trimerization and tetramerization of the unit RNAs afforded catalytically active nano-sized RNA triangles and squares, the structures of which were directly observed by AFM. We have also seceded in design and construction of RNA nanostructures by modular ribozymes and a fluorescent RNA aptamer.

Report

(4 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Research-status Report
  • 2015 Research-status Report
  • Research Products

    (37 results)

All 2018 2017 2016 2015 Other

All Int'l Joint Research (2 results) Journal Article (16 results) (of which Peer Reviewed: 15 results,  Acknowledgement Compliant: 6 results,  Open Access: 3 results) Presentation (19 results) (of which Int'l Joint Research: 5 results,  Invited: 2 results)

  • [Int'l Joint Research] University of California, Santa Barbara(米国)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] University of California, Santa Barbara(米国)

    • Related Report
      2016 Research-status Report
  • [Journal Article] Biogenic triamine and tetraamine activate core catalytic ability of Tetrahymena group I ribozyme in the absence of its large activator module2018

    • Author(s)
      Gulshan Mst Ara、Rahman Md Motiar、Matsumura Shigeyoshi、Higuchi Tsunehiko、Umezawa Naoki、Ikawa Yoshiya
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: 496 Issue: 2 Pages: 594-600

    • DOI

      10.1016/j.bbrc.2018.01.085

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Recognition of cyclic-di-GMP by a riboswitch conducts translational repression through masking the ribosome-binding site distant from the aptamer domain2018

    • Author(s)
      Inuzuka Saki、Kakizawa Hitoshi、Nishimura Kei-ichiro、Naito Takuto、Miyazaki Katsushi、Furuta Hiroyuki、Matsumura Shigeyoshi、Ikawa Yoshiya
    • Journal Title

      Genes to Cells

      Volume: 印刷中 Issue: 6 Pages: 435-447

    • DOI

      10.1111/gtc.12586

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Comparative study of polyethylene polyamines as activator molecules for a structurally unstable group I ribozyme2018

    • Author(s)
      Gulshan Mst Ara、Matsumura Shigeyoshi、Higuchi Tsunehiko、Umezawa Naoki、Ikawa Yoshiya
    • Journal Title

      Bioscience, Biotechnology, and Biochemistry

      Volume: 印刷中 Issue: 8 Pages: 1404-1407

    • DOI

      10.1080/09168451.2018.1465811

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Engineered group I ribozymes as RNA-based modular tools to control gene expression2018

    • Author(s)
      Ikawa Yoshiya、Matsumura, Shigeyoshi
    • Journal Title

      Applied RNA Bioscience

      Volume: - Pages: 203-220

    • Related Report
      2017 Annual Research Report
  • [Journal Article] Programmable formation of catalytic RNA triangles and squares by assembling modular RNA enzymes2017

    • Author(s)
      H. Oi, D. Fujita, Y. Suzuki, H. Sugiyama, M. Endo, S. Matsumura, Y. Ikawa
    • Journal Title

      The Journal of Biochemistry

      Volume: - Pages: 451-462

    • DOI

      10.1093/jb/mvw093

    • NAID

      40021219839

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Rational Engineering of a Modular Group I Ribozyme to Control Its Activity by Self-Dimerization2017

    • Author(s)
      Tanaka Takahiro、Ikawa Yoshiya、Matsumura Shigeyoshi
    • Journal Title

      Methods in Molecular Biology

      Volume: 1632 Pages: 325-340

    • DOI

      10.1007/978-1-4939-7138-1_21

    • ISBN
      9781493971374, 9781493971381
    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Heterodimerization of Group?I Ribozymes Enabling Exon Recombination through Pairs of Cooperative trans-Splicing Reactions2017

    • Author(s)
      Tanaka Takahiro、Hirata Yusuke、Tominaga Yuto、Furuta Hiroyuki、Matsumura Shigeyoshi、Ikawa Yoshiya
    • Journal Title

      ChemBioChem

      Volume: 18 Issue: 16 Pages: 1659-1667

    • DOI

      10.1002/cbic.201700053

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Artificial RNA Motifs Expand the Programmable Assembly between RNA Modules of a Bimolecular Ribozyme Leading to Application to RNA Nanostructure Design2017

    • Author(s)
      Rahman Md Motiar、Matsumura Shigeyoshi、Ikawa Yoshiya
    • Journal Title

      Biology

      Volume: 6 Issue: 4 Pages: 37-37

    • DOI

      10.3390/biology6040037

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Characterization of an RNA receptor motif that recognizes a GCGA tetraloop.2016

    • Author(s)
      Furukawa, A., Maejima, T., Matsumura, S., Ikawa, Y.
    • Journal Title

      Bioscience, Biotechnology, and Biochemistry

      Volume: 印刷中 Issue: 7 Pages: 1386-1389

    • DOI

      10.1080/09168451.2016.1156483

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Optimization of RNA-based c-di-GMP fluorescent sensors through tuning their structural modules.2016

    • Author(s)
      Inuzuka, S., Matsumura, S., Ikawa, Y.
    • Journal Title

      Journal of Bioscience and Bioengineering

      Volume: 印刷中 Issue: 2 Pages: 183-187

    • DOI

      10.1016/j.jbiosc.2016.01.011

    • NAID

      40020927619

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Tecto-GIRz: engineered group I ribozymes the catalytic ability of which can be controlled by self-dimerization.2016

    • Author(s)
      Tanaka, T., Matsumura, S., Furuta, H., Ikawa, Y.
    • Journal Title

      ChemBioChem

      Volume: 印刷中 Issue: 15 Pages: 1448-1455

    • DOI

      10.1002/cbic.201600190

    • Related Report
      2016 Research-status Report
    • Peer Reviewed
  • [Journal Article] Mutational analysis of structural elements in a class-I cyclic di-GMP riboswitch to elucidate its regulatory mechanism.2016

    • Author(s)
      Inuzuka, S., Nishimura, K., Kakizawa, H., Fujita, Y., Furuta, H., Matsumura, S., Ikawa, Y.
    • Journal Title

      The Journal of Biochemistry

      Volume: 印刷中 Issue: 3 Pages: 153-162

    • DOI

      10.1093/jb/mvw026

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Use of a fluorescent aptamer RNA as an exonic sequence to analyze self-splicing ability of a group I intron from structured RNAs2016

    • Author(s)
      Furukawa, A., Tanaka, T., Furuta, H., Matsumura, S., Ikawa, Y.
    • Journal Title

      Biology

      Volume: 5 Issue: 4 Pages: 43-43

    • DOI

      10.3390/biology5040043

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] 分子デザインと進化工学によるRNA構造エンジニアリング2016

    • Author(s)
      井川善也
    • Journal Title

      生物工学会誌

      Volume: 94 Pages: 477-480

    • Related Report
      2016 Research-status Report
    • Peer Reviewed
  • [Journal Article] Prototheca miyajii sp. nov., isolated from a patient with systemic protothecosis2016

    • Author(s)
      Masuda, M., Hirose, N., Ishikawa, T., Ikawa,Y., Nishimura, K.
    • Journal Title

      Int. J. Syst. Evol. Microbiol.

      Volume: 66 Issue: 3 Pages: 1510-1520

    • DOI

      10.1099/ijsem.0.000911

    • Related Report
      2015 Research-status Report
    • Peer Reviewed
  • [Journal Article] Artificial ligase ribozymes isolated by a “design and selection” strategy.2015

    • Author(s)
      Matsumura, S., Ikawa, Y.
    • Journal Title

      Methods in Molecular Biology

      Volume: 1316 Pages: 113-125

    • DOI

      10.1007/978-1-4939-2730-2_10

    • ISBN
      9781493927296, 9781493927302
    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Presentation] Programmable formation of catalytic RNA triangles and squares by assembling modular RNA enzymes2017

    • Author(s)
      Yoshiya Ikawa
    • Organizer
      Gordon Research Conference on RNA Nanotechnology
    • Place of Presentation
      Ventura, California, USA
    • Year and Date
      2017-01-22
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Effects of polyamines on the catalytic properties of a mutant Tetrahymena ribozyme lacking its large peripheral element2017

    • Author(s)
      Ara Mst. Gulshan, Shigeyoshi Matsumura, Yoshiya Ikawa
    • Organizer
      第19回日本RNA学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Expanding the RNA-RNA interaction interface in the Tetrahymena group I ribozyme and its application to RNA-nanostructure desgin2017

    • Author(s)
      Motiar Md. Rahman, Takahiro Tanaka, Hiroki Oi, Shigeyoshi Matsumura, Yoshiya Ikawa
    • Organizer
      第19回日本RNA学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Adaptor modules for T-loop_PK RNA motif that enable us to apply the motif as a new assembly unit for RNA nanostructure design2017

    • Author(s)
      Sohanur Md. Rahman, Junya Ishikawa, Hiroyuki Furuta, Luc Jaeger, Shigeyoshi Matsumura, Yoshiya Ikawa
    • Organizer
      第19回日本RNA学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] リボザイムシステムを用いた小分子を蛍光に変換するRNAコンバーターの構築2017

    • Author(s)
      前島昂弥,鮎川翔太郎,清岡隆司,松村茂祥,木賀大介,井川善也
    • Organizer
      第19回日本RNA学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 改変型RNase Pによるナノ構造体形成および触媒機能の解析2017

    • Author(s)
      能澤友梨,萩原恵,青山理紗子,松村茂祥,井川善也
    • Organizer
      第19回日本RNA学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 三角形型リボザイム三量体を集積ユニットとしたRNAナノ構造の拡張2017

    • Author(s)
      大井宏紀,Yu Kai,杉山弘,遠藤政幸,松村茂祥,井川善也
    • Organizer
      第11回バイオ関連化学シンポジウム
    • Related Report
      2017 Annual Research Report
  • [Presentation] Recognition of c-di-GMP by a riboswitch represses translation through masking the SD element distant from the aptamer domain2017

    • Author(s)
      Yoshiya Ikawa, Saki Inuzuka, Hitoshi Kakizawa, Kei-ichiro Nishimura, Hiroyuki Furuta, Shigeyoshi Matsumura
    • Organizer
      The 44th International Symposium on Nucleic Acids Chemistry
    • Related Report
      2017 Annual Research Report
  • [Presentation] リボザイム閉環三量体によるナノ三角形をユニットとしたRNAナノ構造の拡張2017

    • Author(s)
      大井宏紀,Yu Kai,杉山弘,遠藤政幸,松村茂祥,井川善也
    • Organizer
      ConBio2017 生命科学系学会合同年次大会
    • Related Report
      2017 Annual Research Report
  • [Presentation] RNA as a promising biopolymer to generate neobiological structures and functions2016

    • Author(s)
      Yoshiya Ikawa
    • Organizer
      第68回日本生物工学会2016年大会
    • Place of Presentation
      富山県富山市 富山国際会議場・ANAクラウンプラザホテル富山
    • Year and Date
      2016-09-28
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] モジュール改変型リボザイムの人工集積によるRNAナノ構造の集積と機能制御2016

    • Author(s)
      大井宏紀、藤田大介、鈴木勇輝、杉山弘、遠藤政幸、松村茂祥、井川善也
    • Organizer
      第10回バイオ関連化学シンポジウム
    • Place of Presentation
      石川県金沢市 石川県立音楽堂
    • Year and Date
      2016-09-07
    • Related Report
      2016 Research-status Report
  • [Presentation] RNA構造モジュールの1次元ナノ集積を目指したRNase Pリボザイムの分割と再構築2016

    • Author(s)
      能澤友梨、萩原恵、松村茂祥、井川善也
    • Organizer
      第10回バイオ関連化学シンポジウム
    • Place of Presentation
      石川県金沢市 石川県立音楽堂
    • Year and Date
      2016-09-07
    • Related Report
      2016 Research-status Report
  • [Presentation] 二量化型スプライシング・リボザイムをユニット単位とした一次元RNAナノ集積構造2016

    • Author(s)
      清岡隆司、松村茂祥、井川善也
    • Organizer
      第10回バイオ関連化学シンポジウム
    • Place of Presentation
      石川県金沢市 石川県立音楽堂
    • Year and Date
      2016-09-07
    • Related Report
      2016 Research-status Report
  • [Presentation] Tecto-GIRz: engineered group I ribozyme the catalytic ability of which can be controlled by self-dimerization2016

    • Author(s)
      Takahiro Tanaka, Shigeyoshi Matsumura, Hiroyuki Furuta, Yoshiya Ikawa
    • Organizer
      RNA 2016, The 21st Annual Meeting of the RNA Society
    • Place of Presentation
      京都府京都市 京都国際会議場
    • Year and Date
      2016-06-28
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] Shigeyoshi Matsumura, Narumi Uehara, Daisuke Fujita, Hiroyuki Furuta, Yoshiya Ikawa Programmable formation of catalytic 1D and 2D RNA nanostructures by assembling group I ribozymes2015

    • Author(s)
      Shigeyoshi Matsumura, Narumi Uehara, Daisuke Fujita, Hiroyuki Furuta, Yoshiya Ikawa
    • Organizer
      The international Chemical Congress of Pacific Basin Societies
    • Place of Presentation
      アメリカ、ハワイ州ホノルル Hawaii Convention Center
    • Year and Date
      2015-12-15
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] グループIリボザイムの集積制御によるRNA正多角形の選択的形成とAFM観察2015

    • Author(s)
      大井宏紀、藤田大介、鈴木勇輝、杉山弘、遠藤政幸、松村茂祥、井川善也
    • Organizer
      H27年度 日本化学会近畿支部 北陸地区講演会と研究発表会
    • Place of Presentation
      石川県金沢市 金沢大学角間キャンパス
    • Year and Date
      2015-11-27
    • Related Report
      2015 Research-status Report
  • [Presentation] Programmable formation of catalytic 2D RNA nanostructures by assembling modular RNA enzymes2015

    • Author(s)
      Daisuke Fujita, Hiroki Oi, Yuki Suzuki, Hiroshi Sugiyama, Masayuki Endo, Shigeyoshi Matsumura, Yoshiya Ikawa
    • Organizer
      The 42nd International Symposium on Nucleic Acids Chemistry
    • Place of Presentation
      兵庫県姫路市 あいめっせホール
    • Year and Date
      2015-09-23
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] モジュール型リボザイムの集積制御によるRNA正多角形の選択的形成とAFM観察2015

    • Author(s)
      大井宏紀、藤田大介、鈴木勇輝、杉山弘、遠藤政幸、松村茂祥、井川善也
    • Organizer
      第9回バイオ関連化学シンポジウム
    • Place of Presentation
      熊本大学工学部 黒髪南キャンパス
    • Year and Date
      2015-09-10
    • Related Report
      2015 Research-status Report
  • [Presentation] グループIリボザイムを基盤とした2次元RNAナノ構造体の構築とその酵素活性の制御2015

    • Author(s)
      松村茂祥、藤田大介、大井宏紀、鈴木勇輝、杉山弘、遠藤政幸、井川善也
    • Organizer
      第17回日本RNA学会年会
    • Place of Presentation
      北海道札幌市中央区 ホテルライフォート札幌
    • Year and Date
      2015-07-15
    • Related Report
      2015 Research-status Report

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Published: 2015-04-16   Modified: 2022-06-06  

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