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Experimental evolution of an RNA enzyme using droplet-based microfluidics

Research Project

Project/Area Number 26891009
Research Category

Grant-in-Aid for Research Activity Start-up

Allocation TypeSingle-year Grants
Research Field Evolutionary biology
Research InstitutionUniversity of Toyama

Principal Investigator

MATSUMURA Shigeyoshi  富山大学, 大学院理工学研究部(理学), 助教 (40619855)

Research Collaborator Griffiths Andrew D.  ESPCI ParisTech, 教授
Project Period (FY) 2014-08-29 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥2,730,000 (Direct Cost: ¥2,100,000、Indirect Cost: ¥630,000)
Fiscal Year 2015: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2014: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Keywords人工進化 / RNA酵素 / マイクロ流体システム / エマルジョン / 進化生物学 / 進化分子工学 / RNA / リボザイム / 人工細胞
Outline of Final Research Achievements

In this study, we focused on developing a compartmentalized ribozyme evolution system using microfluidic technology to pursue potential of catalytic RNAs. It is composed of two parts; “compartmentalized ribozyme expression system” and “droplet-based microfluidics”. First, we established the former by optimizing components of an RNA expression system we have previously developed. Second, the latter, an original system which is capable of multi-color fluorescence-based analysis and sorting of droplets, was constructed. Currently, InDrop evolution experiment of ribozymes is undergoing by using the system described above. The drop microfluidic system and devices developed in this study will contribute the basic technology for further artificial RNA evolution experiments.

Report

(3 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Annual Research Report
  • Research Products

    (15 results)

All 2016 2015 2014 Other

All Int'l Joint Research (1 results) Journal Article (6 results) (of which Peer Reviewed: 6 results,  Acknowledgement Compliant: 5 results,  Open Access: 2 results) Presentation (6 results) (of which Int'l Joint Research: 2 results,  Invited: 1 results) Remarks (2 results)

  • [Int'l Joint Research] ESPCI ParisTech(フランス)

    • Related Report
      2015 Annual Research Report
  • [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
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [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
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [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
      2015 Annual Research Report
    • Peer Reviewed / Open Access / 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
      2015 Annual Research 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 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Modulation of group I ribozyme activity by cationic porphyrins2015

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

      Biology (Basel)

      Volume: 4 Issue: 2 Pages: 251-263

    • DOI

      10.3390/biology4020251

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] Addressing origins and evolution of life by microfluidics2016

    • Author(s)
      Matsumura, S.
    • Organizer
      International Symposium on Frontier Biology and Chemistry 2016
    • Place of Presentation
      富山大学 五福キャンパス(富山県富山市)
    • Year and Date
      2016-03-07
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Experimental RNA evolution in droplets: How cellularity contributes the early RNA world evolution2015

    • Author(s)
      Matsumura, S., Coldren, F., Kun, A., Nghe, P., Jossinet, F., Szathmary, E., Griffiths, A., Ryckelynck, M.
    • Organizer
      Pacifichem 2015, The International Chemical Congress of Pacific Basin Societies 2015
    • Place of Presentation
      Hawaii Convention Center(Honolulu, Hawaii, USA)
    • Year and Date
      2015-12-16
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 細胞がもたらす生命の創発:遺伝情報の維持と多様化2015

    • Author(s)
      松村 茂祥
    • Organizer
      BMB2015, 第38回日本分子生物学会年会 第88回日本生化学会大会 合同大会
    • Place of Presentation
      神戸ポートアイランド(兵庫県神戸市)
    • Year and Date
      2015-12-01
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] 細胞構造と群淘汰がもたらす遺伝情報の進化的安定性と多様性2014

    • Author(s)
      松村 茂祥, Coldren, F. M., Kun, A., Nghe, P., Jossinet, F., Szathmary, E., Griffiths, A. D., Ryckelynck, M.
    • Organizer
      第37回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜(神奈川県横浜市)
    • Year and Date
      2014-11-25
    • Related Report
      2014 Annual Research Report
  • [Presentation] Evolutionary stability and diversity of genetic information established by cellularity and cell-based selection2014

    • Author(s)
      Matsumura, S., Coldren, F., Kun, A., Nghe, P., Jossinet, F., Szathmary, E., Griffiths, A., Ryckelynck, M.
    • Organizer
      ISNAC 2014, The 41st International Symposium on Nucleic Acids Chemistry
    • Place of Presentation
      北九州国際会議場(福岡県北九州市)
    • Year and Date
      2014-11-06
    • Related Report
      2014 Annual Research Report
  • [Presentation] Empirical investigation of importance of cellularity in the RNA world evolution using droplet-based microfluidics2014

    • Author(s)
      Matsumura, S., Coldren, F., Kun, A., Nghe, P., Jossinet, F., Szathmary, E., Griffiths, A., Ryckelynck, M.
    • Organizer
      DNA20, The 20th International Conference on DNA Computing and Molecular Programming
    • Place of Presentation
      京都大学医学部芝蘭会館(京都府京都市)
    • Year and Date
      2014-09-25
    • Related Report
      2014 Annual Research Report
  • [Remarks] 富山大学 大学院 理工学研究部 テニュアトラック若手育成部門

    • URL

      http://www3.u-toyama.ac.jp/ritenure/

    • Related Report
      2015 Annual Research Report
  • [Remarks] 富山大学大学院理工学研究部 テニュアトラック若手育成部門

    • URL

      http://www3.u-toyama.ac.jp/ritenure/

    • Related Report
      2014 Annual Research Report

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Published: 2014-09-09   Modified: 2017-05-10  

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