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Development of the system to change enzymatic functions without mutational approaches by using molecular crowding

Research Project

Project/Area Number 16K14041
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
Research Field Bio-related chemistry
Research InstitutionKonan University

Principal Investigator

SUGIMOTO Naoki  甲南大学, 先端生命工学研究所, 教授 (60206430)

Co-Investigator(Kenkyū-buntansha) 高橋 俊太郎  甲南大学, 先端生命工学研究所, 講師 (40456257)
Project Period (FY) 2016-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
Fiscal Year 2017: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Fiscal Year 2016: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Keywords分子クラウディング / 核酸 / 酵素 / 複製 / 転写 / RNA / DNA / ポリメラーゼ / ポリエチレングリコール / 分子進化
Outline of Final Research Achievements

We studied the effect of molecular crowding on DNA or RNA polymerization reactions and found that changes in molecular crowding caused the quantity and quality of polymerized products. These phenomenon were the process of gene regulations without protein. Thus, the structure of template nucleic acids played a role for gene expression in the RNA world where there was no protein. Furthermore, we identified that the regulation system is utilized in the modern cells by analysis of living cells. Therefore, in the process of transition from RNA world to DNA world, the gene regulation system by the structure of the template was took over form RNA to DNA.

Report

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

    (22 results)

All 2018 2017 2016 Other

All Int'l Joint Research (2 results) Journal Article (9 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 9 results,  Open Access: 3 results,  Acknowledgement Compliant: 4 results) Presentation (8 results) (of which Int'l Joint Research: 6 results,  Invited: 1 results) Book (1 results) Remarks (1 results) Patent(Industrial Property Rights) (1 results)

  • [Int'l Joint Research] Reading大学(英国)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] University of Calcutta(インド)

    • Related Report
      2016 Research-status Report
  • [Journal Article] Alkylating probes for the G-quadruplex structure and evaluation of the properties of the alkylated G-quadruplex DNA2018

    • Author(s)
      Sato Norihiro、Takahashi Shuntaro、Tateishi-Karimata Hisae、Hazemi Madoka E.、Chikuni Tomoko、Onizuka Kazumitsu、Sugimoto Naoki、Nagatsugi Fumi
    • Journal Title

      Org. Biomol. Chem.

      Volume: 16 Issue: 9 Pages: 1436-1441

    • DOI

      10.1039/c7ob03179c

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Destabilization of DNA G-Quadruplexes by Chemical Environment Changes during Tumor Progression Facilitates Transcription2018

    • Author(s)
      Tateishi-Karimata Hisae、Kawauchi Keiko、Sugimoto Naoki
    • Journal Title

      Journal of the American Chemical Society

      Volume: 140 Issue: 2 Pages: 642-651

    • DOI

      10.1021/jacs.7b09449

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Topological impact of noncanonical DNA structures on Klenow fragment of DNA polymerase2017

    • Author(s)
      Takahashi Shuntaro、Brazier John A.、Sugimoto Naoki
    • Journal Title

      Proceedings of the National Academy of Sciences

      Volume: 114 Issue: 36 Pages: 9605-9610

    • DOI

      10.1073/pnas.1704258114

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Volumetric contributions of loop regions of G-quadruplex DNA to the formation of the tertiary structure2017

    • Author(s)
      Takahashi Shuntaro、Sugimoto Naoki
    • Journal Title

      Biophysical Chemistry

      Volume: 231 Pages: 146-154

    • DOI

      10.1016/j.bpc.2017.02.001

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Quantitative Analysis of Nucleic Acid Stability with Ligands Under High Pressure to Design Novel Drugs Targeting G-Quadruplexes2017

    • Author(s)
      Takahashi Shuntaro、Sugimoto Naoki
    • Journal Title

      Current Protocols in Nucleic Acid Chemistry

      Volume: 70 Issue: 1

    • DOI

      10.1002/cpnc.39

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Volumetric analysis of formation of the complex of G-quadruplex DNA with hemin using high pressure2017

    • Author(s)
      S. Takahashi, S. Bhowmik and N. Sugimoto
    • Journal Title

      Journal of Inorganic Biochemistry

      Volume: 166 Pages: 199-207

    • DOI

      10.1016/j.jinorgbio.2016.08.011

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Pressure effect on the folding of G-quadruplex DNA modified with hexaethylene glycol2016

    • Author(s)
      S. Takahashi and N. Sugimoto
    • Journal Title

      Molecular Enzymology and Drug Targets

      Volume: 2 Issue: 01

    • DOI

      10.21767/2572-5475.10013

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] G-quadruplexes with tetraethylene glycol-modified deoxythymidines are resistant to nucleases and inhibit HIV-1 reverse transcriptase2016

    • Author(s)
      H. Tateishi-Karimata, T. Muraoka, K. Kinbara, and N. Sugimoto
    • Journal Title

      ChemBioChem

      Volume: 17 Issue: 15 Pages: 1399-1402

    • DOI

      10.1002/cbic.201600162

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] tRNA shifts the G-quadruplex-hairpin conformational equilibrium in RNA towards the hairpin conformer2016

    • Author(s)
      A. B. Rode, T. Endoh, and N. Sugimoto
    • Journal Title

      Angew. Chemie. Int. Ed.

      Volume: 46 Issue: 46 Pages: 14315-14319

    • DOI

      10.1002/anie.201605431

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Presentation] Nucleic Acids Chemistry beyond the Watson-Crick Double Helix (39) : Control of replication of G-quadruplex containing oxidative lesion2018

    • Author(s)
      S. Takahashi, P. Podbevsek, J. Plavec, B. H. Kim, and N. Sugimoto
    • Organizer
      日本化学会第98回春季年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Topological effect of non-canonical DNA structures on DNA replication2017

    • Author(s)
      S.Takahashi, J.A.Brazier, N.Sugimoto
    • Organizer
      第44回国際核酸化学シンポジウム
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] ヘミン - グアニン四重鎖 DNA からなる DNAzyme の反応解析における高圧力の活用2017

    • Author(s)
      高橋 俊太郎, 杉本 直己
    • Organizer
      第58回高圧討論会
    • Related Report
      2017 Annual Research Report
  • [Presentation] “To B or not to B” in Nucleic Acids Chemistry2017

    • Author(s)
      N. Sugimoto
    • Organizer
      Advances in Noncanonical Nucleic Acids 2017
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Stability and function of nucleic acids under molecular crowding conditions2016

    • Author(s)
      Naoki Sugimoto
    • Organizer
      BIT’s 7th World Gene Convention 2016
    • Place of Presentation
      Sheraton Shanghai Waigaoqiao Hotel(上海・中国)
    • Year and Date
      2016-11-03
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] High pressure in RNA world: High pressure dominates the aptamer ligand binding of flavin mononucleotide riboswitch2016

    • Author(s)
      Shuntaro Takahashi, Tamaki Endoh, Ambadas B. Rode, Naoki Sugimoto
    • Organizer
      The 9th International Conference on High Pressure Bioscience and Biotechnology (HPBB2016)
    • Place of Presentation
      University of Toronto(トロント・カナダ)
    • Year and Date
      2016-07-25
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] Does a helicase assist the replication of G-quadruplex DNA?2016

    • Author(s)
      Hiromichi Okura, Shuntaro Takahashi, Naoki Sugimoto
    • Organizer
      The 22th International Round Table on Nucleosides, Nucleotides and Nucleic Acids (XXII IRT)
    • Place of Presentation
      Institut Pasteur (パリ・フランス)
    • Year and Date
      2016-07-18
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] Regulation of gene expressions using the formation of non-canonical structures of nucleic acids2016

    • Author(s)
      H. Tateishi-Karimata, C. Annoni, A. B. Rode, T. Endoh, S. Takahashi, N. Sugimoto
    • Organizer
      ANNA2016 (Advances in Noncanonical Nucleic Acids)
    • Place of Presentation
      National Institute of Chemistry(リュブリャナ・スロベニア)
    • Year and Date
      2016-05-18
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited
  • [Book] 「化学」分子クラウディングワールド―クラウディングによる疾患や分子進化の化学的制御2017

    • Author(s)
      高橋俊太郎、杉本直己
    • Publisher
      化学同人
    • Related Report
      2017 Annual Research Report
  • [Remarks] 甲南大学先端生命工学研究所ホームページ

    • URL

      http://www.konan-fiber.jp/index.php

    • Related Report
      2017 Annual Research Report 2016 Research-status Report
  • [Patent(Industrial Property Rights)] 核酸合成法2017

    • Inventor(s)
      杉本 直己、高橋 俊太郎、大倉 裕道
    • Industrial Property Rights Holder
      学校法人甲南学園
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      2017-120802
    • Filing Date
      2017
    • Related Report
      2017 Annual Research Report

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Published: 2016-04-21   Modified: 2022-06-16  

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