• Search Research Projects
  • Search Researchers
  • How to Use
  1. Back to previous page

Development of new model experimental systems for investigating nucleic acid interactions in the intracellular environment

Research Project

Project/Area Number 24550200
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Chemistry related to living body
Research InstitutionKonan University

Principal Investigator

Nakano Shu-ichi  甲南大学, フロンティアサイエンス学部, 教授 (70340908)

Project Period (FY) 2012-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥5,590,000 (Direct Cost: ¥4,300,000、Indirect Cost: ¥1,290,000)
Fiscal Year 2014: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2013: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2012: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000)
Keywords核酸 / リボザイム / 構造安定性 / 分子クラウディング / 混合溶媒 / モデル実験 / タンパク質 / DNA二重鎖 / 融解温度 / リゾチーム / 脂肪酸結合タンパク質 / ゲル / ポリエチレングリコール
Outline of Final Research Achievements

Model studies under biomimetic conditions are important to understand the effects of the cellular environment on nucleic acid interactions. Neutral water-soluble polymers, such as polyethylene glycol and polysaccharides, are often used as cosolutes in the study of molecular crowding. The present research has developed new model experimental systems for investigating nucleic acid interactions in the intracellular environment. The model sytems enabled to evaluate the effects of various environmental factors, including confined condition, cellular molecules, and altered solvent properties, on the structures and catalytic activities of nucleic acids. The quantitative analysis revealed that the environmental factors that contribute to electrostatic interactions have large impact on the stability of nucleic acid interactions. The observations demonstrate the significance of the model studies for the understanding of the behavior of nucleic acids in the intracellular environment.

Report

(5 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Research-status Report
  • 2013 Research-status Report
  • 2012 Research-status Report
  • Research Products

    (31 results)

All 2016 2015 2014 2013 2012 Other

All Journal Article (10 results) (of which Peer Reviewed: 10 results,  Open Access: 3 results,  Acknowledgement Compliant: 2 results) Presentation (17 results) (of which Int'l Joint Research: 2 results,  Invited: 2 results) Remarks (4 results)

  • [Journal Article] The structural stability and catalytic activity of DNA and RNA oligonucleotides in the presence of organic solvents2016

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

      Biophys. Rev.

      Volume: 8 Issue: 1 Pages: 1-13

    • DOI

      10.1007/s12551-015-0188-0

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Effects of Cosolvents on the Folding and Catalytic Activities of the Hammerhead Ribozyme2015

    • Author(s)
      S. Nakano, Y. Kitagawa, H. Yamashita, D. Miyoshi, N. Sugimoto
    • Journal Title

      ChemBioChem

      Volume: 16 Issue: 12 Pages: 1803-1810

    • DOI

      10.1002/cbic.201500139

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Effects of background anionic compounds on the activity of the hammerhead ribozyme in Mg2+-unsaturated solutions2015

    • Author(s)
      Shu-ichi Nakano, Yuichi Kitagawa, Daisuke Miyoshi, Naoki Sugimoto
    • Journal Title

      J. Biol. Inorg. Chem.

      Volume: 20 Issue: 6 Pages: 1049-1058

    • DOI

      10.1007/s00775-015-1286-y

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Roles of the amino group of purine bases in the thermodynamic stability of DNA base pairing2014

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

      Molecules

      Volume: 19 Issue: 8 Pages: 11613-11627

    • DOI

      10.3390/molecules190811613

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Hammerhead ribozyme activity and oligonucleotide duplex stability in mixed solutions of water and organic compounds2014

    • Author(s)
      Shu-ichi Nakano, Yuichi Kitagawa, Daisuke Miyoshi, Naoki Sugimoto
    • Journal Title

      FEBS Open Bio.

      Volume: 4 Issue: 1 Pages: 643-650

    • DOI

      10.1016/j.fob.2014.06.009

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Preparation of hydrogels for the study of the effects of spatial confinement on DNA2014

    • Author(s)
      S. Nakano, M. Yoshida, D. Yamaguchi, and N. Sugimoto
    • Journal Title

      Transactions of the Materials Research Society of Japan

      Volume: 39 Issue: 4 Pages: 435-438

    • DOI

      10.14723/tmrsj.39.435

    • NAID

      130005004375

    • ISSN
      1382-3469, 2188-1650
    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Effects of molecular crowding on the structures, interactions, and functions of nucleic acids2014

    • Author(s)
      Shu-chi Nakano, Daisuke Miyoshi, and Naoki Sugimoto
    • Journal Title

      Chem Rev.

      Volume: 114 Issue: 5 Pages: 2733-2758

    • DOI

      10.1021/cr400113m

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Quantitative analyses of nucleic acid stability under the molecular crowding condition induced by cosolutes2013

    • Author(s)
      H. Tateishi-Karimata, S. Nakano, and N. Sugimoto
    • Journal Title

      Curr. Protoc. Nucleic Acid Chem.

      Volume: 7 Issue: 1 Pages: 19-19

    • DOI

      10.1002/0471142700.nc0719s53

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Thermodynamics - Hydration Relationships within Loops that Affect G-Quadruplexes under Molecular Crowding Conditions2013

    • Author(s)
      Takeshi Fujimoto, Shu-ichi Nakano, Daisuke Miyoshi, Naoki Sugimoto
    • Journal Title

      Journal of Physical Chemistry B

      Volume: 117 Issue: 4 Pages: 963-972

    • DOI

      10.1021/jp308402v

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Dimerization of Nucleic Acid Hairpins in the Conditions Caused by Neutral Cosolutes2012

    • Author(s)
      S. Nakano, H. Hirayama, D. Miyoshi and N. Sugimoto
    • Journal Title

      J. Phys. Chem. B

      Volume: 16 Issue: 25 Pages: 7406-7415

    • DOI

      10.1021/jp302170f

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Presentation] 生体分子を含んだクラウディング環境がDNAに与える安定性変化のメカニズム2016

    • Author(s)
      中井大樹, 山口大輔, 杉本直己, 中野修一
    • Organizer
      日本化学会第96春季年会
    • Place of Presentation
      同志社大学(京都府京田辺市)
    • Year and Date
      2016-03-24
    • Related Report
      2015 Annual Research Report
  • [Presentation] Effects of protein crowding on the thermal stability of DNA2015

    • Author(s)
      Hiroki Nakai, Daisuke Yamaguchi, Naoki Sugimoto, and Shu-ichi Nakano
    • Organizer
      第38回日本分子生物学会年会(BMB2015)
    • Place of Presentation
      神戸ポートアイランド(兵庫県神戸市)
    • Year and Date
      2015-12-02
    • Related Report
      2015 Annual Research Report
  • [Presentation] Comparison of the effects of PEG, dextran and proteins on the thermal stability of a DNA duplex2015

    • Author(s)
      Hiroki Nakai, Daisuke Yamaguchi, Naoki Sugimoto, and Shu-ichi Nakano
    • Organizer
      第42回国際核酸化学シンポジウム(ISNAC2015)
    • Place of Presentation
      Egret Himeji(兵庫県姫路市)
    • Year and Date
      2015-09-23
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Effect of molecular crowding on ion binding to DNA G-quadruplexes studied by isothermal titration assay2015

    • Author(s)
      Kenta Iwaki, Hayato Sangen, Naoki Sugimoto, Shu-ichi Nakano
    • Organizer
      第42回国際核酸化学シンポジウム(ISNAC2015)
    • Place of Presentation
      Egret Himeji(兵庫県姫路市)
    • Year and Date
      2015-09-23
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] タンパク質を用いた細胞内環境がDNAに与える影響2015

    • Author(s)
      中井大樹、中野修一
    • Organizer
      第6回生命機能研究会
    • Place of Presentation
      龍谷大学大阪梅田キャンパス(大阪府大阪市)
    • Year and Date
      2015-09-12
    • Related Report
      2015 Annual Research Report
  • [Presentation] 細胞内模倣環境がDNA四重鎖のイオン結合におよぼす影響2015

    • Author(s)
      岩木研太、中野修一
    • Organizer
      第6回生命機能研究会
    • Place of Presentation
      龍谷大学大阪梅田キャンパス(大阪府大阪市)
    • Year and Date
      2015-09-12
    • Related Report
      2015 Annual Research Report
  • [Presentation] Studies on the effects of intracellular crowding environment on nucleic acids using model experimental systems2014

    • Author(s)
      S. Nakano, D. Yamaguchi, M. Yoshida, N. Sugimoto
    • Organizer
      第37回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2014-11-25 – 2014-11-27
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] 細胞内分子環境が核酸分子に与える影響 ―モデル実験系を使った物理化学的アプローチから言えること―2014

    • Author(s)
      中野修一
    • Organizer
      生化学若い研究者の会 秋のセミナー
    • Place of Presentation
      大阪大学
    • Year and Date
      2014-11-15
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] Effects of mixed solutions with organic compounds on cation binding to RNA2014

    • Author(s)
      Y. Tanino, H. Yamashita, S. Tanaka, N. Sugimoto, and S. Nakano
    • Organizer
      第41回国際核酸化学シンポジウム
    • Place of Presentation
      北九州国際会議場
    • Year and Date
      2014-11-05 – 2014-11-07
    • Related Report
      2014 Research-status Report
  • [Presentation] Preparation of hydrogels for the study of the effects of spatial confinement on DNA2014

    • Author(s)
      S. Nakano, M. Yoshida, D. Yamaguchi, and N. Sugimoto
    • Organizer
      The IUMRS International Conference in Asia 2014
    • Place of Presentation
      福岡大学
    • Year and Date
      2014-08-24 – 2014-08-30
    • Related Report
      2014 Research-status Report
  • [Presentation] 生命分子の挙動に及ぼす分子環境の効果(54) ゲル繊維に閉じ込められたDNA分子の構造安定性の評価2014

    • Author(s)
      吉田将敏、山口大輔、杉本直己、中野修一
    • Organizer
      日本化学会第94春季年会
    • Place of Presentation
      名古屋大学
    • Related Report
      2013 Research-status Report
  • [Presentation] 分子クラウディング環境におけるRNA相互作用の解明と予測に向けた取り組み2013

    • Author(s)
      中野修一、平山英伸、三好大輔、杉本直己
    • Organizer
      第7回バイオ関連化学シンポジウム
    • Place of Presentation
      名古屋大学
    • Related Report
      2013 Research-status Report
  • [Presentation] Screening of the FABP-binding ligands using delipidated protein2013

    • Author(s)
      H. Hirayama, S. Nagatoishi, N. Sugimoto, S. Nakano
    • Organizer
      第36回日本分子生物学会年会
    • Place of Presentation
      神戸ポートアイランド
    • Related Report
      2013 Research-status Report
  • [Presentation] 細胞の分子環境を模倣したモデル実験系からわかったこと2012

    • Author(s)
      中野修一
    • Organizer
      第3回生命機能研究会
    • Place of Presentation
      兵庫県神戸市
    • Related Report
      2012 Research-status Report
  • [Presentation] 新規分子クラウディングモデル実験系を用いたDNA二重鎖構造の熱的安定性の評価2012

    • Author(s)
      山口大輔、中野修一
    • Organizer
      第6回バイオ関連化学シンポジウム
    • Place of Presentation
      北海道大学
    • Related Report
      2012 Research-status Report
  • [Presentation] Molecular crowding study using nucleotide analogs2012

    • Author(s)
      D. Yamaguchi, H. Oka, M. Fujii, N. Sugimoto, S. Nakano
    • Organizer
      第39回国際核酸化学シンポジウム
    • Place of Presentation
      名古屋大学
    • Related Report
      2012 Research-status Report
  • [Presentation] Model study for the molecular crowding effects on nucleic acid interactions2012

    • Author(s)
      H. Hirayama, Y. Kitagawa, D. Yamaguchi, H. Sangen, N. Sugimoto, S. Nakano
    • Organizer
      第35回日本分子生物学会年会
    • Place of Presentation
      福岡県福岡市
    • Related Report
      2012 Research-status Report
  • [Remarks] バイオ分子機能研究室

    • URL

      http://www.kcc.zaq.ne.jp/konan1st_bmflab/

    • Related Report
      2015 Annual Research Report
  • [Remarks] 補助金研究報告

    • URL

      http://www.kcc.zaq.ne.jp/konan1st_bmflab/Hojyokin_reports.html

    • Related Report
      2015 Annual Research Report
  • [Remarks] バイオ分子機能研究室(研究室ホームページ)

    • URL

      http://www.kcc.zaq.ne.jp/konan1st_bmflab/

    • Related Report
      2013 Research-status Report
  • [Remarks] 研究室のホームページ

    • URL

      http://www.kcc.zaq.ne.jp/konan1st_bmflab/

    • Related Report
      2012 Research-status Report

URL: 

Published: 2013-05-31   Modified: 2019-07-29  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi