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Conformational transition of giant DNA molecules and its biological significance

Research Project

Project/Area Number 20840027
Research Category

Grant-in-Aid for Young Scientists (Start-up)

Allocation TypeSingle-year Grants
Research Field Biophysics/Chemical physics
Research InstitutionKyoto University

Principal Investigator

SAKAUE Takahiro  Kyoto University, 理学研究院, 助教 (30512959)

Project Period (FY) 2008 – 2009
Project Status Completed (Fiscal Year 2009)
Budget Amount *help
¥2,951,000 (Direct Cost: ¥2,270,000、Indirect Cost: ¥681,000)
Fiscal Year 2009: ¥1,352,000 (Direct Cost: ¥1,040,000、Indirect Cost: ¥312,000)
Fiscal Year 2008: ¥1,599,000 (Direct Cost: ¥1,230,000、Indirect Cost: ¥369,000)
KeywordsDNA / 高分子物理学 / 非平衡ダイナミクス / トポロジー / 高分子鎖 / 一分子実験 / 折り畳み / 生体高分子 / translocation / 微小空間 / 細胞モデル / 核モデル / 折り畳み転移 / ソフトマター / ダイナミクス / 非平衡 / 生物物理
Research Abstract

Motivated by the recent progress in the single molecule experiments, we have theoretically studied the behaviors of single (bio) polymers from various viewpoints. Examples include (i) the folding transition of giant DNA molecules, (ii) the decompression and escape dynamics of polymers and (iii) the topological effect in circular DNAs, etc. In addition to the fundamental material properties, we have also discussed their biological implications as well.

Report

(3 results)
  • 2009 Annual Research Report   Final Research Report ( PDF )
  • 2008 Annual Research Report
  • Research Products

    (31 results)

All 2010 2009 2008 Other

All Journal Article (17 results) (of which Peer Reviewed: 9 results) Presentation (11 results) Book (3 results)

  • [Journal Article] Mismatch of bulk viscosity reduces interfacial diffusivity at an aqueous/oil system2010

    • Author(s)
      M. Negishi, T. Sakaue, K. Yoshikawa
    • Journal Title

      Phys. Rev. E vol.81

      Pages: 20901-20901

    • Related Report
      2009 Final Research Report
  • [Journal Article] Sucking genes into pores: Insight into driven translocation2010

    • Author(s)
      T. Sakaue
    • Journal Title

      Phys. Rev. E vol.81

      Pages: 41808-41808

    • NAID

      120005227428

    • Related Report
      2009 Final Research Report
  • [Journal Article] Mismatch of bulk viscosity reduces interfacial diffusivity at an aqueous/oil system2010

    • Author(s)
      M.Negishi, T.Sakaue, K.Yoshikawa
    • Journal Title

      Physical Review E 81

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Cooperation between giant DNA molecules and actin filaments in a microsphere2010

    • Author(s)
      M.Negishi, T.Sakaue., K.Takiguchi, K.Yoshikawa
    • Journal Title

      Physical Review E (In press)

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Sucking genes : Insight into driven translocation2010

    • Author(s)
      T.Sakaue
    • Journal Title

      Physical Review E (In press)

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Nanoscale Swimmers : Hydrodynamic Interactions and Propulsion of Molecular Machines2010

    • Author(s)
      T.Sakaue, A.Mikhailov, R.Kapral
    • Journal Title

      The European Physical Journal B (In press)

    • NAID

      120005289458

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Dynamics of Polymer Decompression: Expansion, Unfolding, and Ejection2009

    • Author(s)
      T. Sakaue, N. Yoshinaga
    • Journal Title

      Phys. Rev. Lett. vol.102

      Pages: 148302-148302

    • Related Report
      2009 Final Research Report
  • [Journal Article] Conformational transition of giant DNA in a confined space surrounded by a phospholipid membrane2009

    • Author(s)
      A. Kato, E. Shindo, T. Sakaue, A. Tsuji, K. Yoshikawa
    • Journal Title

      Biophysical Journal vol.97

      Pages: 1678-1686

    • Related Report
      2009 Final Research Report
  • [Journal Article] Dynamics of Polymer Decompression : Expansion, Unfolding, and Ejection2009

    • Author(s)
      T.Sakaue, N.Yoshinaga
    • Journal Title

      Physical Review Letters 102

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Conformational transition of giant DNA in a confined space surrounded by a phospholipid membrane2009

    • Author(s)
      A.Kato, E.Shindo, T.Sakaue, A.Tsuii, K.Yoshikawa
    • Journal Title

      Biophysical Journal 97

      Pages: 1678-1686

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Dynamics of Polymer Decompression : Expansion, Unfolding and Election2009

    • Author(s)
      T. Sakaue, N. Yoshinaga
    • Journal Title

      Physical Review Letters 102

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Probing Nonequilibrium Fluctuation through Linear Response2008

    • Author(s)
      T. Sakaue, T. Ohta
    • Journal Title

      Phys. Rev. E vol.77

      Pages: 50102-50102

    • Related Report
      2009 Final Research Report
  • [Journal Article] Chain Length Dependence of Folding Transition in a Semiflexible Homo-polymer Chain: Appearance of a Core-shell Structure2008

    • Author(s)
      Y. Higuchi, T. Sakaue, K. Yoshikawa
    • Journal Title

      Chem. Phys. Lett. vol.461

      Pages: 42-42

    • Related Report
      2009 Final Research Report
  • [Journal Article] Probing Nonequilibrium Fluctuations through Linear Response2008

    • Author(s)
      T. Sakaue, T. Ohta
    • Journal Title

      Physical Review E 77

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Chain Length Dependence of Folding Transition in a Seraiflexible Homo-polymer Chain : Appearance of a Core-shell2008

    • Author(s)
      Y. Higuchi, T. Sakaue, K. Yoshikawa
    • Journal Title

      Chemical Physics Letters 461

      Pages: 42-46

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Nanoscale Swimmers: Hydrodynamic Interactions and Propulsion of Molecular Machines

    • Author(s)
      T. Sakaue, A. Mikhailov, R. Kapral
    • Journal Title

      The European Physical Journal B (in press)

    • NAID

      120005289458

    • Related Report
      2009 Final Research Report
  • [Journal Article] Cooperation between giant DNA molecules and actin filaments in a microsphere

    • Author(s)
      M. Negishi, T. Sakaue. K. Takiguchi, K. Yoshikawa
    • Journal Title

      Phys. Rev. E (in press)

    • Related Report
      2009 Final Research Report
  • [Presentation] 非相溶性ブレンドのせん断流下での電場応答2010

    • Author(s)
      坂上貴洋、太田隆夫
    • Organizer
      日本物理学会第65回年次大会
    • Place of Presentation
      岡山大学
    • Year and Date
      2010-03-23
    • Related Report
      2009 Final Research Report
  • [Presentation] 非相溶性ブレンドのせん断流下での電場応答2010

    • Author(s)
      坂上貴洋, 太田隆夫
    • Organizer
      日本物理学会 第65回年次大会
    • Place of Presentation
      岡山大学
    • Year and Date
      2010-03-23
    • Related Report
      2009 Annual Research Report
  • [Presentation] Asymmetric response and fluctuation in nonequilibrium steady state2010

    • Author(s)
      T. Sakaue
    • Organizer
      Open Statistical Physics
    • Place of Presentation
      Open University, UK
    • Year and Date
      2010-03-10
    • Related Report
      2009 Annual Research Report 2009 Final Research Report
  • [Presentation] Two topics on diffusion2009

    • Author(s)
      T. Sakaue
    • Organizer
      The 5th Kyushu University-Pukyong Natl University Joint Symposium on Sciences
    • Place of Presentation
      College of Natural Sciences, Pukyong National University.
    • Year and Date
      2009-11-13
    • Related Report
      2009 Final Research Report
  • [Presentation] Two topics on diffusion2009

    • Author(s)
      坂上貴洋
    • Organizer
      The 5th Kyushu University-Pukyong Natl University Joint Symposium on Sciences
    • Place of Presentation
      College of Natural Sciences, Pukyong National University
    • Year and Date
      2009-11-13
    • Related Report
      2009 Annual Research Report
  • [Presentation] 界面での拡散について2009

    • Author(s)
      坂上貴洋
    • Organizer
      日本物理学会2009年秋季大会
    • Place of Presentation
      熊本大学
    • Year and Date
      2009-09-27
    • Related Report
      2009 Final Research Report
  • [Presentation] 界面での拡散について2009

    • Author(s)
      坂上貴洋
    • Organizer
      日本物理学会 2009年秋季大会
    • Place of Presentation
      熊本大学
    • Year and Date
      2009-09-27
    • Related Report
      2009 Annual Research Report
  • [Presentation] 二次元環状鎖の統計則2009

    • Author(s)
      坂上貴洋, 和田浩史
    • Organizer
      日本物理学会第64回年次大会
    • Place of Presentation
      東京
    • Year and Date
      2009-03-28
    • Related Report
      2008 Annual Research Report
  • [Presentation] Probing nonequilibrium fluctuations through linear response2009

    • Author(s)
      T. Sakaue
    • Organizer
      Self-organization and dynamics of active matter
    • Place of Presentation
      Paris (France)
    • Year and Date
      2009-01-28
    • Related Report
      2008 Annual Research Report
  • [Presentation] Dynamics of polymer expansion and unfolding2008

    • Author(s)
      坂上貴洋, 義永那津人
    • Organizer
      日本物理学会2008年秋季大会
    • Place of Presentation
      盛岡
    • Year and Date
      2008-09-20
    • Related Report
      2008 Annual Research Report
  • [Presentation] Asymmetric responses and fluctuations in nonequilibrium steady state2008

    • Author(s)
      T. Sakaue
    • Organizer
      International Symposium on Non-Equilibrium Soft Matter
    • Place of Presentation
      Kyoto
    • Year and Date
      2008-06-03
    • Related Report
      2008 Annual Research Report
  • [Book] Physical Chemistry of Life Phenomena, chapter 3“Transition in the Higher-order Structure of DNA in Aqueous Solution"2010

    • Author(s)
      T. Sakaue, K. Yoshikawa, Water, Biomolecules
    • Total Pages
      23
    • Publisher
      Springer
    • Related Report
      2009 Final Research Report
  • [Book] Water and Biomolecules : Physical Chemistry of Life Phenomena, chapter 3 "Transition in the Higher-order Structure of DNA in Aqueous Solution"2009

    • Author(s)
      T.Sakaue, K.Yoshikawa
    • Total Pages
      23
    • Publisher
      Springer
    • Related Report
      2009 Annual Research Report
  • [Book] Water and Biomolecules : Physical Chemistry of Life Phenomena (edited by K. Kuwajima), chap. 3 "Transition in the Higher-order structure of DNA in Aqueous Solution"2009

    • Author(s)
      T. Sakaue, K. Yoshikawa
    • Total Pages
      23
    • Publisher
      Springer
    • Related Report
      2008 Annual Research Report

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Published: 2008-04-01   Modified: 2016-04-21  

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