Conformational transition of giant DNA molecules and its biological significance

2009 Fiscal Year Final Research Report

• Project/Area Number: 20840027
• Research Category: Grant-in-Aid for Young Scientists (Start-up)
• Allocation Type: Single-year Grants
• Research Field: Biophysics/Chemical physics
• Research Institution: Kyoto University
• Principal Investigator: SAKAUE Takahiro Kyoto University, 理学研究院, 助教 (30512959)
• Project Period (FY): 2008 – 2009
• Keywords: DNA / 高分子物理学 / 非平衡ダイナミクス / トポロジー

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.

Research Products

• [Journal Article] Mismatch of bulk viscosity reduces interfacial diffusivity at an aqueous/oil system (2010)
  • Author(s): M. Negishi, T. Sakaue, K. Yoshikawa
  • Journal Title: Phys. Rev. E vol.81 Pages: 020901
• [Journal Article] Sucking genes into pores: Insight into driven translocation (2010)
  • Author(s): T. Sakaue
  • Journal Title: Phys. Rev. E vol.81 Pages: 041808
• [Journal Article] Dynamics of Polymer Decompression: Expansion, Unfolding, and Ejection (2009)
  • Author(s): T. Sakaue, N. Yoshinaga
  • Journal Title: Phys. Rev. Lett. vol.102 Pages: 148302
• [Journal Article] Conformational transition of giant DNA in a confined space surrounded by a phospholipid membrane (2009)
  • Author(s): A. Kato, E. Shindo, T. Sakaue, A. Tsuji, K. Yoshikawa
  • Journal Title: Biophysical Journal vol.97 Pages: 1678-1686
• [Journal Article] Probing Nonequilibrium Fluctuation through Linear Response (2008)
  • Author(s): T. Sakaue, T. Ohta
  • Journal Title: Phys. Rev. E vol.77 Pages: 050102
• [Journal Article] Chain Length Dependence of Folding Transition in a Semiflexible Homo-polymer Chain: Appearance of a Core-shell Structure (2008)
  • Author(s): Y. Higuchi, T. Sakaue, K. Yoshikawa
  • Journal Title: Chem. Phys. Lett. vol.461 Pages: 42
• [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)
• [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)
• [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
• [Presentation] Asymmetric response and fluctuation in nonequilibrium steady state (2010)
  • Author(s): T. Sakaue
  • Organizer: Open Statistical Physics
  • Place of Presentation: Open University, UK
  • Year and Date: 2010-03-10
• [Presentation] Two topics on diffusion (2009)
  • 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
• [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
• [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