Apparent persistence length renormalization of bent DNA

Igor M. Kulić, Hervé Mohrbach, Vladimir Lobaskin, Rochish Thaokar, and Helmut Schiessel
Phys. Rev. E 72, 041905 – Published 6 October 2005

Abstract

We derive the single molecule equation of state (force-extension relation) for DNA molecules bearing sliding loops and deflection defects. Analytical results are obtained in the large force limit by employing an analogy with instantons in quantum mechanical tunneling problems. The results reveal a remarkable feature of sliding loops—an apparent strong reduction of the persistence length. We generalize these results to several other experimentally interesting situations ranging from rigid DNA-protein loops to the problem of anchoring deflections in atomic force microscopy stretching of semiflexible polymers. Expressions relating the force-extension measurements to the underlying loop or boundary deflection geometry are provided and applied to the case of the gal repressor dimer protein. The theoretical predictions are complemented and quantitatively confirmed by molecular dynamics simulations.

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  • Received 6 January 2005

DOI:https://doi.org/10.1103/PhysRevE.72.041905

©2005 American Physical Society

Authors & Affiliations

Igor M. Kulić*, Hervé Mohrbach, Vladimir Lobaskin, Rochish Thaokar, and Helmut Schiessel

  • Max-Planck-Institute for Polymer Research, Theory Group, PO Box 3148, D 55021 Mainz, Germany

  • *Present address: Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104, USA.
  • Present address: Instituut-Lorentz, Universiteit Leiden, Postbus 9506, 2300 RA Leiden, The Netherlands.
  • Present address: Department of Chemical Engineering, Indian Institute of Technology, Bombay, Mumbai, 400076, India.

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Issue

Vol. 72, Iss. 4 — October 2005

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