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Journal of Chemical Physics / Volume 136 / Issue 2 / ARTICLES / Biological Molecules, Biopolymers, and Biological Systems

J. Chem. Phys. 136, 025102 (2012); http://dx.doi.org/10.1063/1.3674978 (9 pages)

On binding of DNA-bending proteins to DNA minicircles

Shlomi Medalion and Yitzhak Rabin

Department of Physics and Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel

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(Received 12 May 2011; accepted 14 December 2011; published online 10 January 2012)

We present a theoretical study of binding of DNA-bending proteins to circular DNA, using computer simulations of the wormlike chain model of DNA. We find that the binding affinity is affected by the bending elasticity and the conformational entropy of the polymer and that while protein adsorption is identical on open and closed long DNA molecules, there is significant enhancement of binding on DNA minicircles, compared to their linear counterparts. We also find that the ratio of the radii of gyration of open and closed chains depends on protein concentration for short DNA molecules. Experimental tests of our predictions are proposed.

© 2012 American Institute of Physics

Article Outline

  1. INTRODUCTION
  2. THEORETICAL BACKGROUND
    1. Open wormlike chains
    2. Closure and excluded volume effects
  3. SIMULATION METHOD
  4. RESULTS AND ANALYSIS
    1. Effect of Topology on DNA-protein binding
      1. Effect of chain length
      2. Effect of bending angle
      3. Effect of local stiffness
      4. Effect of number of binding sites
    2. Effect of topology on radius of gyration
  5. DISCUSSION

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KEYWORDS and PACS

Keywords

adsorption, bending, biochemistry, biomechanics, DNA, elasticity, entropy, molecular biophysics, physiological models, proteins, rotation

PACS

ARTICLE DATA

Digital Object Identifier
http://dx.doi.org/10.1063/1.3674978

PUBLICATION DATA

ISSN

0021-9606 (print)  
1089-7690 (online)

Publisher

$abstract.society.value is a Member of CrossRef American Institute of Physics

For access to fully linked references, you need to log in.
    H. Diamant and D. Andelman, Phys. Rev. E 61, 6740 (2000).

    J. Yan and J. Marko, Phys. Rev. E 68, 011905 (2003).

    S. Rappaport and Y. Rabin, Phys. Rev. Lett. 101, 38101 (2008).

    S. Rappaport and Y. Rabin, Phys. Rev. E 80, 052801 (2009).

    S. Medalion, S. Rappaport, and Y. Rabin, J. Chem. Phys. 132, 045101 (2010)JCPSA6000132000004045101000001.

    E. Orlandini and S. Whittington, Rev. Mod. Phys. 79, 611 (2007).

    H. Zhang and J. Marko, Phys. Rev. E 77, 031916 (2008).


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