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Journal of Chemical Physics / Volume 135 / Issue 12 / ARTICLES / Biological Molecules, Biopolymers, and Biological Systems

J. Chem. Phys. 135, 125104 (2011); http://dx.doi.org/10.1063/1.3636383 (10 pages)

Influence of mobile DNA-protein-DNA bridges on DNA configurations: Coarse-grained Monte-Carlo simulations

Renko de Vries

Laboratory of Physical Chemistry and Colloid Science, Wageningen University, P.O. Box 8038, 6700 EK Wageningen, The Netherlands

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(Received 18 May 2011; accepted 21 August 2011; published online 30 September 2011)

A large literature exists on modeling the influence of sequence-specific DNA-binding proteins on the shape of the DNA double helix in terms of one or a few fixed constraints. This approach is inadequate for the many proteins that bind DNA sequence independently, and that are present in very large quantities rather than as a few copies, such as the nucleoid proteins in bacterial cells. The influence of such proteins on DNA configurations is better modeled in terms of a great number of mobile constraints on the DNA. Types of constraints that mimic the influence of various known non-specifically DNA binding proteins include DNA bending, wrapping, and bridging. Using Monte-Carlo simulations, we here investigate the influence of (non-interacting) mobile DNA-protein-DNA bridges on the configurations of a 1000 bp piece of linear DNA, for both homogeneous DNA and DNA with an intrinsic planar bend. Results are compared to experimental data on the bacterial nucleoid protein H-NS that forms DNA-protein-DNA bridges. In agreement with data on H-NS, we find very strong positioning of DNA-protein-DNA bridges in the vicinity of planar bends. H-NS binds to DNA very cooperatively, but for non-interacting bridges we only find a moderate DNA-induced clustering. Finally, it has been suggested that H-NS is an important contributor to the extreme condensation of bacterial DNA into a nucleoid structure, but we find only a moderate compaction of DNA coils with increasing numbers of non-interacting bridges. Our results illustrate the importance of quantifying the various effects on DNA configurations that have been proposed for proteins that bind DNA sequence independently.

© 2011 American Institute of Physics

Article Outline

  1. INTRODUCTION
  2. MODEL AND METHODS
    1. DNA model
    2. Mobile DNA-protein-DNA bridges
    3. Parameter values
    4. Monte-Carlo simulation
  3. RESULTS
    1. Planar curvature
    2. Positioning of single constraint
    3. DNA-induced clustering of bridges
    4. Compaction by multiple constraints
  4. DISCUSSION

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KEYWORDS and PACS

Keywords

bending, biochemistry, biomechanics, DNA, molecular biophysics, molecular configurations, Monte Carlo methods, proteins

PACS

ARTICLE DATA

Digital Object Identifier
http://dx.doi.org/10.1063/1.3636383

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.
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    B. Mergell, M. R. Ejtehadi, and R. Everaers, Phys. Rev. E 68, 021911 (2003).


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