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Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Mar;73(3 Pt 1):031919. Epub 2006 Mar 20.

Modeling DNA loops using the theory of elasticity.

Author information

1
Beckman Institute, Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.

Abstract

An elastic rod model of a protein-bound DNA loop is adapted for application in multi-scale simulations of protein-DNA complexes. The classical Kirchhoff system of equations which describes the equilibrium structure of the elastic loop is modified to account for the intrinsic twist and curvature, anisotropic bending properties, and electrostatic charge of DNA. The effects of bending anisotropy and electrostatics are studied for the DNA loop clamped by the lac repressor protein. For two possible lengths of the loop, several topologically different conformations are predicted and extensively analyzed over the broad range of model parameters describing DNA bending and electrostatic properties. The scope and applications of the model in already accomplished and in future multi-scale studies of protein-DNA complexes are discussed.

PMID:
16605570
DOI:
10.1103/PhysRevE.73.031919
[Indexed for MEDLINE]

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