Alexander Balaeff, L. Mahadevan, and Klaus Schulten.
Modeling DNA loops using the theory of elasticity.
Physical Review E, 73:031919, 2006.
(23 pages).
BALA2006
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 lentghts 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.
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