Alexander Balaeff, Christophe R. Koudella, L. Mahadevan, and Klaus Schulten.
Modeling DNA loops using continuum and statistical mechanics.
Philosophical Transactions of the Royal Society of London A. (Mathematical, Physical and Engineering Sciences), 362:1355-1371, 2004.
BALA2004A
The classical Kirchhoff elastic rod model applied to DNA is
extended to account for sequence dependent intrinsic twist and
curvatures, anisotropic bending rigidities, electrostatic force
interactions and overdamped Brownian motion in a solvent. The
zero temperature equilibrium rod model is then applied to study
the structural basis of the function of the lac repressor protein in
the lac operon of E. coli. The structure of a DNA loop
induced by
the clamping of two distant DNA operator sites by lac repressor is
investigated and the optimal geometries for the loop of length 76
bp are predicted. A mimicked binding of catabolite gene activator
protein (CAP) inside the loop provides solutions that explain
experimentally observed synergy in DNA binding between the
two
proteins. Finally, a combined Monte Carlo and Brownian
dynamics
solver for a wormlike chain model is described and a preliminary
analysis of DNA loop formation kinetics is presented.
Download Full Text
The manuscripts available on our site are provided for your personal
use only and may not be retransmitted or redistributed without written
permissions from the paper's publisher and author. You may not upload any
of this site's material to any public server, on-line service, network, or
bulletin board without prior written permission from the publisher and
author. You may not make copies for any commercial purpose. Reproduction
or storage of materials retrieved from this web site is subject to the
U.S. Copyright Act of 1976, Title 17 U.S.C.
