DNA bending potentials for loop-mediated nucleosome repositioning

¹ Computational Molecular Biophysics, Interdisciplinary Center for Scientific Computing (IWR), Im Neuenheimer Feld 368, University of Heidelberg - D-69120 Heidelberg, Germany, EU
² Biophysics of Macromolecules, Im Neuenheimer Feld 580, German Cancer Research Center (DKFZ) D-69120 Heidelberg, Germany, EU
³ UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory P.O. Box 2008, Oak Ridge, TN 37831-6309, USA
⁴ Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Sciences - 1414 Cumberland Avenue, Knoxville, TN 37996, USA

^a smithjc@ornl.gov

Received: 12 October 2011
Accepted: 4 January 2012

Abstract

Nucleosome repositioning is a fundamental process in gene function. DNA elasticity is a key element of loop-mediated nucleosome repositioning. Two analytical models for DNA elasticity have been proposed: the linear sub-elastic chain (SEC), which allows DNA kinking, and the worm-like chain (WLC), with a harmonic bending potential. In vitro studies have shown that nucleosomes reposition in a discontiguous manner on a segment of DNA and this has also been found in ground-state calculations with the WLC analytical model. Here we study using Monte Carlo simulation the dynamics of DNA loop-mediated nucleosome repositioning at physiological temperatures using the SEC and WLC potentials. At thermal energies both models predict nearest-neighbor repositioning of nucleosomes on DNA, in contrast to the repositioning in jumps observed in experiments. This suggests a crucial role of DNA sequence in nucleosome repositioning.