Volume 97, Number 3, February 2012
|Number of page(s)||6|
|Section||Interdisciplinary Physics and Related Areas of Science and Technology|
|Published online||06 February 2012|
DNA bending potentials for loop-mediated nucleosome repositioning
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
Accepted: 4 January 2012
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.
PACS: 87.15.H- – Dynamics of biomolecules / 87.14.G- – Nucleic acids / 36.20.Ey – Conformation (statistics and dynamics)
© EPLA, 2012
Current usage metrics show cumulative count of Article Views (full-text article views including HTML views, PDF and ePub downloads, according to the available data) and Abstracts Views on Vision4Press platform.
Data correspond to usage on the plateform after 2015. The current usage metrics is available 48-96 hours after online publication and is updated daily on week days.
Initial download of the metrics may take a while.