Coupled dynamics of DNA-breathing and single-stranded DNA binding proteins
Biomolecules
2007-05-23 v2 Statistical Mechanics
Abstract
We study the size fluctuations of a local denaturation zone in a DNA molecule in the presence of proteins that selectively bind to single-stranded DNA, based on a (2+1)-dimensional master equation. By tuning the physical parameters we can drive the system from undisturbed bubble fluctuations to full, binding protein-induced denaturation. We determine the effective free energy landscape of the DNA-bubble and explore its relaxation modes.
Keywords
Cite
@article{arxiv.q-bio/0411053,
title = {Coupled dynamics of DNA-breathing and single-stranded DNA binding proteins},
author = {Tobias Ambjornsson and Ralf Metzler},
journal= {arXiv preprint arXiv:q-bio/0411053},
year = {2007}
}
Comments
REVTeX4, 4 pages, 5 figures, revised version