Bubble dynamics in DNA
Abstract
The formation of local denaturation zones (bubbles) in double-stranded DNA is an important example for conformational changes of biological macromolecules. We study the dynamics of bubble formation in terms of a Fokker-Planck equation for the probability density to find a bubble of size n base pairs at time t, on the basis of the free energy in the Poland-Scheraga model. Characteristic bubble closing and opening times can be determined from the corresponding first passage time problem, and are sensitive to the specific parameters entering the model. A multistate unzipping model with constant rates recently applied to DNA breathing dynamics [G. Altan-Bonnet et al, Phys. Rev. Lett. 90, 138101 (2003)] emerges as a limiting case.
Keywords
Cite
@article{arxiv.cond-mat/0305049,
title = {Bubble dynamics in DNA},
author = {Andreas Hanke and Ralf Metzler},
journal= {arXiv preprint arXiv:cond-mat/0305049},
year = {2009}
}
Comments
9 pages, 2 figures