Europhys. Lett.
Volume 71, Number 5, September 2005
Page(s) 852 - 858
Section Interdisciplinary physics and related areas of science and technology
Published online 29 July 2005
Europhys. Lett., 71 (5), pp. 852-858 (2005)
DOI: 10.1209/epl/i2005-10144-9

Stochastic approach to DNA breathing dynamics

S. K. Banik, T. Ambjörnsson and R. Metzler

NORDITA, Nordic Institute for Theoretical Physics Blegdamsvej 17, DK-2100 Copenhagen Ø, Denmark

received 22 April 2005; accepted in final form 28 June 2005
published online 29 July 2005

We propose a stochastic Gillespie scheme to describe the temporal fluctuations of local denaturation zones in double-stranded DNA as a single-molecule time series. It is demonstrated that the model recovers the equilibrium properties. We also study measurable dynamical quantities such as the bubble size autocorrelation function. This efficient computational approach will be useful to analyse in detail recent single-molecule experiments on clamped homopolymer breathing domains, to probe the parameter values of the underlying Poland-Scheraga model, as well as to design experimental conditions for similar setups.

87.15.Aa - Theory and modeling; computer simulation.
82.37.-j - Single molecule kinetics.
87.14.Gg - DNA, RNA.

© EDP Sciences 2005