Bubble dynamics in DNA

TL;DR

This paper models the formation and dynamics of local denaturation zones (bubbles) in DNA using a Fokker-Planck framework based on the Poland-Scheraga model, providing insights into bubble lifetimes and effects of model parameters.

Contribution

It introduces a Fokker-Planck approach to DNA bubble dynamics and connects it with existing unzipping models, offering a detailed probabilistic analysis.

Findings

Characteristic bubble closing and opening times are derived.

Bubble dynamics are sensitive to model parameters.

The model generalizes previous unzipping approaches.

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.