Bubble dynamics in DNA

The formation of local denaturation zones (bubbles) in double-stranded DNA is an important example of 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 (Altan-Bonnet et al 2003 Phys. Rev. Lett. 90 138101) emerges as a limiting case.