Abstract
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.