Dynamics of a bubble formed in double-stranded DNA

We study the fluctuational dynamics of a tagged base pair in double-stranded DNA. We calculate the drift force which acts on the tagged base pair using a potential model that describes interactions at base pairs level and use it to construct a Fokker-Planck equation. The calculated displacement autocorrelation function is found to be in very good agreement with the experimental result of Altan-Bonnet et al. (Phys. Rev. Lett., 90 (2003) 138101) over the entire time range of measurement. We calculate the most probable displacements which predominately contribute to the autocorrelation function and the half-time history of these displacements.