The dynamics of intermittent strand separation in double-stranded DNA

The transient rupture and reformation of hydrogen bonds between base pairs on distinct chains of double-stranded DNA ("bubble" dynamics) is modeled in terms of the fluctuating distance between the bases. The fluctuations in the distance are assumed to be governed by a simple Langevin equation with a quadratic potential under conditions of high friction. A critical distance of separation L must be achieved before a bubble defect is considered to have been formed. The decay of the dynamic correlations between states of the DNA that have such defects and those that do not has been calculated from the above model and has been found to reproduce the trends in experimental measurements of the same quantity.