Bubble dynamics in double stranded DNA: A Rouse chain based approach

We propose a model for the fluctuation dynamics of the local denaturation zones (bubbles) in double-stranded DNA. In our formulation, the DNA strand is modeled as a one dimensional Rouse chain confined at both the ends. The bubble is formed when the transverse displacement of the chain attains a critical value. This simple model effectively reproduces the autocorrelation function for the tagged base pair in the DNA strand as measured in the seminal single molecule experiment by Altan-Bonnet et al. (2003) [2]. Our model goes beyond a single reaction coordinate description by incorporating the chain dynamics through a confined Rouse chain and thus considers the collective nature of the dynamics. Our model also shows that the autocorrelation function is very sensitive to the relaxation times of the normal modes of the chain, which is obvious since the fluctuation dynamics of the bubble has the contribution from the different normal modes of the chain.