  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
model 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 (Phys. Rev. Lett. 90, 138101 (2003)).
Although our model is mathematically similar to the one proposed by Chatterjee
et al. (J. Chem. Phys. 127, 155104 (2007)) it 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.
