Dynamic model of base pair breathing in a DNA chain with a defect.

We model and analyze a short section of a DNA chain with a defect, with the aim of understanding how the frequency, amplitude, and localization of breathing events depend on the strength of the bonds between base pairs, both along the chain and between the chains. Our results show that the presence of a defect in the chain permits the existence of a localized breather mode. The models we analyze are linear and hence solvable, with solvability extending to the statistical mechanics formulation of the problem. Parameter values for the interaction energy of a base with its nearest neighbors are obtained from AMBER. The results indicate good agreement with both the amplitude and the number of base pairs affected by defect-induced breathing motion.