Inter-strand distance distribution of DNA near melting

Abstract

The distance distribution between complementary base pairs of the two strands of a DNA molecule is studied near the melting transition. Scaling arguments are presented for a generalized Poland-Scheraga type model which includes self-avoiding interactions. At the transition temperature and for a large distance r the distribution decays as 1/r^\kappa with \kappa=1+(c-2)/ \nu. Here \nu is the self-avoiding walk correlation length exponent and c is the exponent associated with the entropy of an open loop in the chain. Results for the distribution function just below the melting point are also presented. Numerical simulations which fully take into account the self-avoiding interactions are in good agreement with the scaling approach.