Inter-strand distance distribution of DNA near melting

TL;DR

This paper analyzes the distribution of inter-strand distances in DNA near melting, combining scaling theory with numerical simulations to understand the effects of self-avoiding interactions on the melting transition.

Contribution

It introduces a generalized Poland-Scheraga model including self-avoiding interactions and derives the inter-strand distance distribution at the melting point.

Findings

Distribution decays as 1/r^ at the transition

Numerical simulations agree with the scaling predictions

Results extend understanding of DNA melting behavior

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.