DNA melting: intra base-pair dynamics and a vector generalization of the Peyrard-Bishop-Dauxois model

Abstract

The Peyrard-Bishop-Dauxois (PBD) model of DNA denaturation, although successful in the description of melting profiles, fails to predict melting entropies, unzipping forces and dynamical properties, e.g. hairpin dynamics. The paper presents an atomistic "toy model" of the intra base-pair motion which suggests that the thermodynamics may be better described by a planar vector - rather than a scalar - order parameter. This leads to correct estimates of melting entropy, unzipping force, hairpin opening rates, and the equilibrium constant of open/closed base pair states during imino proton exchange.