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.