Theoretical study of the effect of salt and the role of strained hydrogen bonds on the thermal stability of DNA polymers.

Abstract

In this paper we show that ionic effects on the thermal stability of interbase hydrogen bonds of an infinitely long DNA polymer with repeating sequence can be analyzed at the molecular level of detail using a modified self-consistent phonon formulation of anharmonic lattice dynamics theory. The interactions of the charged groups of DNA with each other and with the diffuse ionic cloud surrounding it in solution are approximately represented in the framework of Soumpasis's potential of mean force between the interacting charge groups [J. Biomol. Struct. Dyn. 6, 563 (1988); Biopolymers 29, 1089 (1990)]. The tension from the salt-dependent potential of mean forces and other nonbonded forces across the interbase hydrogen bonds generate a strain in the mean H-bond length. This strain alters the dynamic behavior of these hydrogen bonds. The self-consistently determined bond-disruption probabilities are therefore dependent on the bulk salt concentration. Our calculated premelting interbase-hydrogen-bond-disruption probabilities and the extrapolated melting temperature for a B-DNA guanisine-cytosine homopolymer [poly(dG)\ensuremath{\cdot}poly(dC), i.e., polymer G on one strand of hydrogen bonded to polymer C on the other] are in fair agreement with experimental observations over a wide range of salt concentrations.