The energetic basis of the DNA double helix: a combined microcalorimetric approach.

Paulius Vaitiekunas,Peter L. Privalov,Colyn Crane-Robinson

doi:10.1093/nar/gkv812

Abstract

Microcalorimetric studies of DNA duplexes and their component single strands showed that association enthalpies of unfolded complementary strands into completely folded duplexes increase linearly with temperature and do not depend on salt concentration, i.e. duplex formation results in a constant heat capacity decrement, identical for CG and AT pairs. Although duplex thermostability increases with CG content, the enthalpic and entropic contributions of an AT pair to duplex formation exceed that of a CG pair when compared at the same temperature. The reduced contribution of AT pairs to duplex stabilization comes not from their lower enthalpy, as previously supposed, but from their larger entropy contribution. This larger enthalpy and particularly the greater entropy results from water fixed by the AT pair in the minor groove. As the increased entropy of an AT pair exceeds that of melting ice, the water molecule fixed by this pair must affect those of its neighbors. Water in the minor groove is, thus, orchestrated by the arrangement of AT groups, i.e. is context dependent. In contrast, water hydrating exposed nonpolar surfaces of bases is responsible for the heat capacity increment on dissociation and, therefore, for the temperature dependence of all thermodynamic characteristics of the double helix.

Highlights

Understanding that two complementary DNA strands are wound into a double helix and that their separation and copying is the key process in replication of the genetic information [1] immediately raised interest in the energetic basis of this molecular construction, that is the forces between the complementary strands and the work needed for their separation
The enthalpy of DNA dissociation at elevated temperatures, determined by DSC, was found to be in conflict with the enthalpy of association of the complementary strands measured by ITC at lower temperatures: the strand association enthalpies at room temperature were found to be much smaller in magnitude than the melting enthalpies at higher temperatures [14,15,16]
It was concluded that the ‘error in determining the heat capacity increment of DNA duplex melting is so big that it prevents any rigorous thermodynamic analysis of the stability of the nucleic acid duplexes’ [19]

Summary

Introduction

Understanding that two complementary DNA strands are wound into a double helix and that their separation and copying is the key process in replication of the genetic information [1] immediately raised interest in the energetic basis of this molecular construction, that is the forces between the complementary strands and the work needed for their separation. The enthalpy of DNA dissociation at elevated temperatures, determined by DSC, was found to be in conflict with the enthalpy of association of the complementary strands measured by ITC at lower temperatures: the strand association enthalpies at room temperature were found to be much smaller in magnitude than the melting enthalpies at higher temperatures [14,15,16] This suggested, that the enthalpy of double helix formation should be temperature dependent, i.e. unfolding of the double helix should result in a heat capacity increment. It was concluded that the ‘error in determining the heat capacity increment of DNA duplex melting is so big that it prevents any rigorous thermodynamic analysis of the stability of the nucleic acid duplexes’ [19]

Methods

Results

Discussion

Conclusion