Soliton-like states for opening in polynucleotide double helices

Abstract

Abstract The polar hydrogens of the nucleobases in DNA and synthetic duplexes exchange with solvent hydrogens under conditions in which these molecules are ordered and remote from any denaturation transitions. This behavior of both natural and synthetic polynucleotide duplexes has led to the proposal that ordered double helices contain small amounts of open states, in which bases are unpaired, and that these open states mediate the exchange of otherwise inaccessible hydrogen-bonded protons. In this paper we conclude from analysis of the experimental data that these open configurations can consist of mobile segments on the order of ten base pairs in length. We suggest that these extended open states may be described in terms of solitons, which are now being recognized as important conformational excitations in polymers and other chain compounds.