Symmetry reduction in homopolymeric DNA: implications for DNA fine structure

Abstract

Theoretical modelling of DNA duplexes with homopolymeric base sequences shows that AT bases are unusual in two respects. First, their most stable B-family conformation exhibits dinucleotide symmetry characterised by a 20° phase change between successive sugars in the adenosine strand. Secondly, by passing over a small energy barrier they can adopt an even more strongly dinucleotidic conformation with successive C2'-endo and O1'-endo sugars within the thymidine strand. This conformation is almost as stable as the previous minimum. The first of these features is lost if the adenine amino group is removed or displaced, or a second amino group is added. If thymine is replaced by uracil, the asymmetry of the most stable minimum is conserved, but the second minimum is strongly destabilised. These unusual features of AT bases may be related to the ability of AT tracts to induce curvature within DNA.