Sequence dependence of the curvature of DNA: a test of the phasing hypothesis

Abstract

Certain DNA molecules derived from both prokaryotic and eukaryotic organisms display markedly abnormal electrophoretic behavior on polyacrylamide gels. These molecules share a common element of sequence which involves collections of A/T residues that are approximately in phase with the helix repeat. This sequence periodicity has led to the suggestion that such phasing is important in generating the abnormal behavior. We have demonstrated that such phasing is, in fact, essential, thus ruling out alternative models which invoke any form of isotropic or centrosymmetric flexibility as the source of the phenomenon. We have also shown that the abnormal behavior is not a simple consequence of marginal thermodynamic stability. The most plausible explanation for the observed behavior is that stable, local distortions of the helix axis result in macroscopic curvature when such distortions are propagated in phase with the helix repeat.