Supercoiling couples DNA curvature to the overall shape and the internal motion of the DNA molecule in solution

Abstract

If particular sequence stretches in the DNA deflect the helix axis in phase with the helix screw, a curvature of the molecule is induced globally and becomes macroscopically measurable. Several sequences are able to induce this effect. Best analyzed are short tracts of the homopolymer dA : dT. The ability to induce curvature is assumed to be a consequence of such tracts to adopt a stable B′-DNA conformation which is distinct from the normal B-form. The B′-form structure having a large propeller twist is stabilized by stacking interactions. The structure forms due to the exocyclic chemical groups of the base adenine. Short curved DNA segments can act as mediators for the ordering of large domains in superhelical DNA. Permanently curved inserts have an influence on the solution structure and on the internal motions of superhelical plasmid DNA. The dynamics of superhelical DNA are strongly influenced by sequence- or protein-induced bending. In superhelical plasmids containing curved inserts, the amplitude of the internal motion is decreased compared with non-curved controls. Furthermore, the relative arrangement of curved sequences in the plasmids can influence the overall shape of the superhelical DNA. Linearized forms of the plasmids having no superhelical stress do not show these effects.