DNA-bending on ligand binding; change of DNA persistence length

Abstract

This paper simulates the helix-characteristic changes of apparent DNA persistence length caused by randomly distributed helix bends as induced, e.g., by DNA-bound ligand molecules. The parameters varied are the constant angle gamma of helix bending and the size alpha of the DNA drug binding site, but also the degree of DNA-ligand binding cooperativity and the helix-unwinding angle. If the size of the binding site is comparable with the helix pitch, the influence of phasing between helix bends and helix screw upon the apparent persistence length is obvious. In the accompanying paper experimental data are analyzed in terms of this theoretical background.