LIGAND-BINDING ISOTHERM FOR DNA IN THE PRESENCE OF SUPERCOIL-INDUCED NON-B FORM - A THEORETICAL-ANALYSIS

A binding isotherm in the form of a modified McGhee-Von Hippel equatio n is proposed, on the basis of thermodynamical considerations, to incl ude the non-cooperative binding of extended ligands to supercoiled DNA , where a stretch of non-B form may be present under superhelical stre ss. It is then studied, on the basis of a non-linear Scatchard plot, h ow the presence of an intercalating ligand can relax the supercoiled m olecule and thus destabilise the non-B stretch, which may be recognise d by the existence of a significant kink in the Scatchard plot.