TOD

Abstract

Stretching experiments on DNA in the presence of DNA binding ligands have been shown to reveal insight into biological processes of DNA-ligand binding. We generalize the Poland-Scheraga model to consider DNA denaturation in the presence of an external stretching force and DNA-binding ligands which bind to double-stranded DNA by intercalating between two adjacent base pairs. We obtain the phase diagram of DNA denaturation as a function of temperature, stretching force, and the chemical potential of the DNA-binding ligand. Force-extension relations are compared with recent DNA stretching experiments in the presence of DNA intercalating ethidium and ruthenium complexes.