Theoretical Treatment of Melting of Complexes of DNA with Ligands Having Several Types of Binding Sites on Helical and Single-stranded DNA

Abstract

We treat theoretically conformational transitions in DNA-ligand complexes allowing for the existence of different binding parameters of the ligand to different DNA conformations. The parameters of binding are determined from the best fit of the theory to experimental data for the difference between transition point (Tm) and the width of transition curve (delta T) for the complexes and for naked DNA. The analysis shows that Ethidium Bromide (EB) and Actinomycin D (AMD) each may form at least five types of complexes: three types (one "strong" and two "weak") with helix DNA and two types ("strong" and "weak") with single-stranded DNA. The parameters of the complexes have been obtained. Some testable experimental predictions of the theory are also discussed.