Role of the Moiety Chirality in Determining the DNA Binding Characteristics of Threading Intercalators

Abstract

Threading intercalators are small molecules that bind to DNA by threading their ancillary groups through the DNA bases to intercalate their middle planar section between the DNA base pairs. The high binding affinity and slow dissociation rates of threading intercalators have put them in the class of prospective anti-cancer drugs. In this study we explore the binding of a specific threading intercalator, the binuclear ruthenium complex ΛΛ-P (ΛΛ-[µ-bidppz(phen)4Ru2]4+) using optical tweezers. A single DNA molecule is held at a constant force and ΛΛ-P is introduced to the system in varying concentrations until equilibrium is achieved. Measurements of DNA extension at various concentrations of ΛΛ-P as a function of time provide the DNA equilibrium binding affinity and binding kinetics for this molecule. Preliminary data analysis at constant force suggests that ΛΛ-P exhibits significantly faster binding kinetics compared to the very similar ΔΔ-P [μ-bidppz(phen)4Ru2]4+. These complexes have the same chemical structure and only differ in their chirality, which suggests that the left handed (ΛΛ) threading moieties require less DNA structural distortion for threading compared with the right handed (ΔΔ) threading moieties.