The Role of the Threading Moiety in DNA Threading Intercalation by Ruthenium Dimer Complexes

Abstract

There is significant interest in ruthenium dimer complexes due to their novel DNA binding properties. The binuclear ruthenium complex ΔΔ-[μ-bidppz(bipy)4Ru2]4+ that we investigate in this study binds to DNA by threading intercalation, in which one of the bulky ruthenium moieties threads through the DNA base pair stack to reach its bound state. The extremely slow dissociation from DNA of this threading intercalator gives it properties needed for chemotherapy drugs, while also making it difficult to study in traditional bulk experiments. In this study we use optical tweezers in order to quantify the threading kinetics as well as the equilibrium behavior of this ruthenium dimer complex to understand how changing the ancillary ligands coordinated to ruthenium (threading moiety) affects the process of threading. To observe the slow threading process, the DNA was held at a constant force in the presence of the ligand and the DNA extension was measured as a function of time until the extension reached equilibrium. When the concentration of the ligand is increased during these constant force measurements, the total extension of the DNA will also increase until it becomes saturated at some concentration as all of the ligand binding sites are filled. These measurements of the equilibrium DNA extension allow for a full quantitative description of the binding kinetics and equilibrium behavior of the complex. The preliminary data suggests that the ΔΔ-[μ-bidppz(bipy)4Ru2]4+ complex with its bicyclic bipyridine ligand, shows significantly faster kinetics compared to the ΔΔ-[μ-bidppz(phen)4Ru2]4+, complex with a tricyclic phenanthroline ligand counterpart.