Binding Kinetics of DNA Intercalation by Small Rhodium Complexes

Abstract

We characterize the kinetics and DNA binding properties of the small rhodium based molecules, [Rh(bpy)2(chrysi)]3+ (chrysi) and [Rh(bpy)2(phi)]3+ (phi). Both motifs bind to DNA. Phi contains an aromatic ring system known to intercalate between adjacent bases in a fairly sequence-neutral manner. Intercalation is weaker for chrysi due to the presence of an additional aromatic ring. Instead, chrysi has been shown to bind to DNA mismatches preferentially, ejecting and replacing the bases along the helical stack. We used optical tweezers on single DNA hairpin and long DNA molecules. Hairpin unfolding experiments on mismatch-containing sequences show that chrysi binds preferentially to sequences containing mismatches, stabilizing the hairpin. Long double stranded DNA was stretched at a constant external force in the presence of the ligand and a change in DNA extension was observed to be driven directly by ligand intercalation. Under the influence of increasing force, intercalation of the phi ligand into matched DNA is observed as expected. Surprisingly this intercalation into matched DNA was also observed for the chrysi ligand. Further analysis revealed the dissociation constants (Kd) of the chrysi and phi complexes to be on the order of 1 μM, though phi showed a significantly stronger intercalating affinity than chrysi.