Binding properties of ruthenium(II) polypyridyl complexes [Ru(bpy)2(L)]2+(L=7-F-dppz and 7OCH3–-dppz) with poly(A)-poly(U) under dilute and molecular crowding conditions

Abstract

Two ruthenium(II) polypyridyl complexes, [Ru(bpy)2(7-F-dppz)]2+ (Ru1, bpy = 2,2′-bipyridine, 7-F-dppz = 7-fluorodipyrido[3,2-a:2′,3′-c]phenazine) and [Ru(bpy)2(7OCH3–-dppz)]2+ (Ru2, 7OCH3–-dppz = 7‑methoxy-dipyrido-[3,2-a,2′,3′-c]-phenazine), were synthesized. The binding properties of Ru1 and Ru2 to duplex RNA poly(A)-poly(U) have been explored through spectroscopic techniques and viscometry. Spectral titration and viscosity experiments show that the binding mode of Ru1 and Ru2 to double-stranded RNA(dsRNA) in dilute solution and molecular crowded environment are intercalation, and that the binding affinity of Ru1 for poly(A)-poly(U) is greater than that of Ru2. Thermal denaturation experiments showed that two complexes have good thermal stability for dsRNA in two environments. Fluorescence titrations showed that Ru1 and Ru2 could act as molecular "light switch" for duplex poly(A)-poly(U) in both environments. Surprisingly, the binding effect of ligands and poly(A)-poly(U) was significantly reduced under crowded condition, and the thermal stability of RNA duplex was less significant than that of dilute solution. The reason of this result is due to the water activity in molecular crowded environment, the increased viscosity of the medium leading to a decrease in the affinity of the ligand for the RNA duplex, and also the electronic effect of the ligand on the binding affinity of the poly(A)-poly(U). Results of the present work facilitate our understanding of the two environments as well as the interaction between ruthenium(II) polypyridyl complexes and dsRNA is influenced by the electronegativity of the substituents.