Binding properties of ruthenium(II) complexes [Ru(phen)2(dicnq)]2+ and [Ru(bpy)2(dicnq)]2+ with the RNA triplex poly(U)·poly(A)*poly(U)

Abstract

Using phen or bpy (phen = 1,10-phenanthroline, bpy = 2,2′-bipyridine) as ancillary ligands and dicnq (dicnq = 6,7-dicyanodipyrido[2,2-d:2′,3′-f]quinoxaline) as the main ligand, two new Ru(II) polypyridyl complexes containing cyano groups, [Ru(phen)2dicnq]2+ (Ru1) and [Ru(bpy)2dicnq]2+ (Ru2) have been synthesized as binders for poly(U)·poly(A)*poly(U) triplex. The binding properties of Ru1 and Ru2 with the triplex has been studied by spectroscopic methods and viscosity measurements. Analysis of the electronic absorption spectra suggests that the binding of intercalating Ru1 with the triplex is greater than that of Ru2, which is also supported by spectroscopic titrations and viscosity measurements. Thermal denaturation studies suggest that the two complexes stabilize the Watson-Crick base-paired duplex of the triplex structure almost without affecting the stability of the Hoogsteen base-paired third strand, suggesting that the electron-withdrawing effect of cyano group hardly increases the binding strengths of the third strand and the template duplex of the triplex under study here. Changes in the CD (CD = circular dichroism) spectra of the triplex indicate that the binding-induced CD perturbation of the triplex structure is more marked with Ru1. The main results obtained here indicate that small differences in the ancillary ligands play important roles in the triplex binding when ruthenium(II) complexes contain the same intercalative ligands.