Oxidation of DNA and RNA by oxoruthenium(IV) metallointercalators: Visualizing the recognition properties of dipyridophenazine by high-resolution electrophoresis

The binding specificity for the intercalating Ru(tpy)(dppz)O2+ complex (tpy = 2,2',2 "-terpyridine; dppz = dipyridophenazine) was investigated fur duplex DNA, HN-I TAR DNA and RNA? and tRNA(Phe) Unlike other dppz compounds studied to date, this compound cleaves nucleic acids at short range, and the resulting cleavage pattern dan therefore be directly related to the recognition properties of the dppz ligand. To assign the intercalative recognition sites, a comparison was first made between the cleavage patterns of Ru(tpy)(dppz)O2+ and Hu(tpy)(bpy)O2+ (bpy = 2,2'-bipyridine), which differs from Ru(tpy)(dppz)O2+ only by the absence of the intercalative dppz functionality. Cleavage sites common to both complexes were assigned to binding properties other than intercalation, whereas any additional sites observed for Ru(tpy)(dppz)O2+ were strongly implicated as the sites of intercalative recognition. It was necessary, however, to distinguish between those sites which represent a strong binding affinity and those sites which were instead made more accessible to cleavage by binding of another equivalent of the Intercalating complex at a remote site. We therefore investigated the cleavage pattern of Ru(tpy)(bpy)O2+ with and without the classical intercalator Pt(tpy)(HET)(+) (HET = 2-hydroxyethanethiolate) to determine the effect of decoupling the intercalative recognition and oxidation chemistry, In this experiment, sites where cleavage inhibition was observed were indicative of intercalative recognition by the platinum complex, whereas sites where cleavage enhancement was observed strongly suggested that intercalative binding at a remote site had altered the structure of the nucleic acid. Comparison of the cleavage patterns of Ru(tpy)(bpy)O2+ and Ru(tpy)(dppz)O2+ for a duplex oligonucleotides. tRNA, and stem-loop structures suggests a recognition pattern for the dppz ligand very similar to that pf classical intercalators.