The binding specificity for the intercalating Ru(tpy)(dppz)O2+ complex (tpy = 2,2‘,2‘‘-terpyridine; dppz = dipyridophenazine) was investigated for duplex DNA, HIV-1 TAR DNA and RNA, and tRNAPhe. Unlike other dppz compounds studied to date, this compound cleaves nucleic acids at short range, and the resulting cleavage pattern can 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 Ru(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 of classical intercalators.

The effects of steric hindrance on the oxidation of DNA by polypyridyl oxoruthenium(IV) complexes have been investigated. The complexes oxidize DNA by activation either of the 1' ribose C-H bond or by oxo transfer to the guanine nucleobase. A method is presented for determining the relative rates of activation of individual sites from the dependence of the extent of cleavage on the oxidant concentration. This analysis shows that hybridization of the labeled strand to its complement attenuates the rate of oxidation of guanine more effectively than the rate of sugar oxidation. Accordingly, higher ratios of guanine/sugar oxidation are observed in single strands. Among the individual guanine residues, however, the relative reactivities are not altered by hybridization; a similar result is obtained for sugar oxidation. This result implies that sequence-dependent chemical reactivity is partly responsible for the different extents of cleavage observed within the sequence. The ability of hybridization to protect guanine from oxidation is also apparent in hairpin studies, where the stem guanines are much less reactive than the loop guanines, and altered sugar conformations in the loop lead to modulated reactivity. Finally, a set of sterically differentiated complexes shows greater steric effects for oxidation of guanine compared to oxidation of sugar, as expected from the relative rates of the single strand and duplexes.

The photochemistry of Pt2(pop)44- with nucleic acids has been studied using radiolabeled oligomers of DNA and RNA and high-resolution electrophoresis (pop is P2O5H22-). Photolysis of Pt2(pop)44- with duplex DNA produces an even cleavage ladder and relatively little enhancement of cleavage upon treatment with piperidine. In contrast, the cleavage pattern is far less regular with single-stranded DNA, and there is a large enhancement in cleavage upon treatment with piperidine. Accordingly, photolysis of Pt2(pop)44- with the DNA hairpin 5'-d[ATCCTATTTATAGGAT] produces a much larger piperidine enhancement at the loop and end nucleotides than in the stem. There is an additional piperidine enhancement that occurs selectively at guanine residues either in RNA or in DNA at low Mg2+ concentrations that is attributed to outer-sphere electron transfer on the basis of the known excited-state redox potentials of Pt2(pop)44- and the expected oxidative chemistry of guanine. The extent of guanine oxidation is higher compared to the extent of sugar oxidation at low Mg2+ concentrations, which can be attributed to a shallower distance dependence for electron transfer compared to that for atom transfer. The effects of Mg2+ and piperidine or aniline treatment were examined on stem-loop structures of DNA and RNA and gave partial images of the expected secondary structures.

He was wedded to the unglamorous carbon cycle while younger [scientists] were achieving fame and opulent grants in such fair fields as neurobiology, virology, and the wonderful new wilderness of nucleic acids.

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