Oxidation of DNA Hairpins by Oxoruthenium(IV): Effects of Sterics and Secondary Structure

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Abstract
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.