Comparison of the cleavage profiles of oligonucleotide duplexes with or without phosphorothioate linkages by using a chemical nuclease probe

A single nuclease-resistant linkage in DNA as a versatile tool for the characterization of DNA lesions: application to the guanine oxidative lesion "G+34" generated by metalloporphyrin/KHSO(5) reagent

The oxidation of an oligonucleotide containing a single nuclease-resistant phosphodiester link, a stereoisomerically pure methylphosphonate, by manganese (Mn-TMPyP) or iron (Fe-TMPyP) porphyrin associated to KHSO(5) allowed the isolation and characterization of a guanine lesion corresponding to an increase of mass of 34 amu as compared to guanine ("G+34"), namely, 5-carboxamido-5-formamido-2-iminohydantoin. Enzymatic digestion of the damaged oligonucleotide afforded, apart from the undamaged nucleotide monomer pool, a unique dinucleotide doubly modified with a methylphosphonate and an oxidized guanine base that is suitable for NMR analysis. The method can be applied to the study of any DNA lesion. More importantly, the method can be extended to the analysis of DNA damage in a sequence context. Any preselected residue in a DNA sequence may be individually analyzed by the easy introduction of a single nuclease-resistant link at the 3'- or 5'-position.

Use of short duplexes for the analysis of the sequence-dependent cleavage of DNA by a chemical nuclease, a manganese porphyrin

A manganese porphyrin, manganese(III)-bis(aqua)-meso-tetrakis(4-N-methylpyridiniumyl)porphyrin, in the presence of KHSO5 is able to perform deoxyribose or guanine oxidation depending on its mode of interaction with DNA. These two reactions involve an oxygen-atom transfer or an electron transfer, respectively. The oxidative reactivity of the manganese-oxo porphyrin was compared on short oligonucleotide duplexes of different sequences. The major mechanism of DNA damage is due to deoxyribose hydroxylation at a site of strong interaction, an (A.T)3 sequence. Guanine oxidation by electron transfer was found not to be competitive with this major mechanism. It was found that a single intrastrand guanine was three orders of magnitude less reactive than an (A.T)3 sequence. The reactivity of a 5'-GG sequence was found to be intermediate and was estimated to be two orders of magnitude less than that of an (A.T)3 site. Short oligonucleotide duplexes, as double-stranded-DNA models, proved to be convenient tools for the study of the comparative reactivity of this reagent toward different sequences of DNA. However, they showed a particular reactivity at their terminal base pairs (the "end effect") that biased their modeling capacity for double-helix-DNA models.