Influence of an 8-oxoadenine lesion on the structural and dynamic featuresof a 30-mer DNA fragment with and without a mismatch

Purpose: To elucidate the influence of the oxidative lesion 7,8-dihydro-8-o xoadenine (8-oxoA) on the structural and dynamic features of a 30-mer DNA f ragment, and to understand if differences occur when C is positioned opposi te 8-oxoA instead of T. Materials and methods: Two 30-mer DNA oligomers with or without the 8-oxoA and two complementary oligomers with C or T base opposite the lesion site w ere synthesized and annealed. Duplexes named AT, A*T, AC and A*C were chara cterized by means of circular dichroism and UV denaturation measurements. g amma -Ray footprinting experiments were performed to give insight into thei r fine three-dimensional structure. Elastic torsional constants were derive d by following the decay of the fluorescence polarization anisotropy (FPA) of the ethidium-DNA complexes measured by multifrequency-phase fluorometry. Results: The introduction of one oxidative lesion in a 30-mer DNA oligomer with and without a mismatch did not cause relevant changes in their overall conformation and slightly modified their elastic properties. Small energet ic differences were revealed by thermodynamic analysis in the sample bearin g both the oxidative lesion and the mismatch. Minor variations in the cleav age pattern due to the hydroxyl radicals in the A*T sample were observed an d present along the entire DNA fragment length. In the A*C sample, by contr ast, there was a major modification in the cleavage pattern extending for a bout 11 bases around the lesion, especially towards the 5'-end. Conclusions : Differences in the fine structure and in the elastic properti es between the A*T and A*C samples were observed, while their overall confo rmation was unchanged. The results are consistent with the hypothesis that the observed local changes of the double helix structure in A*C are due to the pairing of the oxidized adenine in a syn conformation with the cytosine .