The ensemble reactions of hydroxyl radical exhibit no specificity for primary or secondary structure of DNA.

Hydroxyl radical reacts at numerous sites within nucleic acids to form a wide range of derivatives yet the conformational specificity of only one of these processes, direct strand fragmentation, has received much attention to date. Since the deleterious effects of this radical are not likely limited to strand fragmentation in vivo, this report examined the conformational specificity expressed in a more general manner. For this, modification of DNA was induced by the hydroxyl radical generating system of H2O2 and Fe-EDTA. The ensemble rate of oxidation (nucleobase + deoxyribose backbone) was determined from the overall consumption of a series of oligonucleotides that were designed to model random coils and double helixes containing complementary and noncomplementary base pairing. The resulting pseudo-first order rate constants derived from this model system were relatively unaffected by nucleotide sequence or secondary structure and varied from only 0.022 to 0.048 s-1. Consequently, the indiscriminant nature of hydroxyl radical appears to persist beyond strand fragmentation to include nucleobase oxidation as well.