The effects of secondary structure and O2 on the formation of direct strand breaks upon UV irradiation of 5-bromodeoxy-uridine-containing oligonucleotides

Background 5-Bromodeoxyuridine is a radiosensitizing agent that is currently being evaluated in clinical trials as an adjuvant in the treatment of a variety of cancers. γ-Radiolysis and UV irradiation of oligonucleotides containing 5-bromodeoxyuridine result in the formation of direct strand breaks at the 5′-adjacent nucleotide by oxidation of the respective deoxyribose. We investigated the effects of DNA secondary structure and O 2 on the induction of direct strand breaks in 5-bromodeoxyuridine-containing oligonucleotides. Results The efficiency of direct strand break formation in duplex DNA is dependent upon O 2 and results in fragments containing 3′-phosphate and the labile 3′-ketodeoxyadenosine termini. The ratio of the 3′-termini is also dependent upon O 2 and structure. Deuterium product isotope effects and tritium-transfer studies indicate that hydrogen-atom abstraction from the C1′- and C2′-positions occurs in an O 2 - and structure-dependent manner. Conclusions The reaction mechanisms by which DNA containing 5-bromodeoxyuridine is sensitized to damage by UV irradiation are dependent upon whether the substrate is hybridized and upon the presence or absence of O 2 . Oxygen reduces the efficiency of direct strand break formation in duplex DNA, but does not affect the overall strand damage. It is proposed that the σ radical abstracts hydrogen atoms from the C1′- and C2′-positions of the 5′-adjacent deoxyribose moiety, whereas the nucleobase peroxyl radical selectively abstracts the C1′-hydrogen atom from this site. This is the second example of DNA damage amplification by a nucleobase peroxyl radical, and might be indicative of a general reaction pattern for this family of reactive intermediates.