DNA Damage Induced via 5,6-Dihydrothymid-5-yl in Single-Stranded Oligonucleotides

Abstract

5,6-Dihydrothymid-5-yl ( 4 ) is generated via Norrish type I cleavage of isopropyl ketone 7 . Ketone 7 was site specifically incorporated into chemically synthesized polythymidylates and an oligonucleotide containing all four native deoxyribonucleotides. No damage is induced in oligonucleotides containing 7 upon photolysis under anaerobic conditions. In the presence of O 2, strand breaks and alkaline labile lesions are formed at the original site of 7, and at nucleotides adjacent to the 5‘-phosphate of 7 . Kinetic isotope effect experiments reveal that direct strand scission at the thymidine adjacent to the 5‘-phosphate of 4 arises from C1‘ hydrogen atom abstraction. The observed KIE (∼3.9) is attributed to hydrogen atom abstraction from C1‘ by the peroxyl radical 35 derived from 4 . Enzymatic end group analysis and measurement of free base release are consistent with a process involving C1‘ hydrogen atom abstraction. Cleavage experiments carried out in the presence of t -BuOH (1.05 M) and NaN 3 (10 mM) indicate that damage does not result from hydroxyl radical, but that 1 O 2 is responsible for a significant amount of the observed strand damage.