Unexpected Complexity in the Products Arising from NaOH-, Heat-, Amine-, and Glycosylase-Induced Strand Cleavage at an Abasic Site in DNA

Hydrolytic loss of nucleobases from the deoxyribose backbone of DNA is one of the most common unavoidable types of damage in synthetic and cellular DNA. The reaction generates abasic sites in DNA and it is important to understand the properties of these lesions. The acidic nature of the α-protons of the ring-opened abasic aldehyde residue facilitates β-elimination of the 3’-phosphoryl group. This reaction is expected to generate a DNA strand break with a phosphoryl group on the 5’-terminus and a trans-α,β-unsaturated aldehyde residue on the 3’-terminus; however, a handful of studies have identified noncanonical sugar remnants on the 3’-terminus, suggesting that the products arising from strand cleavage at AP sites in DNA may be more complex than commonly thought. We characterized the strand cleavage induced by treatment of an abasic site-containing DNA oligonucleotide with heat, NaOH, piperidine, spermine, and the base excision repair glycoslyases Fpg and Endo III. The results showed that, under multiple conditions, cleavage at an abasic site in a DNA oligomer generated noncanonical sugar remnants including cis-α,β-unsaturated aldehyde, 2-deoxyribose, and 3-thio-2,3-dideoxyribose products on the 3’-terminus of the strand break.