α-anomeric deoxynucleotides, anoxic products of ionizing radiation, are substrates for the endonuclease IV-type AP endonucleases

α-Anomeric 2′-deoxynucleosides (αdN) are one of the products formed by ionizing radiation (IR) in DNA under anoxic conditions. α-2′-Deoxyadenosine (αdA) and α-thymidine (αT) are not recognized by DNA glycosylases, and are likely removed by the alternative nucleotide incision repair (NIR) pathway. Indeed, it has been shown that αdA is a substrate for the Escherichia coli Nfo and human Ape1 proteins. However, the repair pathway for removal of αdA and other αdN in yeast is unknown. Here we report that αdA when present in DNA is recognized by the Saccharomyces cerevisiae Apn1 protein, a homologue of Nfo. Furthermore, αT is a substrate for Nfo and Apn1. Kinetic constants indicate that αdA and αT are equally good substrates, as a tetrahydrofuranyl (THF) residue, for Nfo and Apn1. Using E. coli and S. cerevisiae cell-free extracts, we have further substantiated the role of the nfo and apn1 gene products in the repair of αdN. Surprisingly, we found that bacteria and yeast NIR-deficient mutants are not sensitive to IR, suggesting that DNA strand breaks with terminal 3′-blocking groups rather than αdN might contribute to cell survival. We propose that the novel substrate specificities of Nfo and Apn1 play an important role in counteracting oxidative DNA base damage.