The recognition of DNA containing an AP site by E.coli endonuclease VI (exonuclease III)

The major apurinic/apyrimidinic (AP) DNA-repair endonuclease of Escherichia coli is the endonuclease VI (exonuclease III) protein. To elucidate the substrate specificity of the AP endonuclease, we used the double- and single-stranded oligo deoxyribonucleotides containing an AP residue such as 2-deoxyribosylformamide (1), 2-deoxyribose (2), 1,2-dideoxyribofuranose (3), and propanediol (4) as the substrate. The endonuclease VI cleaved the phosphodiester bond 5' at these AP sites of the duplexes. The endonucleolytic activity was not influenced by the kind of nucleotide residue on the opposite side of the AP site. Further, it was observed that the AP endonuclease cleaved single-stranded oligomers containing an AP site.