TI - The major human AP endonuclease ( Ape1 ) is involved in the nucleotide incision repair pathway . AB - In nucleotide incision repair ( NIR ) , an endonuclease nicks oxidatively damaged DNA in a DNA glycosylase -independent manner , providing the correct ends for DNA synthesis coupled to the repair of the remaining 5'-dangling modified nucleotide . This mechanistic feature is distinct from DNA glycosylase-mediated base excision repair . Here we report that Ape1 , the major apurinic/apyrimidinic endonuclease in human cells , is the damage - specific endonuclease involved in NIR . We show that Ape1 incises DNA containing 5 , 6-dihydro-2'-deoxyuridine , 5 , 6-dihydrothymidine , 5-hydroxy-2'-deoxyuridine , alpha-2'-deoxyadenosine and alpha-thymidine adducts , generating 3'-hydroxyl and 5'-phosphate termini . The kinetic constants indicate that Ape1 -catalysed NIR activity is highly efficient . The SUBstrate specificity and protein conformation of Ape1 is modulated by MgCl2 concentrations , thus providing conditions under which NIR becomes a major activity in cell -free extracts . While the N-terminal region of Ape1 is not required for AP endonuclease function , we show that it regulates the NIR activity . The physiological relevance of the mammalian NIR pathway is discussed .