Human DNA apurinic/apyrimidinic endonuclease (APE1) plays a key role in the DNA base excision repair process. In this study, we further characterized the exonuclease activity of APE1. The magnesium requirement and pH dependence of the exonuclease and endonuclease activities of APE1 are significantly different. APE1 showed a similar K m value for matched, 3 mispaired, or nucleoside analog -L-dioxolane-cytidine terminated nicked DNA as well as for DNA containing a tetrahydrofuran, an abasic site analog. The k cat for exonuclease activity on matched, 3 mispaired, and -L-dioxolane-cytidine nicked DNA are 2.3, 61.2, and 98.8 min ؊1 , respectively, and 787.5 min ؊1 for APE1 endonuclease. Site-directed APE1 mutant proteins (E96A, E96Q, D210E, D210N, and H309N), which target amino acid residues in the endonuclease active site, also showed significant decrease in exonuclease activity. DNA base excision repair is the main pathway to repair DNA base damages caused by oxidation, radiation, and the loss of bases (1, 2). There are several enzymes that participate in this pathway, including DNA polymerase , DNA ligase III-XRCC1 complex (1, 2), and apurinic/apyrimidinic endonuclease (APE1) 1 to protect the genome integrity (1-3). The DNA repair activity of APE1 resides in the C-terminal region (4, 5). It endonucleolytically makes a nick immediately adjacent to 5Ј of an apurinic/apyrimidinic (AP) site and generates a hydroxyl group at the 3Ј terminus upstream of the nick and a 5Ј-deoxyribose phosphate moiety downstream (6). DNA polymerase  further processes the product of APE1 by inserting a nucleotide into the gap and releasing the 5Ј-deoxyribose phosphate by its intrinsic lyase activity (7). The repair process is then completed by either DNA ligase I or DNA ligase III/XRCC1 to seal the nicked DNA (1). During DNA base excision repair, DNA polymerase  is the major polymerase that incorporates a nucleotide into the gapped DNA (1). However, DNA polymerase  is a lower fidelity polymerase (8) in comparison to the replicating DNA polymerases ␦ or ⑀ (9). ⌻he error rate of polymerase  is about 1 in 4000 incorporations (1).APE1 is a versatile multifunctional protein (10). In addition to its endonuclease activity, it also possesses 3Ј-phosphatase, 3Ј-phosphodiesterase, RNase H, and 3Ј-5Ј-exonuclease activities (10). APE1 knockout mice die in the early embryonic stage (11), which indicates this protein is critical for development. Previously we reported (12) that the 3Ј-5Ј-exonuclease activity of APE1 is the major exonuclease activity in the human cell nucleus for the removal of the nucleoside analog -L-dioxolanecytidine (L-OddC, BCH-4556, Troxacitabine, and Troxatyl) from the 3Ј termini of DNA. L-OddC is a novel nucleoside analog with L-configuration that is currently under phase III clinical trial and is showing promising activity for the treatment of leukemia (13,14). The incorporation of L-OddC into DNA terminates DNA chain elongation because of the lack of the 3Ј-hydroxyl group on the sugar moiety of L-OddC. The cytotoxicity ...