Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

An exonucleolytic activity of human apurinic/apyrimidinic endonuclease on 3′ mispaired DNA


Human apurinic/apyrimidinic endonuclease (APE1) is an essential enzyme in DNA base excision repair that cuts the DNA backbone immediately adjacent to the 5′ side of abasic sites to facilitate repair synthesis by DNA polymerase β (ref. 1). Mice lacking the murine homologue of APE1 die at an early embryonic stage2. Here we report that APE1 has a DNA exonuclease activity on mismatched deoxyribonucleotides at the 3′ termini of nicked or gapped DNA molecules. The efficiency of this activity is inversely proportional to the gap size in DNA. In a base excision repair system reconstituted in vitro, the rejoining of nicked mismatched DNA depended on the presence of APE1, indicating that APE1 may increase the fidelity of base excision repair and may represent a new 3′ mispaired DNA repair mechanism. The exonuclease activity of APE1 can remove the anti-HIV nucleoside analogues 3′-azido-3′-deoxythymidine and 2′,3′-didehydro-2′, 3′-dideoxythymidine from DNA, suggesting that APE1 might have an impact on the therapeutic index of antiviral compounds in this category.

Your institute does not have access to this article

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Rate of APE1 exonucelase activity on different DNA substrates.
Figure 2: Activity of APE1 mismatch repair on DNA with different gap sizes.
Figure 3: In vitro reconstitution of the BER system.
Figure 4: The contribution of APE1 exonuclease to removal of DNA 3′ mispairs in nuclear extracts of human cells.


  1. Wilson, D. M., Takeshita, M., Grollman, A. P. & Demple, B. Incision activity of human apurinic endonuclease (Ape) at abasic site analogs in DNA. J. Biol. Chem. 270, 16002–16007 (1995).

    CAS  Article  Google Scholar 

  2. Xanthoudakis, S., Smeyne, R. J., Wallace, J. D. & Curran, T. The redox/DNA repair protein, Ref-1, is essential for early embryonic development in mice. Proc. Natl Acad. Sci. USA 93, 8919–8923 (1996).

    ADS  CAS  Article  Google Scholar 

  3. Lindahl, T. Suppression of spontaneous mutagenesis in human cells by DNA base excision–repair. Mutat. Res. 462, 129–135 (2000).

    CAS  Article  Google Scholar 

  4. Loeb, L. A. & Preston, B. D. Mutagenesis by apurinic/apyrimidinic sites. Annu. Rev. Genet. 20, 201–230 (1986).

    CAS  Article  Google Scholar 

  5. Matsumoto, Y. & Kim, K. Excision of deoxyribose phosphate residues by DNA polymerase β during DNA repair. Science 269, 699–702 (1995).

    ADS  CAS  Article  Google Scholar 

  6. Kunkel, T. A. The mutational specificity of DNA polymerase-β during in vitro DNA synthesis. Production of frameshift, base substitution, and deletion mutations. J. Biol. Chem. 260, 5787–5796 (1985).

    CAS  PubMed  Google Scholar 

  7. Loeb, K. R. & Loeb, L. A. Significance of multiple mutations in cancer. Carcinogenesis 21, 379–385 (2000).

    CAS  Article  Google Scholar 

  8. Demple, B., Herman, T. & Chen, D. S. Cloning and expression of APE, the cDNA encoding the major human apurinic endonuclease: definition of a family of DNA repair enzymes. Proc. Natl Acad. Sci. USA 88, 11450–11454 (1991).

    ADS  CAS  Article  Google Scholar 

  9. Robson, C. N., Milne, A. M., Pappin, D. J. & Hickson, I. D. Isolation of cDNA clones encoding an enzyme from bovine cells that repairs oxidative DNA damage in vitro: homology with bacterial repair enzymes. Nucleic Acids Res. 19, 1087–1092 (1991).

    CAS  Article  Google Scholar 

  10. Chou, K. M., Kukhanova, M. & Cheng, Y. C. A novel action of human apurinic/apyrimidinic endonuclease. Excision of l-configuration deoxyribonucleoside analogs from the 3′ termini of DNA. J. Biol. Chem. 275, 31009–31015 (2000).

    CAS  Article  Google Scholar 

  11. Grove, K. L. et al. Anticancer activity of β-l-dioxolane-cytidine, a novel nucleoside analogue with the unnatural L configuration. Cancer Res. 55, 3008–3011 (1995).

    CAS  PubMed  Google Scholar 

  12. Wilson, S. H. & Kunkel, T. A. Passing the baton in base excision repair. Nature Struct. Biol. 7, 176–178 (2000).

    CAS  Article  Google Scholar 

  13. Bennett, R. A., Wilson, D. M., Wong, D. & Demple, B. Interaction of human apurinic endonuclease and DNA polymerase β in the base excision repair pathway. Proc. Natl Acad. Sci. USA 94, 7166–7169 (1997).

    ADS  CAS  Article  Google Scholar 

  14. Husain, I. et al. Purification and characterization of DNA ligase III from bovine testes. Homology with DNA ligase II and vaccinia DNA ligase. J. Biol. Chem. 270, 9683–9690 (1995).

    CAS  Article  Google Scholar 

  15. Cheng, Y. C., Gao, W. Y., Chen, C. H., Vazquez-Padua, M. & Starnes, M. C. DNA polymerases versus HIV reverse transcriptase in AIDS therapy. Ann. NY Acad. Sci. 616, 217–223 (1990).

    ADS  CAS  Article  Google Scholar 

  16. Bouayadi, K. et al. Overexpression of DNA polymerase β sensitizes mammalian cells to 2′,3′-deoxycytidine and 3′-azido-3′-deoxythymidine. Cancer Res. 57, 110–116 (1997).

    CAS  PubMed  Google Scholar 

  17. Skalski, V., Liu, S. H. & Cheng, Y. C. Removal of anti-human immunodeficiency virus 2′,3′-dideoxynucleoside monophosphates from DNA by a novel human cytosolic 3′-5′ exonuclease. Biochem. Pharmacol. 50, 815–821 (1995).

    CAS  Article  Google Scholar 

  18. Zhu, Q. Y., Scarborough, A., Polsky, B. & Chou, T. C. Drug combinations and effect parameters of zidovudine, stavudine, and nevirapine in standardized drug-sensitive and resistant HIV type 1 strains. AIDS Res. Hum. Retrovir. 12, 507–517 (1996).

    CAS  Article  Google Scholar 

  19. Strauss, P. R., Beard, W. A., Patterson, T. A. & Wilson, S. H. Substrate binding by human apurinic/apyrimidinic endonuclease indicates a Briggs-Haldane mechanism. J. Biol. Chem. 272, 1302–7. (1997).

    CAS  Article  Google Scholar 

  20. McCullough, A. K., Dodson, M. L. & Lloyd, R. S. Initiation of base excision repair: glycosylase mechanisms and structures. Annu. Rev. Biochem. 68, 255–285 (1999).

    CAS  Article  Google Scholar 

  21. Chen, D. S., Herman, T. & Demple, B. Two distinct human DNA diesterases that hydrolyze 3′-blocking deoxyribose fragments from oxidized DNA. Nucleic Acids Res. 19, 5907–5914 (1991).

    CAS  Article  Google Scholar 

  22. Bhagwat, A. S., Sanderson, R. J. & Lindahl, T. Delayed DNA joining at 3′ mismatches by human DNA ligases. Nucleic Acids Res. 27, 4028–4033 (1999).

    CAS  Article  Google Scholar 

  23. Hoss, M. et al. A human DNA editing enzyme homologous to the Escherichia coli DnaQ/MutD protein. EMBO J. 18, 3868–3875 (1999).

    CAS  Article  Google Scholar 

  24. Mazur, D. J. & Perrino, F. W. Identification and expression of the TREX1 and TREX2 cDNA sequences encoding mammalian 3′–5′ exonucleases. J. Biol. Chem. 274, 19655–19660 (1999).

    CAS  Article  Google Scholar 

  25. Mazur, D. J. & Perrino, F. W. Excision of 3′ termini by the Trex1 and TREX2 3′-5′ exonucleases: characterization of the recombinant proteins. J. Biol. Chem. 276, 17022–17029 (2001).

    CAS  Article  Google Scholar 

Download references


We thank Z. Hatahet and J. B. Sweasy for discussion; M. Kelley and B. Demple for providing the APE clones; A. Tomkinson for human DNA ligase I; and J. Sweasy for human DNA polymerase β.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Yung-Chi Cheng.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Chou, KM., Cheng, YC. An exonucleolytic activity of human apurinic/apyrimidinic endonuclease on 3′ mispaired DNA. Nature 415, 655–659 (2002).

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI:

Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing