3'-5' exonuclease activity of human apurinic/apyrimidinic endonuclease 1 towards DNAs containing dNMP and their modified analogs at the 3 end of single strand DNA break

Biochemistry (Mosc). 2006 Feb;71(2):200-10. doi: 10.1134/s0006297906020131.


Human DNA apurinic/apyrimidinic (AP-) endonuclease 1 (APE1) is involved in the base excision repair (BER) pathway. The enzyme hydrolyzes DNA from the 5 side of the AP site. In addition to endonuclease activity, APE1 also possesses other slight activities including 3 -5 exonuclease activity. The latter is preferentially exhibited towards mispaired (non-canonical) nucleotides, this being the reason why APE1 is considered as a proofreading enzyme correcting the misincorporations introduced by DNA polymerase beta. We have studied 3 -5 exonuclease activity of APE1 towards dCMP and dTMP residues and modified dCMP analogs with photoreactive groups at the 3 end of the nicked DNA. Photoreactive dNMP residues were incorporated at the 3 end of the lesion using DNA polymerase beta and photoreactive dNTPs. The dependence of exonuclease activity on the "canonicity" of the base pair formed by dNMP flanking the nick at the 3 end, on the nature of the group flanking the nick at the 5 end, and on the reaction conditions has been determined. Optimal reaction conditions for the 3 -5 exonuclease hydrolysis reaction catalyzed by APE1 in vitro have been established, and conditions when photoreactive residues are not removed by APE1 have been chosen. These reaction conditions are suitable for using photoreactive nicked DNAs bearing 3 -photoreactive dNMP residues for photoaffinity labeling of proteins in cellular/nuclear extracts and model APE1-containing systems. We recommend using FAPdCTP for photoaffinity modification in APE1-containing systems because the FAPdCMP residue is less prone to exonuclease degradation, in contrast to FABOdCTP, which is not recommended.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Pair Mismatch
  • Cytidine Triphosphate / analogs & derivatives
  • Cytidine Triphosphate / chemistry
  • Cytidine Triphosphate / metabolism
  • DNA Damage*
  • DNA Repair*
  • DNA-(Apurinic or Apyrimidinic Site) Lyase / chemistry*
  • DNA-(Apurinic or Apyrimidinic Site) Lyase / metabolism
  • Deoxyribonucleotides / chemistry*
  • Deoxyribonucleotides / metabolism
  • Exodeoxyribonucleases / chemistry*
  • Exodeoxyribonucleases / metabolism
  • Humans
  • Nucleic Acid Heteroduplexes / chemistry
  • Nucleic Acid Heteroduplexes / metabolism
  • Nucleotides / metabolism*
  • Photochemistry
  • Rats
  • Thymine Nucleotides / metabolism


  • Deoxyribonucleotides
  • Nucleic Acid Heteroduplexes
  • Nucleotides
  • Thymine Nucleotides
  • Cytidine Triphosphate
  • Exodeoxyribonucleases
  • APEX1 protein, human
  • DNA-(Apurinic or Apyrimidinic Site) Lyase
  • thymidine 5'-triphosphate