Abasic and oxidized ribonucleotides embedded in DNA are processed by human APE1 and not by RNase H2

Nucleic Acids Res. 2017 Nov 2;45(19):11193-11212. doi: 10.1093/nar/gkx723.


Ribonucleoside 5'-monophosphates (rNMPs) are the most common non-standard nucleotides found in DNA of eukaryotic cells, with over 100 million rNMPs transiently incorporated in the mammalian genome per cell cycle. Human ribonuclease (RNase) H2 is the principal enzyme able to cleave rNMPs in DNA. Whether RNase H2 may process abasic or oxidized rNMPs incorporated in DNA is unknown. The base excision repair (BER) pathway is mainly responsible for repairing oxidized and abasic sites into DNA. Here we show that human RNase H2 is unable to process an abasic rNMP (rAP site) or a ribose 8oxoG (r8oxoG) site embedded in DNA. On the contrary, we found that recombinant purified human apurinic/apyrimidinic endonuclease-1 (APE1) and APE1 from human cell extracts efficiently process an rAP site in DNA and have weak endoribonuclease and 3'-exonuclease activities on r8oxoG substrate. Using biochemical assays, our results provide evidence of a human enzyme able to recognize and process abasic and oxidized ribonucleotides embedded in DNA.

MeSH terms

  • Binding Sites / genetics
  • DNA / genetics
  • DNA / metabolism*
  • DNA Repair
  • DNA-(Apurinic or Apyrimidinic Site) Lyase / genetics
  • DNA-(Apurinic or Apyrimidinic Site) Lyase / metabolism*
  • HeLa Cells
  • Humans
  • Kinetics
  • Models, Genetic
  • Oxidation-Reduction
  • Protein Binding
  • Recombinant Proteins / metabolism
  • Ribonuclease H / genetics
  • Ribonuclease H / metabolism*
  • Ribonucleotides / genetics
  • Ribonucleotides / metabolism*
  • Substrate Specificity


  • Recombinant Proteins
  • Ribonucleotides
  • DNA
  • ribonuclease HII
  • Ribonuclease H
  • APEX1 protein, human
  • DNA-(Apurinic or Apyrimidinic Site) Lyase