Molecular Biology

, Volume 52, Issue 6, pp 922–928 | Cite as

Excision of Carbohydrate-Modified dNMP Analogues from DNA 3' end by Human Apurinic/Apyrimidinic Endonuclease 1 (APE1) and Tyrosyl-DNA Phosphodiesterase 1 (TDP1)

  • N. S. Dyrkheeva
  • N. A. Lebedeva
  • Yu. V. Sherstyuk
  • T. V. Abramova
  • V. N. Silnikov
  • O. I. LavrikEmail author


We have studied the excision efficiency of human apurinic/apyrimidinic endonuclease 1 (APE1) and tyrosyl-DNA phosphodiesterase 1 (TDP1) on matched or mismatched bases located at the 3' end of DNA primers. We have used model DNA duplexes, which mimic DNA structures that occur during either replication (DNA with a 3' recessed end) or repair (DNA with a single-strand break). Both APE1 and TDP1 are more efficient in removing ribose-modified dNMP residues from mismatched pairs rather than canonical pairs. Thus, both of these enzymes may act as proofreading factors during the repair synthesis catalyzed by DNA polymerases including DNA polymerase β (Polβ). The design of new DNA polymerase inhibitors, which act as DNA or RNA chain terminators, is one of the main strategies in the development of antiviral agents. The excision efficacy of APE1 and TDP1 has also been studied for 3'-modified DNA duplexes that contain ddNMP or phosphorylated morpholino nucleosides (MorB) commonly used as terminators in the DNA synthesis. We have also investigated the insertion of ddNTP and morpholino nucleotides catalyzed by Polβ and human immunodeficiency virus reverse transcriptase. This experiment has pointed to MorCyt, cytosine-containing morpholino nucleoside, as a potential antiviral agent.


proofreading of DNA synthesis morpholino nucleoside triphosphates АРЕ1 TDP1 HIV reverse transcriptase 



  1. 1.
    Cihlar T., Ray A.S. 2010. Nucleoside and nucleotide HIV reverse transcriptase inhibitors: 25 years after zidovudine. Antiviral Res. 85, 39–58.CrossRefGoogle Scholar
  2. 2.
    Shelton J., Lu X., Hollenbaugh J.A., Hyun Cho J., Amblard F., Schinazi R.F. 2016. Metabolism, biochemical actions, and chemical synthesis of anticancer nucleosides, nucleotides, and base analogs. Chem. Rev. 116, 14379–14455.CrossRefGoogle Scholar
  3. 3.
    Lebedeva N.A., Seredina T.A., Silnikov V.N., Abramova T.V., Levina A.S., Khodyreva S.N., Rechkunova N.I., Lavrik O.I. 2005. Analysis of interactions of DNA polymerase β and reverse transcriptases of human immunodeficiency and mouse leukemia viruses with dNTP analogs containing a modified sugar residue. Biochemistry (Moscow). 70 (1), 1–8.Google Scholar
  4. 4.
    Abramova T.V., Bakharev P.A., Vasilyeva S.V., Silnikov V.N. 2004. Synthesis of morpholine nucleoside triphosphates. Tetrahedron Lett. 45, 4361–4364.CrossRefGoogle Scholar
  5. 5.
    Blum M., De Robertis E.M., Wallingford J.B., Niehrs C. 2015. Morpholinos: Antisense and sensibility. Dev. Cell. 35, 145–149.CrossRefGoogle Scholar
  6. 6.
    Stein C.A. 2016. Eteplirsen approved for Duchenne muscular dystrophy: The FDA faces a difficult choice. Mol. Ther. 24, 1884–1885.CrossRefGoogle Scholar
  7. 7.
    Chou K.-M., Cheng Y.-C. 2002. An exonucleolitic activity of human apurinic/apyrimidinic endonuclease on 3'-mispaired DNA. Nature. 415. 655–659.CrossRefGoogle Scholar
  8. 8.
    Lebedeva N.A., Khodyreva S.N., Favre A., Lavrik O.I. 2003. AP endonuclease 1 has no biologically significant 3'-5' exonuclease activity. Biochem. Biophys. Res. Communs. 300, 182–187.CrossRefGoogle Scholar
  9. 9.
    Dyrkheeva N.S., Khodyreva S.N., Sukhanova M.V., Safronov I.V., Dezhurov S.V., Lavrik O.I. 2006. 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 (Moscow). 71 (2), 200–210.Google Scholar
  10. 10.
    Dyrkheeva N.S., Lomzov A.A., Pyshnyi D.V., Khodyreva S.N., Lavrik O.I. 2006. Efficiency of exonucleolytic action of apurinic/apyrimidinic endonuclease 1 towards matched and mismatched dNMP at the 3' terminus of different oligomeric DNA structures correlates with thermal stability of DNA duplexes. Biochim. Biophys. Acta. 764, 699–706.CrossRefGoogle Scholar
  11. 11.
    Lebedeva N.A., Rechkunova N.I., Ishchenko A.A., Saparbaev M., Lavrik O.I. 2013. The mechanism of human tyrosyl-DNA phosphodiesterase 1 in the cleavage of AP site and its synthetic analogs. DNA Repair (Amst.). 12, 1037–1042.CrossRefGoogle Scholar
  12. 12.
    Lebedeva N.A., Rechkunova N.I., El-Khamisy S.F., Lavrik O.I. 2012. Tyrosyl-DNA phosphodiesterase 1 initiates repair of apurinic/apyrimidinic sites. Biochimie. 94, 1749–1753.CrossRefGoogle Scholar
  13. 13.
    Pommier Y., Huang S.Y., Gao R., Das B.B., Murai J., Marchand C. 2014. Tyrosyl-DNA-phosphodiesterases (TDP1 and TDP2). DNA Repair. 19, 114–129.CrossRefGoogle Scholar
  14. 14.
    Menon V., Povirk L.F. 2016. End-processing nucleases and phosphodiesterases: An elite supporting cast for the non-homologous end joining pathway of DNA double-strand break repair. DNA Repair (Amst.). 43, 57–68.CrossRefGoogle Scholar
  15. 15.
    Moor N.A., Vasil’eva I.A., Anarbaev R.O., Antson A.A., Lavrik O.I. 2015. Quantitative characterization of protein–protein complexes involved in base excision DNA repair. Nucleic Acids Res. 43, 6009–6022.CrossRefGoogle Scholar
  16. 16.
    Lebedeva N.A., Anarbaev R.O., Sukhanova M.V., Vasil’eva I.A., Rechkunova N.I., Lavrik O.I. 2015. Poly(ADP-ribose)polymerase 1 stimulates the AP-site cleavage activity of tyrosyl-DNA phosphodiesterase 1. Biosci. Rep. 35, 1–9.CrossRefGoogle Scholar
  17. 17.
    Vohtancev I.P., Sherstyuk Y.V., Silnikov V.N., Abra-mova T.V. 2018. Effective synthesis of 5-iodo derivatives of pyrimidine morpholino nucleosides. Org. Prep. Proc. Int. 50, 332–342.CrossRefGoogle Scholar
  18. 18.
    Abramova T.V., Belov S.S., Tarasenko Y.V., Silnikov V.N. 2014. Solid-phase-supported synthesis of morpholinoglycine oligonucleotide mimics. Beilstein J. Org. Chem. 10, 1151–1158.CrossRefGoogle Scholar
  19. 19.
    Tarasenko Y.V., Abramova T.V., Mamatuk V.I., Silnikov V.N. 2016. Effective synthesis of fluorescently labeled morpholino nucleoside triphosphate derivatives. Nucleosides Nucleotides Nucleic Acids. 35, 32–42.CrossRefGoogle Scholar
  20. 20.
    Chou K.M., Kukhanova M., Cheng Y.C. 2000. 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.CrossRefGoogle Scholar
  21. 21.
    Lindahl T. 2000. Suppression of spontaneous mutagenesis in human cells by DNA base excision repair. Mutat. Res. 462, 129–135.CrossRefGoogle Scholar
  22. 22.
    Dyrkheeva N.S., Lebedeva N.A., Lavrik O.I. 2016. AP endonuclease 1 as a key enzyme in repair of apurinic/apyrimidinic sites. Biochemistry (Moscow). 81 (9), 951–967.Google Scholar
  23. 23.
    Lavrik O.I., Prasad R., Beard W.A., Safronov I.V., Dobrikov M.I., Srivastava D.K., Shishkin G.V., Wood T.G., Wilson S.H. 1996. dNTP binding to HIV-1 reverse transcriptase and mammalian DNA polymerase β as revealed by affinity labeling with a photoreactive dNTP analog. J. Biol. Chem. 271, 21891–21897.CrossRefGoogle Scholar

Copyright information

© Pleiades Publishing, Inc. 2018

Authors and Affiliations

  • N. S. Dyrkheeva
    • 1
  • N. A. Lebedeva
    • 1
  • Yu. V. Sherstyuk
    • 1
  • T. V. Abramova
    • 1
  • V. N. Silnikov
    • 1
  • O. I. Lavrik
    • 1
    • 2
    • 3
    Email author
  1. 1.Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of SciencesNovosibirskRussia
  2. 2.Novosibirsk State UniversityNovosibirskRussia
  3. 3.Altai State UniversityBarnaulRussia

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