Advertisement

Biochemistry (Moscow)

, Volume 77, Issue 10, pp 1162–1171 | Cite as

Kinetic mechanism of the interaction of Saccharomyces cerevisiae AP-endonuclease 1 with DNA substrates

  • E. S. Dyakonova
  • V. V. Koval
  • A. A. Ishchenko
  • M. K. Saparbaev
  • R. Kaptein
  • O. S. FedorovaEmail author
Article

Abstract

The apurinic/apyrimidinic endonuclease from Saccharomyces cerevisiae Apn1 is one of the key enzymes involved in base excision repair of DNA lesions. A major function of the enzyme is to cleave the upstream phosphodiester bond of an apurinic/apyrimidinic site (AP-site), leading to the formation of a single-strand break with 3′-hydroxyl (OH) and 5′-deoxyribose phosphate (dRP) termini. In this study, the pre-steady-state kinetics and conformational dynamics of DNA substrates during their interaction with Apn1 were investigated. A stopped-flow method with detection of the fluorescence intensity of 2-aminopurine and pyrrolocytosine located adjacent or opposite to the damage was used. It was found that upon interaction with Apn1, both DNA strands undergo a number of rapid changes. The location of fluorescent analogs of heterocyclic bases in DNA does not influence the catalytic step of the reaction. Comparison of data obtained for yeast Apn1 and reported data (Kanazhevskaya, L. Yu., Koval, V. V., Vorobjev, Yu. N., and Fedorova, O. S. (2012) Biochemistry, 51, 1306–1321) for human Ape1 revealed some differences in their interaction with DNA substrates.

Key words

Apn1 base excision repair (BER) stopped-flow method 2-aminopurine pyrrolocytosine 

Abbreviations

Ape1

human apurinic/apyrimidinic endonuclease

Apn1

apurinic/apyrimidinic endonuclease from Saccharomyces cerevisiae

AP-site

abasic site

2-aPu

2-aminopurine

BER

base excision repair

F

synthetic analog of AP-site ((3-hydroxytetrahydrofuran-2-yl)methyl phosphate)

PyrC

pyrrolocytosine (3-[β-D-2-ribofuranosyl]-6-methylpyrrolo[2,3-d]pyrimidin-2(3H)-one)

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Mitra, S., Izumi, T., Boldogh, I., Bhakat, K. K., Hill, J. W., and Hazra, T. K. (2002) Free Radic. Biol. Med., 33, 15–28.PubMedCrossRefGoogle Scholar
  2. 2.
    Sukhanova, M. V., Khodyreva, S. N., Lebedeva, N. A., Prasad, R., Wilson, S. H., and Lavrik, O. I. (2005) Nucleic Acids Res., 33, 1222–1229.PubMedCrossRefGoogle Scholar
  3. 3.
    Dianov, G. L., and Parsons, J. L. (2007) DNA Repair, 6, 454–460.PubMedCrossRefGoogle Scholar
  4. 4.
    Fritz, G., Grosch, S., Tomicic, M., and Kaina, B. (2003) Toxicology, 193, 67–78.PubMedCrossRefGoogle Scholar
  5. 5.
    Daley, J. M., Zakaria, C., and Ramotar, D. (2010) Mut. Res., 705, 217–227.CrossRefGoogle Scholar
  6. 6.
    David, S. (2005) Nature, 434, 569–570.PubMedCrossRefGoogle Scholar
  7. 7.
    Kreklau, E. L., Limp-Foster, M., Liu, N., Xu, Y., Kelley, M. R., and Erickson, L. C. (2001) Nucleic Acids Res., 29, 2558–2566.PubMedCrossRefGoogle Scholar
  8. 8.
    Boiteux, S., and Guillet, M. (2004) DNA Repair, 3, 1–12.PubMedCrossRefGoogle Scholar
  9. 9.
    Kanazhevskaya, L. Yu., Koval, V. V., Vorobjev, Yu. N., and Fedorova, O. S. (2012) Biochemistry, 51, 1306–1321.PubMedCrossRefGoogle Scholar
  10. 10.
    Timofeyeva, N. A., Koval, V. V., Ishchenko, A. A., Saparbaev, M. K., and Fedorova, O. S. (2011) Biochemistry (Moscow), 76, 273–282.CrossRefGoogle Scholar
  11. 11.
    Kanazhevskaya, L. Yu., Koval, V. V., Zharkov, D. O., Strauss, P. R., and Fedorova, O. S. (2010) Biochemistry, 49, 6451–6461.PubMedCrossRefGoogle Scholar
  12. 12.
    Hosfield, D. J., Guan, Y., Haas, B. J., Cunningham, R. P., and Tainer, J. A. (1999) Cell, 98, 397–408.PubMedCrossRefGoogle Scholar
  13. 13.
    Ramotar, D., Popoff, S. C., Gralla, E. B., and Demple, B. (1991) Mol. Cell. Biol., 11, 4537–4544.PubMedGoogle Scholar
  14. 14.
    Lakovic, J. (1986) Principles of Fluorescence Spectroscopy [Russian translation], Mir, Moscow.Google Scholar
  15. 15.
    Dunlap, C. A., and Tsai, M. D. (2002) Biochemistry, 41, 11226–11235.PubMedCrossRefGoogle Scholar
  16. 16.
    Sinkeldam, R. W., Greco, N. J., and Tor, Y. (2010) Chem. Rev., 110, 2579–2619.PubMedCrossRefGoogle Scholar
  17. 17.
    Tamulaitis, G., Zaremba, M., Szczepanovski, R. H., Bochtler, M., and Siksnys, V. (2007) Nucleic Acids Res., 35, 4792–4799.PubMedCrossRefGoogle Scholar
  18. 18.
    Rachofsky, E. L., Seibert, E., Stivers, J. T., Osman, R., and Ross, A. (2001) Biochemistry, 40, 957–967.PubMedCrossRefGoogle Scholar
  19. 19.
    Dash, C., Rausch, J. W., and Le Grice, S. F. J. (2004) Nucleic Acids Res., 32, 1539–1547.PubMedCrossRefGoogle Scholar
  20. 20.
    Thompson, K. C., and Miyake, N. (2005) J. Phys. Chem. B., 109, 6012–6019.PubMedCrossRefGoogle Scholar
  21. 21.
    Hardman, S. J. O., Botchway, S. W., and Thompson, K. C. (2008) Photochem. Photobiol., 84, 1473–1479.PubMedCrossRefGoogle Scholar
  22. 22.
    Gasteiger, E., Gattiker, A., Hoogland, C., Ivanyi, I., Appel, R. D., and Bairoch, A. ExPASy: the proteomics server for in-depth protein knowledge and analysis.Google Scholar
  23. 23.
    Fasman, G. D. (1975) in Handbook of Biochemistry and Molecular Biology — Nucleic Acids,Vol. 1, GRC Press, Cleveland.Google Scholar
  24. 24.
    Hoehn, S. T., Turner, C. J., and Stubbe, J. (2001) Nucleic Acids Res., 29, 3413–3423.PubMedCrossRefGoogle Scholar
  25. 25.
    Fedorova, O. S., Nevinsky, G. A., Koval, V. V., Ishchenko, A. A., Vasilenko, N. L., and Douglas, K. T. (2002) Biochemistry, 41, 1520–1528.PubMedCrossRefGoogle Scholar
  26. 26.
    Kuzmic, P. (1996) Anal. Biochem., 237, 260–273.PubMedCrossRefGoogle Scholar
  27. 27.
    Koval, V. V., Kuznetsov, N. A., Zharkov, D. O., Ishchenko, A. A., Douglas, K. T., Nevinsky, G. A., and Fedorova, O. S. (2004) Nucleic Acids Res., 32, 926–935.PubMedCrossRefGoogle Scholar
  28. 28.
    Biro, F. N., Zhai, J., Doucette, C. W., and Hingorani, M. M. (2010) J. Vis. Exp., 37, pii: 1874, doi: 10.3791/1874.Google Scholar
  29. 29.
    Zhai, J., and Hingorani, M. M. (2010) Proc. Natl. Acad. Sci. USA, 107, 680–685.PubMedCrossRefGoogle Scholar

Copyright information

© Pleiades Publishing, Ltd. 2012

Authors and Affiliations

  • E. S. Dyakonova
    • 1
    • 2
  • V. V. Koval
    • 1
    • 2
  • A. A. Ishchenko
    • 3
  • M. K. Saparbaev
    • 3
  • R. Kaptein
    • 2
    • 4
  • O. S. Fedorova
    • 1
    • 2
    Email author
  1. 1.Institute of Chemical Biology and Fundamental MedicineSiberian Branch of the Russian Academy of SciencesNovosibirskRussia
  2. 2.Novosibirsk State UniversityNovosibirskRussia
  3. 3.UMR 8200 C.N.R.S. Institut Gustave RoussyGroupe “Reparation de l’ADN” Univ. Paris-Sud XIVillejuif CedexFrance
  4. 4.Bijvoet Center for Biomolecular ResearchUtrecht UniversityUtrechtThe Netherlands

Personalised recommendations