Russian Journal of Bioorganic Chemistry

, Volume 38, Issue 4, pp 376–382 | Cite as

Oligomerization of site-specific nicking endonuclease BspD6I at high protein concentrations

  • S. A. Sekerina
  • A. V. Grishin
  • A. Yu. Ryazanova
  • R. I. Artyukh
  • E. A. Rogulin
  • A. K. Yunusova
  • T. S. Oretskaya
  • L. A. Zheleznaya
  • E. A. Kubareva


The ability of site-specific nicking endonuclease BspD6I (Nt.BspD6I) to oligomerize at concentrations > 0.5 μM (>0.035 mg/mL) is studied. Three states of Nt.BspD6I are registered via electrophoretic studies both in the presence and in the absence of DNA. Estimation of their molecular mass allows assigning them as a monomer, a dimer and a trimer. Both dimeric and monomeric Nt.BspD6I are shown to hydrolyze its DNA substrate with the same specificity. Calculation of the electrostatic potential distribution on the Nt.BspD6I globule surface shows that the protein molecule is a dipole. The Nt.BspD6I oligomeric forms are likely to be the result of ionic protein-protein interactions.


heterodimeric restriction endonucleases nicking endonuclease oligomerization protein docking 



Protein Data Bank




nicking endonuclease


theoretical molecular weight


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Van Ness, J., Van Ness, L.K., and Galas, D.J., Proc. Natl. Acad. Sci. USA, 2003, vol. 100, pp. 4504–4509.PubMedCrossRefGoogle Scholar
  2. 2.
    Yang, J., Zhang, Z., Zhang, X.A., and Luo, Q., Bio-Techniques, 2010, vol. 49, pp. 817–821.Google Scholar
  3. 3.
    Wang, H. and Hays, J.B., Mol. Biotechnol., 2001, vol. 19, pp. 133–140.PubMedCrossRefGoogle Scholar
  4. 4.
    Bath, J., Green, S.J., and Turberfield, A.J., Angew. Chem. Int. Ed. Engl., 2005, vol. 44, pp. 4358–4361.PubMedCrossRefGoogle Scholar
  5. 5.
    Kuhn, H. and Frank-Kamenetskii, M.D., Nucleic Acids Res., 2008, vol. 36, p. e40.Google Scholar
  6. 6.
    Tan, E., Erwin, B., Dames, S., Voelkerding, K., and Niemz, A., Clin. Chem., 2007, vol. 53, pp. 2017–2020.PubMedCrossRefGoogle Scholar
  7. 7.
    Chen, J., Zhang, J., Li, J., Fu, F., Yang, H.H., and Chen, G., Chem. Commun. (Camb.), 2010, vol. 28, pp. 5939–5941.CrossRefGoogle Scholar
  8. 8.
    Zheleznaya, L.A., Perevyazova, T.A., Al’dzhanova, D.V., and Matvienko, N.I., Biochemistry (Mosc.), 2001, vol. 69, pp. 1123–1127.Google Scholar
  9. 9.
    Yunusova, A.K., Rogulin, E.A., Artyukh, R.I., Zheleznaya, L.A, and Matvienko, N.I., Biochemistry (Mosc.), 2006, vol. 71, pp. 815–820.CrossRefGoogle Scholar
  10. 10.
    Perevyazova, T.A., Rogulin, E.A., Zheleznaya, L.A., and Matvienko, N.I., Biochemistry (Mosc.), 2003, vol. 68, pp. 984–987.CrossRefGoogle Scholar
  11. 11.
    Higgins, L.S., Besnier, C., and Kong, H., Nucleic Acids Res., 2001, vol. 29, pp. 2492–2501.PubMedCrossRefGoogle Scholar
  12. 12.
    Kachalova, G.S., Artyukh, R.I., Zheleznaya, L., and Matvienko, N.I., Acta Crystallogr. Sect. F. Struct. Biol. Cryst. Commun., 2005, vol. 61, pp. 332–334.PubMedCrossRefGoogle Scholar
  13. 13.
    Goodsell, D.S. and Olson, A.J., Annu. Rev. Biophys. Biomol. Struct., 2000, vol. 29, pp. 105–153.PubMedCrossRefGoogle Scholar
  14. 14.
    Nooren, I.M.A. and Thornton, J.M.J., Mol. Biol., 2003, vol. 325, pp. 991–1018.CrossRefGoogle Scholar
  15. 15.
    Bading, H., Nucleic Acids Res., 1988, vol. 16, pp. 5241–5248.PubMedCrossRefGoogle Scholar
  16. 16.
    Schägger, H. and Jagow, G., Anal. Biochem., 1991, vol. 199, pp. 223–231.PubMedCrossRefGoogle Scholar
  17. 17.
    Niepman, M. and Zheng, J., Electrophoresis, 2006, vol. 27, pp. 3949–3951.CrossRefGoogle Scholar
  18. 18.
    Krause, F., Electrophoresis, 2006, vol. 27, pp. 2759–2781.PubMedCrossRefGoogle Scholar
  19. 19.
    Schägger, H., Nat. Protoc., 2006, vol. 1, pp. 16–22.PubMedCrossRefGoogle Scholar
  20. 20.
    Ryazanova, A.Yu., Molochkov, N.V., Abrosimova, L.A., Alekseevskii, A.V., Karyagina, A.S., Protsenko, A.S., Friedhoff, P., Oretskaya, T.S., and Kubareva, sE.A., Mol. Biol. (Mosk.), 2010, vol. 44, pp. 911–921.Google Scholar
  21. 21.
    Ahmad, S. and Sarai, A., J. Mol. Biol., 2004, vol. 341, pp. 65–71.PubMedCrossRefGoogle Scholar
  22. 22.
    Ali, M.H. and Imperiali, B., Bioorg. Med. Chem., 2005, vol. 13, pp. 5013–5020.PubMedCrossRefGoogle Scholar
  23. 23.
    Rogulin, E.A., Perevyazova, T.A., Zheleznaya, L.A., and Matvienko, N.I., Biochemistry (Mosc.), 2004, vol. 69, pp. 1123–1127.CrossRefGoogle Scholar

Copyright information

© Pleiades Publishing, Ltd. 2012

Authors and Affiliations

  • S. A. Sekerina
    • 1
  • A. V. Grishin
    • 1
  • A. Yu. Ryazanova
    • 1
  • R. I. Artyukh
    • 2
  • E. A. Rogulin
    • 2
  • A. K. Yunusova
    • 2
  • T. S. Oretskaya
    • 1
  • L. A. Zheleznaya
    • 2
  • E. A. Kubareva
    • 1
  1. 1.Chemistry Department, Faculty of Bioengineering and Bioinformatics and A. N. Belozersky Institute of Physico-Chemical BiologyMoscow State UniversityMoscowRussia
  2. 2.Institute of Theoretical and Experimental BiophysicsPushchinoRussia

Personalised recommendations