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Biochemistry (Moscow)

, Volume 76, Issue 1, pp 157–166 | Cite as

Photoactivated DNA analogs of substrates of the nucleotide excision repair system and their interaction with proteins of NER-competent extract of HeLa cells. Synthesis and application of long model DNA

  • A. N. Evdokimov
  • I. O. PetrusevaEmail author
  • P. E. Pestryakov
  • O. I. Lavrik
Article

Abstract

Long linear DNA analogs of nucleotide excision repair (NER) substrates have been synthesized. They are 137-mer duplexes containing in their internal positions nucleotides with bulky substitutes imitating lesions with fluorochloroazidopyridyl and fluorescein groups introduced using spacer fragments at the 4N and 5C positions of dCMP and dUMP (Fap-dC- and Flu-dU-DNA) and DNA containing a (+)-cis-stereoisomer of benzo[a]pyrene-N2-deoxyguanidine (BP-dG-DNA, 131 bp). The interaction of the modified DNA duplexes with the proteins of NER-competent HeLa extract was investigated. The substrate properties of the model DNA in the reaction of specific excision were shown to vary in the series Fap-dC-DNA << Flu-dU-DNA < BP-dG-DNA. During the experiments on affinity modification of the proteins of NER-competent extract, Fap-dC-DNA (137 bp) containing a 32P-label in the photoactive nucleotide demonstrated properties of a highly efficient and selective probe. The set of the main targets of labeling included polypeptides of the extract with the same values of apparent molecular weights (35–90 kDa) as when using the shorter (48 bp) Fap-dC-DNA. Besides, some of the extract proteins were shown capable of specific and effective interaction with the long analog of NER substrate. Electrophoretic mobility of these proteins coincided with the mobilities of DNA-binding subunits of XPC-HR23B and PARP1 (∼127 and T]115 kDa, respectively). The 115-kDa target protein was identified as PARP1 using NAD+-based functional testing. The results suggest that the linear Fap-dC-DNA is an unrepairable substrate analog that can compete with effective NER substrates in the binding of the proteins responsible for lesion recognition and excision.

Key words

long bulky substituted DNA duplexes protein factors of NER preincision complexes photoaffinity modification 

Abbreviations

BP-dG

(+)-cis-benzo[a]pyrene-N2-deoxyguanine

Fap-dCTP

exo-N-{;2-[N-(4-azido-2,5-difluoro-3-chloropyridin-6-yl)-3-aminopropionyl]aminoethyl}-2′-deoxycytidine-5′-triphosphate

HR23B

58-kDa polypeptide, a minor subunit of functional heterodimer XPC-HR23B

NER

nucleotide excision repair

ONT

deoxyoligonucleotide

PARP1

poly-(ADP-ribose)-polymerase-1

RPA

human replication A factor

XPC

xeroderma pigmentosum complementation group C factor

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References

  1. 1.
    Scharer, O. D. (2003) Angew. Chem. Int. Ed., 42, 2946–2974.CrossRefGoogle Scholar
  2. 2.
    Dip, R., Camenisch, U., and Naegeli, H. (2004) DNA Rep., 3, 1409–1423.CrossRefGoogle Scholar
  3. 3.
    Gillet, L. C., and Scharer, O. D. (2006) Chem. Rev., 106, 253–276.CrossRefPubMedGoogle Scholar
  4. 4.
    Sugasawa, K., Okamoto, T., Shimizu, Y., Masutani, C., Iwai, S., and Hanaoka, F. (2001) Genes Dev., 15, 507–521.CrossRefPubMedGoogle Scholar
  5. 5.
    Hey, T., Lipps, G., Sugasawa, K., Iwai, S., Hanaoka, F., and Krauss, G. (2002) Biochemistry, 41, 6583–6587.CrossRefPubMedGoogle Scholar
  6. 6.
    Tapias, A., Auriol, J., Forget, D., Enzlin, J. H., Scharer, O. D., Coin, F., Coulombe, B., and Egly, J. M. (2004) J. Biol. Chem., 279, 19074–19083.CrossRefPubMedGoogle Scholar
  7. 7.
    DellaVecchia, M. J., Croteau, D. L., Skorvaga, M., Dezhurov, S. V., Lavrik, O. I., and van Houten, B. (2004) J. Biol. Chem., 279, 45245–45256.CrossRefPubMedGoogle Scholar
  8. 8.
    Buterin, T., Meyer, C., Giese, B., and Naegeli, H. (2005) Chem. Biol., 12, 913–922.CrossRefPubMedGoogle Scholar
  9. 9.
    Trego, K. S., and Turchi, J. J. (2006) Biochemistry, 45, 1961–1969.CrossRefPubMedGoogle Scholar
  10. 10.
    Gillet, L. C., Alzeer, J., and Scharer, O. D. (2005) Nucleic Acids Res., 33, 1961–1969.CrossRefPubMedGoogle Scholar
  11. 11.
    Dezhurov, S. V., Khodyreva, S. N., Plekhanova, E. S., and Lavrik, O. I. (2005) Bioconjug. Chem., 16, 215–222.CrossRefPubMedGoogle Scholar
  12. 12.
    Alzeer, J., and Scharer, O. D. (2006) Nucleic Acids Res., 34, 4458–4466.CrossRefPubMedGoogle Scholar
  13. 13.
    Maltseva, E. A., Rechkunova, N. I., Petruseva, I. O., Sil’nikov, V. N., Vermeulen, V., and Lavrik, O. I. (2006) Biochemistry (Moscow), 71, 270–278.CrossRefGoogle Scholar
  14. 14.
    Petruseva, I. O., Tikhanovich, I. S., Chelobanov, B. P., and Lavrik, O. I. (2008) J. Mol. Recognit., 21, 154–162.CrossRefPubMedGoogle Scholar
  15. 15.
    Maltseva, E. A., Rechkunova, N. I., Gillet, L. C., Petruseva, I. O., Scharer, O. D., and Lavrik, O. I. (2007) Biochim. Biophys. Acta, 1770, 781–789.PubMedGoogle Scholar
  16. 16.
    Krasikova, Yu. S., Rechkunova, N. I., Maltseva, E. A., Petruseva, I. O., Sil’nikov, V. N., Zatsepin, T. S., Oretskaya, T. S., Scharer, O. D., and Lavrik, O. I. (2008) Biochemistry (Moscow), 73, 886–896.CrossRefGoogle Scholar
  17. 17.
    Maltseva, E. A., Rechkunova, N. I., Gillet, L. C., Petruseva, I. O., Scharer, O. D., and Lavrik, O. I. (2007) Biochim. Biophys. Acta, 1770, 781–789.PubMedGoogle Scholar
  18. 18.
    Maltseva, E. A., Rechkunova, N. I., Petruseva, I. O., Vermeulen, W., Scharer, O. D., and Lavrik, O. I. (2008) Bioorg. Chem., 36, 77–84.CrossRefPubMedGoogle Scholar
  19. 19.
    Petruseva, I. O., Tikhanovich, I. S., Maltseva, E. A., Safronov, I. V., and Lavrik, O. I. (2009) Biochemistry (Moscow), 74, 491–501.CrossRefGoogle Scholar
  20. 20.
    Reardon, J. T., and Sancar, A. (2006) Meth. Enzymol., 408, 189–213.CrossRefPubMedGoogle Scholar
  21. 21.
    Sugasawa, K., Akagi, J., Nishi, R., Iwai, S., and Hanaoka, F. (2009) Mol. Cell, 36, 642–653.CrossRefPubMedGoogle Scholar
  22. 22.
    Mocquet, V., Kropachev, K., Kolbanovskiy, M., Kolbanovskiy, A., Tapias, A., Cai, Y., Broyde, S., Geacintov, N. E., and Egly, J. M. (2007) EMBO J., 26, 2923–2932.CrossRefPubMedGoogle Scholar
  23. 23.
    Kropachev, K., Kolbanovskii, M., Cai, Y., Rodriguez, F., Kolbanovskii, A., Liu, Y., Zhang, L., Amin, S., Patel, D., Broyde, S., and Geacintov, N. E. (2009) J. Mol. Biol., 386, 1193–1203.CrossRefPubMedGoogle Scholar
  24. 24.
    Nishi, R., Okuda, Y., Watanabe, E., Mori, T., Iwai, S., Masutani, C., Sugasawa, K., and Hanaoka, F. (2005) Mol. Cell. Biol., 25, 5664–5674.CrossRefPubMedGoogle Scholar
  25. 25.
    Calsou, P., Frit, P., and Salles, B. (1996) J. Biol. Chem., 271, 27601–27607.CrossRefPubMedGoogle Scholar
  26. 26.
    Buterin, T., Hess, M. T., Gunz, D., Geacintov, N. E., Mullenders, L. H., and Naegeli, H. (2002) Cancer Res., 62, 4229–4235.PubMedGoogle Scholar
  27. 27.
    Khodyreva, S. N., and Lavrik, O. I. (2005) Curr. Med. Chem., 12, 641–655.CrossRefPubMedGoogle Scholar
  28. 28.
    Rechkunova, N. I., and Lavrik, O. I. (2010) Subcell Biochem., 50, 251–277.CrossRefPubMedGoogle Scholar
  29. 29.
    Guggenheim, E. R., Xu, D., Zhang, C. X., Chang, P. V., and Lippard, S. J. (2009) Chembiochem, 10, 141–157.CrossRefPubMedGoogle Scholar
  30. 30.
    Wu, X., and Lieber, M. R. (1996) Mol. Cell. Biol., 16, 5186–5193.PubMedGoogle Scholar
  31. 31.
    Ilina, E. S., Khodyreva, S. N., Berezhnoy, A. E., Larin, S. S., and Lavrik, O. I. (2010) Mutat. Res., 685, 90–96.PubMedGoogle Scholar
  32. 32.
    Lavrik, O. I., Prasad, R., Sobol, R. W., Horton, J. K., Ackerman, E. J., and Wilson, S. H. (2001) J. Biol. Chem., 276, 25541–25548.CrossRefPubMedGoogle Scholar
  33. 33.
    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.CrossRefPubMedGoogle Scholar
  34. 34.
    Sukhanova, M., Khodyreva, S., and Lavrik, O. (2009) Mutat. Res., 685, 80–89.PubMedGoogle Scholar
  35. 35.
    Zhu, G., Chang, P., and Lippard, S. J. (2010) Biochemistry, 49, 6177–6183.CrossRefPubMedGoogle Scholar

Copyright information

© Pleiades Publishing, Ltd. 2011

Authors and Affiliations

  • A. N. Evdokimov
    • 1
    • 2
  • I. O. Petruseva
    • 1
    Email author
  • P. E. Pestryakov
    • 1
  • O. I. Lavrik
    • 1
    • 2
  1. 1.Institute of Chemical Biology and Fundamental MedicineSiberian Branch of the Russian Academy of SciencesNovosibirskRussia
  2. 2.Novosibirsk State UniversityNovosibirskRussia

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