PL EN


Preferencje help
Widoczny [Schowaj] Abstrakt
Liczba wyników
Tytuł artykułu

Quantum Chemical Study of the Nature of Stacking Interactions of 2-Oxo-adenine with Native B-DNA Purines

Identyfikatory
Warianty tytułu
Języki publikacji
EN
Abstrakty
EN
The scan of intermolecular interaction energy surfaces for stacked complexes of 2-oxoadenine (AA) with purine bases was performed using the density-fitting approach at the MP2 level of theory with correlation-consistent Dunning's basis sets. Moreover, the convergence of stabilization energy to the basis-set limit was analyzed using two-point extrapolation formula proposed by Halkier et al. Four different complexes in two different context alignments appearing in B-DNA were considered, namely 5c-A/A-3', 5'-A/AA-3', 5c-AA/A-3', 5c-G/A-3', 5'-G/AA-3', 5'-A/G-3' and 5'-AA/G-3'. The results of ab initio calculation allow to arrive at conclusion that oxidation of adenine at C2 position does not lead to significant changes in the structural parameters of stacked complexes. However, the modification of adenine by hydroxyl radical affects noticeably the stabilization energy only for 5'-G/AA-3' complex. In order to explain the source of this large stabilization effect, the intermolecular interaction energy decomposition was performed at the MP2/aug-cc-pVDZ level of theory for the minima on the interaction energy surfaces of adenine (2-oxo-ad e nine) with guanine. It was found that the observed larger stabilization energy for 5'-G/AA-3' compared to 5'-G/A-3' arises from the electrostatic interactions.
Rocznik
Strony
2269--2279
Opis fizyczny
Bibliogr. 37 poz., rys.
Twórcy
autor
autor
  • Department of Physical Chemistry, Collegium Medicum, Nicolaus Copernicus University, Kurpińskiego 5, 85-950 Bydgoszcz, Poland, piotr.cysewski@cm.umk.pl
Bibliografia
  • 1. Hunter C.A., J. Mol. Biol., 230, 1025 (1993).
  • 2. Calladine C.R., J. Mol. Biol., 161, 343 (1982).
  • 3. Drew H.R., Wing R.M., Takana T., Broka C., Tanaka S., Itakura K. and Dickerson R.E., Proc. Natl. Acad. Sci. U.S.A., 78, 2179 (1981).
  • 4. Kennard O. and Hunter W.N., Angew. Chem. Int. Ed. Engl., 30, 1254 (1991).
  • 5. Wilson W.D. and Jones R.L., Intercalation Chemistry, Wittingham M.S., Jacobsen A.J., Eds., Academic Press, New York, 1982, Chapter 14.
  • 6. Kasai H., Crain P.F., Kuchino Y., Nishimura S., Ootsuyana A. and Tanooka H., Carcinogenesis, 7, 1849(1986).
  • 7. Fridovich L, Arch. Biochem. Biophys., 247, l (1986).
  • 8.   Floyd R.A., Watson J.J., Harris J., West M. and Wong P.K., Biochem. Biophys. Res. Commun., 137, 841 (1986).
  • 9. Breimer L.H., Mol.Carcinogenesis, 3, 188 (1990).
  • 10. Harman D., Proc. Natl. Acad. U. S. A* 78, 7124 (1981).
  • 11. Ames B.N., Science, 221, 1256 (1983).
  • 12. Pryor W.A., Annu. Rev. Physiol., 48, 657 (1986).
  • 13. Wood M.L., Estave A., Momingstar M.L., Kuziamko G. and Essigmann J.M., Nuc. Acids Res., 20, 6023 (1992).
  • 14. Vieria A.J.S.C. and Stenken S., J. Am. Chem. Soc., 112, 6986 (1990).
  • 15. Doetsch P.W., Zastawny T.H., Martin A.M. and Dizdaroglu M., Biochemistry, 34, 737 (1995).
  • 16. Frelon S., Douki T. and Cadet J., Free Radic. Res., 36, 499 (2002).
  • 17. Cooke M.S., Evans M.D., Dizdaroglu M. and Lunec J., The FASEB Journal, 17, 1195 (2003).
  • 18. Jurečka R, Šponer J., Černy J. and Hobza R, Phys. Chem. Chem. Phys., 8, 1985 (2006).
  • 19. Langner K.M., Sokaiski W.A. and Leszczyński J., J. Chem. Phys., in press.
  • 20. Sedlak R., Jurečka R and Hobza R, J. Chem. Phys., 127, 075104 (2007).
  • 21. Lu X.J. and Olso W.K., Nuc. Acids Res., 31, 5108 (2003).
  • 22. Olson W. K., Bansal M., Burley S.K., Dickerson R.E., Gerstein M., Harvey S.C., Heinemann U., Lu X. J., Neidle S., Shakked Z., Sklenar H., Suzuki M., Tung C.S., Westh E., Wolberger C. and Berman H.M., J. Mol. Biol., 313, 229 (2001).
  • 23. Nucleic Acids Databases: http://ndbserver.rutgers.edu/atlas
  • 24. Hunter C.A. and Lu X., J. Mol. Biol., 265, 603 (1997).
  • 25. Schmidt M.W., Baldridge K.K., Boatz J.A., Elbert S.T., Gordon M.S., Jensen J.H., Koseki S.,Matsunaga N., Nguyen K.A., Su S., Windus T.L., Dupuis M. and Montgomery J.A., J. Comput. Chem., 14, 1347(1993).
  • 26. Czyżnikowska Ż., Zaleśny R., Góra R. W., Ziółkowski M. and Cysewski R., Chem, Phys. Lett., submitted.
  • 27. Dunning T.H. Jr., J. Chem. Phys., 90, 1007 (1989).
  • 28. Werner H.-J., Manby F.R. and Knowles P.J., J. Chem. Phys., 118, 8149 (2003).
  • 29. Poily R., Werner H.-J., Manby F.R. and Knowles P.J., Mol. Phys., 102, 2311 (2004).
  • 30. Halkier A., Helgaker T., Jorgensen R, Klopper W., Koch H. and Olsen J., Chem. Phys. Lett., 286, 243 (1998).
  • 31. Halkier A., Helgaker T., Jorgensen R, Klopper W. and Olsen J., Chem. Phys. Lett., 302, 437 (1999).
  • 32. Werner H.-J., Knowles P.J., Lindh R., Manby F.R., Schutz M., Celani R., Korona T., Rauhut G.,Amos R.D., Bernhardsson A., Berning A., Cooper D.L., Deegan M.J.O., Dobbyn A.J., Eckert F.,Hampel C., Hetzer G., Lloyd A.W, McNicholas S.J., Meyer W, Mura M.E., Nieklass A., Palmieri R,Pitzer R., Schumann U., Stoll H., Stone A.J., Tarroni R. and Thorsteinsson T, MOLPRO, version 2006.1.
  • 33. Boys S.F. and Bernardi F., Mol. Phys., 19, 553 (1970).
  • 34. Góra R. W, EDS v2.2.1 package (1998-2003).
  • 35. Góra R.W, Bartkowiak W, Roszak S. and Leszczyński J., J. Chem. Phys., 117, 1031 (2002).
  • 36. Toczyłowski R.R. and Cybulski S.M., J. Chem. Phys., 123, 154312 (2005).
  • 37. Haley T.R, Gravbill E.R. and Cybulski S.M., J. Chem. Phys., 124, 204301 (2006).
Typ dokumentu
Bibliografia
Identyfikator YADDA
bwmeta1.element.baztech-article-BUJ6-0025-0025
JavaScript jest wyłączony w Twojej przeglądarce internetowej. Włącz go, a następnie odśwież stronę, aby móc w pełni z niej korzystać.