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Vol. 25 No. 7 (2013): Vol 25 Issue 7

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Theoretical Study on the Site and Regularity of Chiral Ru(II) Polypyridyl Complexes Binding to Mismatched DNA-Base-Pair

https://doi.org/10.14233/ajchem.2013.13839
Si Yan Liao
Department of Chemistry, Guangzhou Medical College, Guangzhou 510182, P.R. China ; The Key Laboratory of Bioinorganic and Synthetic Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P.R. China
Hai Liang Lu
The Key Laboratory of Bioinorganic and Synthetic Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P.R. China
Ti Fang Miao
College of Chemistry and Materials Science, Huaibei Normal University, Huaibei 235000, P.R. China ; College of Chemistry and Materials Science, Huaibei Normal University, Huaibei 235000, P.R. China
Kang Cheng Zheng
The Key Laboratory of Bioinorganic and Synthetic Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P.R. China

Corresponding Author(s) : Si Yan Liao

siyanliao@163.com

Asian Journal of Chemistry, Vol. 25 No. 7 (2013): Vol 25 Issue 7

Abstract

In order to perform theoretical studies on the interactions between Ru(II) complexes and DNA, a combined methodology of molecular mechanics (MM+), quantum chemistry (DFT) and molecular docking was applied to establish the valuable model and hereby to study the interaction of Ru(II) complexes with mismatched DNA containing sheared G×A base pairs. The groove selectivity, base pair recognition, binding energy at different base pair site and binding configuration were investigated, using well-known DNA intercalator [Ru(phen)2(dppz)]2+ as a molecular probe. On the basis of these testing researches, a series of chiral Ru(II) complexes D, L-[Ru(bpy)2L]2+ [L = o-hpip, m-hpip, p-hpip] {hpip = 2-(hydroxyphenyl)imidazo[4,5-f][1,10-phenanthroline]} were selected to carry out a significant study on their DNA-groove selectivity, DNA-binding energy and binding configuration at the specific base-pair site which has been specially recognized by [Ru(phen)2(dppz)]2+ molecular probe. The effects of chirality, different position of substitute group and intramolecular hydrogen bond of these studied complexes on the complex-DNA interaction were also discussed and the related regularities were well revealed. The obtained results help to understanding the control regulations and the action mechanism between the complex and DNA and further directing the design and synthesis of this kind of Ru(II) polypyridyl complex.

Keywords

Ru(II) polypyridyl complex DNA Molecular mechanism DFT calculation Docking analysis
Yan Liao, S., Liang Lu, H., Fang Miao, T., & Cheng Zheng, K. (2013). Theoretical Study on the Site and Regularity of Chiral Ru(II) Polypyridyl Complexes Binding to Mismatched DNA-Base-Pair. Asian Journal of Chemistry, 25(7), 3902–3908. https://doi.org/10.14233/ajchem.2013.13839
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References
  1. D.L. Grady, R.L. Ratliff, D.L. Robinson, E.C. McCanlies, J. Meyne and R.K. Moyzis, Proceed. Nat. Acad. Sci., 89, 1695 (1992).
  2. S.H. Chou, L. Zhu and B.R. Reid, J. Mol. Biol., 244, 250 (1994).
  3. S.H. Chou, L. Zhu and B.R. Reid, J. Mol. Biol., 267, 1055 (1997).
  4. Y.G. Gao, H. Robinson, R. Sanishvili, A. Joachimiak and A.H. Wang, Biochemistry, 38, 16452 (1999).
  5. J.K. Barton, Science, 233, 727 (1986).
  6. B. Norden, P. Lincoln, B. Akerman and E. Tuite, In eds.: A. Sigel and H. Sigel, Metal Ions in Biological Systems, Marcel Dekker, New York (1996).
  7. A.E. Friedman, J.C. Chambron, J.P. Sauvage, N.J. Turro and J.K. Barton, J. Am. Chem. Soc., 112, 4960 (1990).
  8. L.N. Ji, X.H. Zou and J.G. Liu, Coord. Chem. Rev., 216, 513 (2001).
  9. K.E. Erkkila, D.T. Odom and J.K. Barton, Chem. Rev., 99, 2777 (1999).
  10. H.Y. Mei and J.K. Barton, J. Am. Chem. Soc., 108, 7414 (1986).
  11. M. Eriksson, M. Leijon, C. Hiort, B. Norden and A. Graeslund, J. Am. Chem. Soc., 114, 4933 (1992).
  12. M. Eriksson, M. Leijon, C. Hiort, B. Norden and A. Graeslund, Biochemistry, 33, 5031 (1994).
  13. D.Z.M. Coggan, I.S. Haworth, P.J. Bates, A. Robinson and A. Rodger, Inorg. Chem., 38, 4486 (1999).
  14. F. Gao, H. Chao and L.N. Ji, Chem. Biodiversity, 5, 1962 (2008).
  15. Z. Xiong and P. Yang, J. Mol. Struct (Theochem.), 582, 107 (2002).
  16. S.D. Wettig, D.O. Wood, P. Aich and J.S. Lee, J. Inorg. Biochem., 99, 2093 (2005).
  17. H. Chen, P. Yang, C. Yuan and X. Pu, Eur. J. Inorg. Chem., 3141 (2005).
  18. B.M. Zeglis, V.C. Pierre and J.K. Barton, Chem. Commun., 4565 (2007).
  19. G. Pourtois, D. Beljonne, C. Moucheron, S. Schumm, A. Kirsch-De Mesmaeker, R. Lazzaroni and J.L. Bredas, J. Am. Chem. Soc., 126, 683 (2004).
  20. J. Li, J.C. Chen, L.C. Xu, K.C. Zheng and L.N. Ji, J. Organomet. Chem., 692, 831 (2007).
  21. N. Kurita and K. Kobayashi, Comp. Chem., 24, 351 (2000).
  22. P. Yang, D. Han and Z. Xiong, J. Mol. Struct.: Theochem., 540, 211 (2001).
  23. Z. Xiong and P. Yang, J. Mol. Struct.: Theochem., 620, 129 (2003).
  24. C. Metcalfe and J.A. Thomas, Chem. Soc. Rev., 32, 215 (2003).
  25. Y.J. Liu, H. Chao, L.F. Tan, Y.X. Yuan, W. Wei and L.N. Ji, J. Inorg. Biochem., 99, 530 (2005).
  26. J.G. Liu, B.H. Ye, H. Li, Q.X. Zhen, L.N. Ji and Y.H.P. Fu, J. Inorg. Biochem., 76, 265 (1999).
  27. W.J. Mei, J. Liu, K.C. Zheng, L.J. Lin, H. Chao, A.X. Li, F.C. Yun and L.N. Ji, Dalton Trans., 1352 (2003).
  28. S. Shi, J. Liu, J. Li, K.C. Zheng, C.P. Tan, L.M. Chen and L.N. Ji, Dalton Trans., 2038 (2005).
  29. S. Shi, J. Liu, J. Li, K.C. Zheng, X.M. Huang, C.P. Tan, L.M. Chen and L.N. Ji, J. Inorg. Biochem., 100, 385 (2006).
  30. E.F. Pettersen, T.D. Goddard, C.C. Huang, G.S. Couch, D.M. Greenblatt, E.C. Meng and T.E. Ferrin, J. Computat. Chem., 25, 1605 (2004).
  31. M. Challacombe, P.M.W. Gill, B. Johnson, W. Chcn, M.W. Wong, J.L. Andres, C. Gonzalcz, M. Head-Gordon, E.S. Rcploglc and J.A. Poplc, Gaussian 03, Revision D. 01; Gaussian. Inc.: Pittsburgh PA (2005).
  32. P.T. Lang, D. Moustakas, S. Brozell, N.C., S. Mukherjee, S.P., K. Raha, D.S., R. Rizzo, D.C., B. Shoichet and I. Kuntz, DOCK,Version 6.2, University of California,University of California, San Francisco, USA (2008).
  33. SYBYL 6.9, St Louis Tripos Associates, Inc. (2001).
  34. C. Huang, DMS, University of California, San Francisco (2008)
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