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Molecular modeling on the recognition of DNA sequence and conformational repair of sheared DNA by novel chiral metal complex D,L-[Co(phen)2hpip]3+

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Abstract

A study on the recognition of DNA sequence and conformational repair of sheared DNA by Novel Chiral Metal complex D,L-[Co(phen)2hpip]3+ (phen=1,10 phenanthroline, hpip=2-[2-hydroxyphenyl] imidazole [4,5-f][1,10] phenanthroline) is carried out with molecular simulations. The results reveal that two isomers of the complex could both recognize the normal DNA in the minor groove orientation, while recognize the sheared DNA in the major groove orientation and both isomers could convert the conformation of mismatched bases from sheared form to parallel form. Further analysis shows that the steric details of complex’s intercalation to base stack determine the results of recognition, which is induced by the steric collision among ancillary ligand phen, bases and DNA backbone, and by the steric crowding occurring in the process of structural expansion of bases and DNA backbone. Detailed analysis reveals that the conformational repair of mismatched bases relates not only to the steric interactions, but also the π-π stack among normal bases, mismatched bases and hpip ligand.

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References

  1. Harfe, B. D., Jinks-Robertson, S., DNA mismatch repair and genetic instability, Annu. Rev. Genet., 2000, 34: 359–399.

    Article  CAS  Google Scholar 

  2. Buermeyer, A. B., Deschenes, S. M., Baker, S. M. et al., Mammalian DNA mismatch repair, Annu. Rev. Genet., 1999, 33: 533–564.

    Article  CAS  Google Scholar 

  3. Chen, H. L., Yang, P., Progress in the studies of mismatched nucleic acid, Progress in Chemistry (in Chinese), 2002, 14: 133–139.

    Google Scholar 

  4. Chen, H. L., Yang, P., Progress in the studies of recognition and repair of mismatched nucleic acid, Progress in Chemistry (in Chinese), 2002, 14: 239–245.

    CAS  Google Scholar 

  5. Erkkila, K. E., Odom, D. T., Barton, J. K., Recognition and reaction of metallointercalators with DNA, Chem. Rev., 1999, 19: 2777–2795.

    Google Scholar 

  6. Qi, D. F., Tann, C. M., Haring, D. et al., Generation of new enzymes via covalent modification of existing proteins, Chem. Rev., 2001, 101: 3081–3111.

    Article  CAS  Google Scholar 

  7. Friedman, A. E., Kumar, C. V., Turro, N. J. et al., Luminescence of ruthenium(II) polypyridyls: evidence for intercalative binding to Z-DNA, Nucleic Acid Res., 1991, 19(10): 2595–2602.

    CAS  Google Scholar 

  8. Turro, C., Bossmann, S. H., Jenkins, Y. et al., Proton transfer quenching of the MLCT excited state of Ru(phen)2dppz2+ in homogeneous solution and bound to DNA, J. Am. Chem. Soc., 1995, 117: 9026–9032.

    CAS  Google Scholar 

  9. Yun, B. H., Kim, J. O., Lee, B. W. et al., Simultaneous binding of ruthenium(II) [(1,10-phenanthroline)2dipyridophenazine]2+ and minor groove binder 4′,6-diamidino-2-phenylindole to poly[d(A-T)2] at high binding densities: Observation of fluorescence resonance energy trasfer across the DNA stem, J. Phys. Chem. B, 2003, 107: 9858–9864.

    Article  CAS  Google Scholar 

  10. Gisselfalt, K., Lincoln, P., Norden, B. et al., Interactions of tris(phenanthroline)ruthenium(II) enantiomers with DNA: Effects on helix flexibility studied by the electrophoretic behavior of reptating DNA in agarose gel, J. Phys. Chem. B, 2000, 104: 3651–3659.

    Article  Google Scholar 

  11. Barton, J. K., Raphael, A. L., Photoactivated stereospecific cleavage of double-helical DNA by cobalt(III) complexes, J. Am. Chem. Soc., 1984, 106: 2466–2468.

    CAS  Google Scholar 

  12. Jackson, B. A., Alekseyev, V. Y., Barton, J. K., A versatile mismatch recognition agent: Specific cleavage of a plasmid DNA at a single base mispair, Biochemistry, 1999, 38: 4655–4662.

    Article  CAS  Google Scholar 

  13. Collins, J. G., Sleeman, A. D., Aldrich-Wright, J. R. et al., A 1H NMR study of the DNA binding of ruthenium(II) polypyridyl complexes, Inorg. Chem., 1998, 37: 3133–3141.

    Article  CAS  Google Scholar 

  14. Xiong, Z. H., Yang, P., Molecular modeling on recognition of sheared and normal DNA by novel metal complex L-and D-[Co(phen)2hpip]3+, J. Mol. Struc. (Theochem.), 2003, 620: 129–138.

    CAS  Google Scholar 

  15. Xiong, Z. H., Yang, P., Molecular modeling on recognition of DNA sequence by Λ-,Δ-[Co(phen)2hpip]3+, Chem. J. Chinese U. (in Chinese), 2002, 23(Supp.): 57–63.

    Google Scholar 

  16. http://www.ncbi.nlm.nih.gov/Entrez.

  17. Yang, P., Han, D. X., Molecular modeling of the binding mode of chiral metal complex Δ-and Λ-[Co(phen)2dppz]3+ with DNA, Science in China, Ser. B, 2000, 43(5): 516–523.

    CAS  Google Scholar 

  18. Xiong, Z. H., Yang, P., Studies of the interaction between sheared DNA and Λ-or Δ-[Ru(phen)2dppz]n+ by molecular modeling, J. Mol. Struc. (Theochem.), 2002, 582: 107–117.

    CAS  Google Scholar 

  19. Chen, H. L., Yang, P., A novel cobalt(III) mixed-polypyridy complex: Synthesis characterization and DNA binding, Chinese J. Chem., 2002, 20(6): 1529–1535.

    CAS  Google Scholar 

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Authors and Affiliations

  1. Institute of Molecular Science, Key Laboratory of Chemical Biology of Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, China

    Wu Yanbo, Zhang Cuiping & Yang Pin

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  1. Wu Yanbo
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  2. Zhang Cuiping
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  3. Yang Pin
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Correspondence to Yang Pin.

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Wu, Y., Zhang, C. & Yang, P. Molecular modeling on the recognition of DNA sequence and conformational repair of sheared DNA by novel chiral metal complex D,L-[Co(phen)2hpip]3+ . SCI CHINA SER B 49, 177–185 (2006). https://doi.org/10.1007/s11426-006-0177-z

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  • DOI: https://doi.org/10.1007/s11426-006-0177-z

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