Share This Article:

A model study on the stacking interaction of phenanthroline ligand with nucleic acid base pairs: An ab initio, MP2 and DFT studies

Abstract Full-Text HTML Download Download as PDF (Size:336KB) PP. 153-158
DOI: 10.4236/jbpc.2011.22019    4,697 Downloads   9,608 Views   Citations


The stacking of phenanthroline(phen) ligand within base pair sequences is one of the important factors for the stabilization of metalphen complex within DNA. The stacking ability of this ligand has been assessed to deduce the base pair selectivity as well as to identify the favored region of intercalation. Different level of theories have been used to predict the favorable regions for stacking interaction of phen ligand with base pair, but the results of MP2/6-31+G(d,p) is found to be reasonably good for monitoring such interactions.

Conflicts of Interest

The authors declare no conflicts of interest.

Cite this paper

Hazarika, P. , Bezbaruah, B. , Das, P. , Medhi, O. and Medhi, C. (2011) A model study on the stacking interaction of phenanthroline ligand with nucleic acid base pairs: An ab initio, MP2 and DFT studies. Journal of Biophysical Chemistry, 2, 153-158. doi: 10.4236/jbpc.2011.22019.


[1] Denny, W.A., Baguley, B., Neidle, S. and Waring, M. (1994) Molecular aspects of anti-cancer drug-DNA interaction. British Journal of Clinical Pharmacology, 37, 103.
[2] Mukherjee, A., Lavery, R., Bagchi, B. and Hynes, J.T. (2008) On the molecular mechanism of drug intercalation into DNA: A simulation study of the intercalation pathway, free energy, and DNA structural changes. Journal of the American Chemical Society, 130, 9747-9755. doi:10.1021/ja8001666
[3] Rehmann, J.P. and Barton, J.K. (1990) H NMR studies of tris (phenanthroline) metal complexes bound to oligonucleotides: Characterization of binding modest. Biochemistry, 29, 1701-1709. doi:10.1021/bi00459a006
[4] Coggan, D.Z.M., Haworth, I.S., Bates, P.J., Robinson, A. and Rodger, A. (1999) DNA binding of ruthenium tris(1, 10-phenanthroline): Evidence for the dependence of binding mode on metal complex concentration. Inorganic Chemistry, 38, 4486-4497. doi:10.1021/ic990654c
[5] Barton, J.K., Basile, L.A., Danishefsky, A. and Alexandrescu, A. (1984) Chiral probes for the handedness of DNA helices: Enantiomers of tris(4, 7 diphenylphenanthroline) ruthenium (II). Proceedings of National Acadamy of Sciences of USA, 81, 1961-1965. doi:10.1073/pnas.81.7.1961
[6] Haworth, I.S., Elcock, A.H., Freeman, J., Rodger, A. and Richards, W.G. (1991) Sequence selective binding to the DNA major groove: tris(1, 10-phenanthroline) metal complexes binding to poly(dG-dC) and poly(dA-dT). Journal of Biomolecular Structure and Dynamics, 9, 23-44.
[7] Satyanarayana, S., Dabrowiak, J.C. and Chaires, J.B. (1992) Neither DELTA- nor LAMBDA-tris(phenanthroline) ruthenium (II) binds to DNA by classical intercalation. Biochemistry, 31, 9319-9324. doi:10.1021/bi00154a001
[8] Eriksson, M., Leijon, M., Hiort, C, Nordén, B. and Graslund, A. (1994) Binding of DELTA- and LAMBDA- [Ru(phen)3]2+ to [d(CGCGATCGCG)]2 Studied by NMR. Biochemistry, 33, 5031-5040. doi:10.1021/bi00183a005
[9] Lyng, R., Rodger, A. and Nordén, B. (1991) The circular dichroism of drug-DNA systems. Poly(dG-dC) B-DNA. Biopolymers, 31, 1709-1720.
[10] Lyng, R., Rodger, A. and Nordén, B. (1992) The circular dichroism of drug-DNA systems poly(dA-dT) B-DNA. Biopolymers, 32, 1201-1214. doi:10.1002/bip.360320910
[11] Lincoln, P. and Nordén, B. (1998) DNA Binding Geometries of Ruthenium (II) Complexes with 1, 10-phenanthroline and 2, 2’-bipyridyl ligands studied with linear dichroism spectra. Borderline cases of intercalation. Journal of Physical Chemistry, 102, 9583-9594. doi:10.1021/jp9824914
[12] Cho, C.B., Cho, T.S., Kim, S.K., Kim, B.J., Han, S.W. and Jung, M.J. (2000) Binding mode of [Ruthenium (II) (1, 10-Phenanthroline)2L]2+ to poly(dG)?poly(dC)?poly (dC)+ triplex DNA. Korean Chemical Society, 21, 995-999.
[13] Coury, J.E., Anderson, J.R., McFail-Isom, L., Williams, L.D. and Bottomley, L.A. (1997) Scanning force microscopy of small ligand-nucleic acid complexes: tris(o-phenanthroline)ruthenium (II) as a test for a new assay. Journal of the American Chemical Society, 119, 3792-3796. doi:10.1021/ja9623774
[14] Hiort, C., Nordén, B., Rodger, A. (1990) Enantiopreferential DNA binding of [ruthenium (II) (1, 10-phenanthroline)3]2+ studied with linear and circular dichroism. Journal of the American Chemical Society, 112, 1971-1982. doi:10.1021/ja00161a050
[15] Kumar, C.V., Barton, J.K. and Turro, N.J. (1985) Photophysics of ruthenium complexes bound to double helical DNA. Journal of the American Chemical Society, 107, 5518-5523. doi:10.1021/ja00305a032
[16] Patel, D. and Shapiro, L. (1985) Molecular recognition in noncovalent antitumor agent-DNA complexes: NMR studies of the base and sequence dependent recognition of the DNA minor groove by netropsin. Biochiemie, 67, 887-915. doi:10.1016/S0300-9084(85)80181-4
[17] Pyle, A.M., Rehman, R.M., Kumar, C.V., Turro, N.J. and Barton, J.K. (1989) Mixed-ligand complexes of ruthenium (11): Factors governing binding to DNA. Journal of the American Chemical Society, 111, 3051-3058. doi:10.1021/ja00190a046
[18] Kumar, S.V., Sakore, T.D. and Sobell, H.M. (1984) Structure of a novel drug-nucleic acid crystalline complex: 1, 10-phenanthroline-platinum (II) ethylenediamine-5’-phosphoryl-thymidylyl (3’-5’) deoxyadenosine. Journal of Biomolecular Structure and Dynamics, 2, 333-344.
[19] Barton, J.K., Goldberg, J., Kumar, C.V. and Turro, N.J. (1986) Binding modes and base specificity of tris(phenanthroline)ruthenium(II) enantiomers with nucleic acids: Tuning the stereoselectivity. Journal of the American Chemical Society, 108, 2081-2088. doi:10.1021/ja00268a057
[20] Kirshenbaum, M.R., Tribolet, R. and Barton, J.K. (1988). Rh(DIP)3(3+) a shape-selective metal complex which targets cruciforms. Nucleic Acid Research, 16, 7943-7960. doi:10.1093/nar/16.16.7943
[21] Hill, J.G. and Platts, J.A. (2009) Local electron correlation descriptions of the intermolecular stacking interactions between aromatic intercalators and nucleic acids. Chemical Physical Letter, 479, 279-283. doi:10.1016/j.cplett.2009.08.021
[22] Riley, K.E. and Hobza, P. (2007) Assessment of the MP2 method, along with several basis sets, for the computation of interaction energies of biologically relevant hydrogen bonded and dispersion bound complexes. Journal of Physical Chemistry A, 111, 8257-8263. doi:10.1021/jp073358r
[23] Grimme, S. (2003) Improved second-order M?ller- Plesset perturbation theory by separate scaling of parallel-and antiparallel-spin pair correlation energies. Journal of Chemical Physics, 118, 9095-9102. doi:10.1063/1.1569242
[24] Janet, E. and Bene, D. (1988) Ab initio molecular orbital study of the structures and energies of neutral and charged bimolecular complexes of water with the hydrides AHn (A = nitrogen, oxygen, fluorine, phosphorus, sulfur, and chlorine). Journal of Physical Chemistry. A, 92, 2874-2880.
[25] McDonald, D.Q. and Still, W.C. (1994) Conformational free energies from simulation: Stochastic dynamics/monte carlo simulations of a homologous series of Gellman’s diamides. Journal of the American Chemical Society, 116, 11550-11553. doi:10.1021/ja00104a039
[26] Hobza, P. and Zahradnik, R. (1988) Intermolecular interactions between medium-sized systems. Nonempirical and empirical calculations of interaction energies. Successes and failures. Chemical Review, 88, 871-897. doi:10.1021/cr00088a004
[27] Hobza, P., Sponer, J. and Leszczynski, J. (1997) Comment on electron-correlated calculations of electric properties of nucleic acid bases. Journal of Physical Chemistry B, 101, 8038-8039. doi:10.1021/jp970622f
[28] Frisch, M.J., Trucks, G.W., Schlegel, H.B., Gill, P.M.W., Johnson, B.G., Robb, M.A., Cheeseman, J.R., Keith, T., Petersson, G.A., Montgomery, J.A., Raghavachari, K., Al- Laham, M.A., Zakrzewaki, V.G., Ortiz, J.V., Foresmann, J.B., Ciolowski, J., Stefanov, B.B., Nama- yakkara, A., Challacombe, M., Peng, C.Y., Ayala, P.Y., Chen, W., Wong, M.W., Andres, J.L., Replogle, E.S., Gomperts, R., Martin, R.L., Fox, D.J., Binkley, J.S., Defrees, D.J., Baker, J., Stewart, J.P., Head-Gordon, M., Gonzalez, C. and Pople,
[29] Medhi, C. and Kalita, R. (2008) Join Molecule, Department of Chemistry , Gauhati University.

comments powered by Disqus

Copyright © 2018 by authors and Scientific Research Publishing Inc.

Creative Commons License

This work and the related PDF file are licensed under a Creative Commons Attribution 4.0 International License.