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Handbook of Computational Chemistry pp 1277–1308Cite as

Metal Interactions with Nucleobases, Base Pairs, and Oligomer Sequences; Computational Approach

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Abstract

This review summarizes computational studies devoted to interactions of metal cations with nucleobases, nucleotides, and short oligonucleotides considered as DNA/RNA models. Since this topic is complex, basically only the results obtained using ab initio and DFT methods are discussed. Part I focuses mainly on the interactions of the isolated bases with metal cations in bare, hydrated, and ligated forms. First, interactions of bare cations with nucleobases in gas phase approach are mentioned. Later, solvation effects using polarizable continuum models are analyzed and a comparison with explicitly hydrated ions is presented. In Part II, adducts of alkali metal, metal of alkaline earth, and zinc group metal cations with canonical base pairs are discussed. A separate section is devoted to platinum complexes related to anticancer treatment. Stacked bases and larger systems are discussed in last section. Here, semiempirical methods and molecular modeling are also discussed due to extensive size of studied complexes.

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References

  • Ai, H. Q., Yang, A. B., & Li, Y. G. (2008). Theoretical study on the interactions between Zn2+ and adenine isomers in aqueous phase. Acta Physico-Chimica Sinica, 24, 1047.

    CAS  Google Scholar 

  • Allen, R. N., Shukla, M. K., Burda, J. V., & Leszczynski, J. (2006). Theoretical study of interaction of urate with Li+, Na+, K+, Be2+, Mg2+, and Ca2+ metal cations. The Journal of Physical Chemistry A, 110, 6139.

    Article  CAS  Google Scholar 

  • Andrushchenko, V., & Bouř, P. (2009). Infrared absorption detection of metal ion-deoxyguanosine monophosphate binding: Experimental and theoretical study. The Journal of Physical Chemistry B, 113, 283.

    Article  CAS  Google Scholar 

  • Anwander, E. H. S., Probst, M. M., & Rode, B. M. (1990). The influence of Li+, Na+, Mg2+, Ca2+, and Zn2+ ions on the hydrogen bonds of the Watson-Crick base pair. Biopolymers, 29, 757.

    Article  CAS  Google Scholar 

  • Arpalahti, J., & Lippert, B. (1990). Coordination of Aquated cis-Pt(II) Diamines to purine nucleosides. Kinetics of complex formation. Inorganic Chemistry, 29, 104.

    Google Scholar 

  • Baik, M.-H., Friesner, R. A., & Lippard, S. J. (2002). Theoretical study on the stability of N-glycosyl bonds: Why does N7-platination not promote depurination? Journal of the American Chemical Society, 124, 4495.

    Article  CAS  Google Scholar 

  • Baik, M. H., Friesner, R. A., & Lippard, S. J. (2003). Theoretical study of cisplatin binding to purine bases: Why does cisplatin prefer guanine over adenine? Journal of the American Chemical Society, 125, 14082.

    Article  CAS  Google Scholar 

  • Banas, P., Jurecka, P., Walter, N. G., Sponer, J., & Otyepka, M. (2009). Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM. Methods, 49, 202.

    Article  CAS  Google Scholar 

  • Bancroft, D. P., Lepre, C. A., & Lippard, S. J. (1990). Journal of the American Chemical Society, 112, 6860.

    Article  CAS  Google Scholar 

  • Bandyopadhyay, D., & Bhattacharyya, D. (2003). Different modes of interaction between hydrated magnesium ion and DNA functional groups: Database analysis and ab initio studies. Journal of Biomolecular Structure and Dynamics, 21, 447.

    Article  CAS  Google Scholar 

  • Basch, H., Krauss, M., Stevens, W. J., & Cohen, D. (1986). Binding of Pt(NH3)3 2+ to nucleic acid bases. Inorganic Chemistry, 25, 684.

    Article  CAS  Google Scholar 

  • Besker, N., Coletti, C., Marrone, A., & Re, N. (2007). Binding of antitumor ruthenium complexes to DNA and proteins: A theoretical approach. The Journal of Physical Chemistry B, 111, 9955.

    Article  CAS  Google Scholar 

  • Boys, S. F., & Bernardi, F. (1970). The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors. Molecular Physics, 19, 553.

    Google Scholar 

  • Burda, J. V., & Leszczynski, J. (2003). How strong can the bend be on a DNA helix from cisplatin? DFT and MP2 quantum chemical calculations of cisplatin-bridged DNA purine bases. Inorganic Chemistry, 42, 7162.

    Article  CAS  Google Scholar 

  • Burda, J. V., Sponer, J., & Hobza, P. (1996). Ab initio study of the interaction of guanine and adenine with various mono- and bivalent metal cations (Li+, Na+, K+, Rb+, Cs+; Cu+, Ag+, Au+; Mg2+, Ca2+, Sr2+, Ba2+; Zn2+, Cd2+, and Hg2+). Journal of Physical Chemistry, 100, 7250.

    Article  CAS  Google Scholar 

  • Burda, J. V., Sponer, J., Leszczynski, J., & Hobza, P. (1997). Interaction of DNA base pairs with various metal cations (Mg2+, Ca2+, Sr2+, Ba2+, Cu+, Ag+, Au+, Zn2+, Cd2+, and Hg2+): Nonempirical ab initio calculations on structures, energies, and nonadditivity of the interaction. The Journal of Physical Chemistry B, 101, 9670.

    Article  CAS  Google Scholar 

  • Burda, J. V., Sponer, J., & Leszczynski, J. (2000). The interactions of square platinum(II) complexes with guanine and adenine: A quantum-chemical ab initio study of metalated tautomeric forms. Journal of Biological Inorganic Chemistry, 5, 178.

    Article  CAS  Google Scholar 

  • Burda, J. V., Sponer, J., & Leszczynski, J. (2001). The influence of square planar platinum complexes on DNA base pairing. An ab initio DFT study. Physical Chemistry Chemical Physics, 3, 4404.

    Google Scholar 

  • Burda, J. V., Sponer, J., Hrabadkova, J., Zeizinger, M., & Leszczynski, J. (2003). The influence of N-7 guanine modifications on the strength of Watson-Crick base pairing and guanine N-1 acidity: Comparison of gas-phase and condensed-phase trends. The Journal of Physical Chemistry B, 107, 5349.

    Article  CAS  Google Scholar 

  • Burda, J. V., Pavelka, M., & Simanek, M. (2004). Theoretical model of copper Cu(I)/Cu(II) hydration. DFT and ab initio quantum chemical study. Journal of Molecular Structure-Theochem, 683, 183.

    Google Scholar 

  • Burda, J. V., Shukla, M. K., & Leszczynski, J. (2005). Theoretical model of the aqua-copper [Cu(H2O)(5)](+) cation interactions with guanine. Journal of Molecular Modeling, 11, 362.

    Article  CAS  Google Scholar 

  • Chu, V. B., Bai, Y., Lipfert, J., Herschlag, D., & Doniach, S. (2008). A repulsive field: advances in the electrostatics of the ion atmosphere. Current Opinion in Chemical Biology, 12, 619–625.

    Article  CAS  Google Scholar 

  • Chval, Z., & Sip, M. (2003). Transition states of cisplatin binding to guanine and adenine: Ab initio reactivity study. Collection of Czechoslovak Chemical Communications, 68, 1105.

    Article  CAS  Google Scholar 

  • Colominas, C., Luque, F. J., & Orozco, M. (1996). Tautomerism and protonation of guanine and cytosine. Implications in the formation of hydrogen-bonded complexes. Journal of the American Chemical Society, 118, 6811.

    Google Scholar 

  • Del Bene, J. E. (1984). Molecular orbital study of the Li+ complexes of the DNA bases. Journal of Physical Chemistry, 88, 5927.

    Article  Google Scholar 

  • Del Bene, J. E. (1985). Molecular orbital theory of the hydrogen bond. Journal of Molecular Structure, 124, 201.

    Article  Google Scholar 

  • Deubel, D. V. (2003). Reactivity of osmium tetraoxide towards nitrogen heterocycles: Implications for the molecular recognition of DNA mismatch. Angewandte Chemie International Edition, 42, 1974.

    Article  CAS  Google Scholar 

  • Draper, D. E., Grilley, D., & Soto, A. M. (2005). Annual Review of Biophysics and Biomolecular Structure, 34, 221.

    Article  CAS  Google Scholar 

  • Egli, M., & Gessner, R. V. (1995). Stereoelectronic effects of deoxyribose O4′ on DNA conformation. Proceedings of the National Academy of Sciences of the United States of America, 92, 180.

    Article  CAS  Google Scholar 

  • Egli, M., Williams, L. D., Frederick, C. A. & Rich, A. (1991). DNA-Nogalamycin Interactions, Biochemistry, 30, 1364–1372.

    Article  CAS  Google Scholar 

  • Elmahdaoui, L., & Tajmirriahi, H. (1995). A Comparative-study Of Atp and Gtp complexation with trivalent Al, Ga and Fe cations - Determination of cation-binding site and nucleotide conformation by FTIR difference spectroscopy. Journal of Biomolecular Structure and Dynamics, 13, 69.

    Article  CAS  Google Scholar 

  • Fuentes-Cabrera, M., Sumpter, B. G., & Sponer, J. E. (2007). Theoretical study on the structure, stability, and electronic properties of the guanine-Zn-cytosine base pair in M-DNA. The Journal of Physical Chemistry B, 111, 870.

    Article  CAS  Google Scholar 

  • Futera, Z., Klenko, J., Sponer, J. E., Sponer, J., & Burda, J. V. (2009). Interactions of the “piano-stool” ruthenium(II)(eta(6)-arene)(en)Cl (+) complexes with water and nucleobases; ab initio and DFT study. Journal of Computational Chemistry, 30, 1758.

    Article  CAS  Google Scholar 

  • Gresh, N., Šponer, J. E., Špaková, N., Leszczynski J., & Šponer, J.(2003). Theoretical study of binding of hydrated cations Zn(II) and Mg(II) to guanosine 5′ monophosphate. Towards polarizable molecular mechanics for DNA and RNA. The Journal of Physical Chemistry B, 107, 8669.

    Google Scholar 

  • Gu, J. D., & Leszczynski, J. (2000). A remarkable alteration in the bonding pattern: An HF and DFT study of the interactions between the metal cations and the Hoogsteen hydrogen-bonded G-tetrad. The Journal of Physical Chemistry A, 104, 6308.

    Article  CAS  Google Scholar 

  • Hud, N. V., Smith, F. W., Anet, F. A. L., & Feigon, J. (1996). The selectivity for K+ versus Na+ in DNA quadruplexes is dominated by relative free energies of hydration: A thermodynamic analysis by 1H NMR. Biochemistry, 35, 15383.

    Article  CAS  Google Scholar 

  • Hud, N. V., Schultze, P., & Feigon, J. (1998). Journal of the American Chemical Society, 120, 6403.

    Article  CAS  Google Scholar 

  • Ida, R., & Wu, G. (2008). Direct NMR detection of alkali metal ions bound to G-quadruplex DNA. Journal of the American Chemical Society, 130, 3590.

    Article  CAS  Google Scholar 

  • Kabeláč, M., & Hobza, P. (2006). Na+, Mg2+, and Zn2+ binding to all tautomers of adenine, cytosine, and thymine and the eight most stable keto/enol tautomers of guanine: A correlated ab initio quantum chemical study. The Journal of Physical Chemistry B, 110, 14515.

    Article  Google Scholar 

  • Korolev, N., Lyubartsev, A. P., & Nordenskiold, L. (2002). Application of the Poisson Boltzmann polyelectrolyte model for analysis of equilibria between single-, double-, and triple-stranded polynucleotides in the presence of K+, Na+, and Mg2+ ions. Journal of Biomolecular Structure and Dynamics, 20, 275.

    Article  CAS  Google Scholar 

  • Kosenkov, D., Gorb, L., Shishkin, O. V., Sponer, J., & Leszczynski, J. (2008). Tautomeric equilibrium, stability, and hydrogen bonding in 2′-deoxyguanosine monophosphate complexed with Mg2+. The Journal of Physical Chemistry B, 112, 150.

    Article  CAS  Google Scholar 

  • Lide, D. R. (1977). CRC Handbook of chemistry and physics. Cleveland: CRC.

    Google Scholar 

  • Lilley, D. M. J., & Eckstein, F. (2008). Ribozymes and RNA catalysis. Cambridge: Royal Society of Chemistry.

    Google Scholar 

  • Lipinski, J. (1989). Electronic structure of platinum(ii) antitumor complexes and their interactions with nucleic acid bases. Part ii. Journal of Molecular Structure (Theochem), 201, 295.

    Google Scholar 

  • Marino, T., Toscano, M., Russo, N., & Grand, A., (2004). Gas-phase interaction between DNA and RNA bases and copper(II) ion: A density functional study. International Journal of Quantum Chemistry, 98, 347.

    Article  CAS  Google Scholar 

  • Martinez, J. M., Elmroth, S. K. C., & Kloo, L. (2001). Influence of sodium ions on the dynamics and structure of single-stranded DNA oligomers: A molecular dynamics study. Journal of the American Chemical Society, 123, 12279.

    Article  CAS  Google Scholar 

  • Matsubara, T., & Hirao, K. (2002). Density functional study of the binding of the cyclen-coordinated M(II) (M = Zn, Cu, Ni) complexes to the DNA base. Why is Zn better to bind? Journal of Molecular Structure-Theochem, 581, 203.

    Google Scholar 

  • Meyer, M., Steinke, T., & Brandl, M. (2001). Density functional study of guanine and uracil quartets and of guanine quartet/metal ion complexes. Journal of Computational Chemistry, 22, 109.

    Article  CAS  Google Scholar 

  • Monajjemi, M., Ghiasi, R., Ketabi, S., Passdar, H., & Mollaamin, F. (2004). A theoretical study of metal-stabilised rare tautomers stability: N4 metalated cytosine (M=Be2+, Mg2+, Ca2+, Sr2+ and Ba2+) in gas phase and different solvents. Journal of Chemical Research-S, 2004(1), 11. http://stl.publisher.ingentaconnect.com/content/stl/jcr

  • Montrel, M., Chuprina, V. P., Poltev, V. I., Nerdal, W., & Sletten, E. (1998). Sequence-dependent binding of metal ion to DNA oligomeres. A comparison of molecular electrostatic potentials with NMR data. Journal of Biomolecular Structure and Dynamics, 16, 631.

    Google Scholar 

  • Noguera, M., Bertran, J., & Sodupe, M. (2004). A quantum chemical study of Cu2+ interacting with guanine-cytosine base pair. Electrostatic and oxidative effects on intermolecular proton-transfer processes. The Journal of Physical Chemistry A, 108, 333.

    Google Scholar 

  • Noguera, M., Branchadell, V., Constantino, E., Rios-Font, R., Sodupe, M., & Rodriguez-Santiago, L. (2007). On the bonding of first-row transition metal cations to guanine and adenine nucleobases. The Journal of Physical Chemistry A, 111, 9823.

    Article  CAS  Google Scholar 

  • Noguera, M., Bertran, J., & Sodupe, M. (2008). Cu2+/+ cation coordination to adenine-thymine base pair. Effects on intermolecular proton-transfer processes. The Journal of Physical Chemistry B, 112, 4817.

    Google Scholar 

  • Parr, R. G., & Pearson, R. G. (1983). Absolute hardness: Companion parameter to absolute electronegativity. Journal of the American Chemical Society, 105, 7512.

    Article  CAS  Google Scholar 

  • Pavelka, M., & Burda, J. V. (2005). Theoretical description of copper Cu(I)/Cu(II) complexes in mixed ammine-aqua environment. DFT and ab initio quantum chemical study. Chemical Physics, 312, 193.

    Google Scholar 

  • Pavelka, M., Šimánek, M., Šponer, J., & Burda, J. V. (2006). Copper cation interactions with biologically essential types of ligands: A computational DFT study. The Journal of Physical Chemistry A, 110, 4795.

    Article  CAS  Google Scholar 

  • Pavelka, M., Shukla, M. K., Leszczynski, J., & Burda, J. V. (2008). Theoretical study of hydrated copper(II) interactions with guanine: A computational density functional theory study. The Journal of Physical Chemistry A, 112, 256.

    Article  CAS  Google Scholar 

  • Petrov, A. S., Lamm, G., & Pack, G. R. (2005). Calculation of the binding free energy for magnesium - RNA interactions. Biopolymers, 77, 137.

    Article  CAS  Google Scholar 

  • Poltev, V. I., Malenkov, G. G., Gonzales, E. J., Teplukhin, A. V., Rein, R., Shibata, M., & Miller, J. H. (1996). Modeling DNA hydration: Comparison of calculated and experimental hydration properties of nuclic acid bases. Journal of Biomolecular Structure and Dynamics, 13, 717.

    Article  CAS  Google Scholar 

  • Potaman, V. N., & Soyfer, V. N. (1994). Divalent metal cations upon coordination to the N7 of purines differentially stabilize the PyPuPu DNA triplex due to unequal Hoogsteen-type hydrogen bond enhancement. Journal of biomolecular structure and dynamics, 11, 1035.

    Article  CAS  Google Scholar 

  • Pyykko, P. (1988). Relativistic effects in structural chemistry. Chemical Reviews, 88, 563.

    Article  CAS  Google Scholar 

  • Raber, J., Zhu, C., & Eriksson, L. A., (2005). Theoretical study of cisplatin binding to DNA: The importance of initial complex stabilisation. ournal of Physical Chemistry, 109, 11006.

    Google Scholar 

  • Rosenberg, B., Van Camp, L., & Krigas, T. (1965). Inhibition of cell division in Escherichia coli by electrolysis products from a platinum electrode. Nature, 205, 698.

    Article  CAS  Google Scholar 

  • Rosenberg, B., Van Camp, L., Trosko, J. L., & Mansour, V. H. (1969). Platinum drugs; a new class of potent antitumor agents. Nature, 222, 385.

    Article  CAS  Google Scholar 

  • Rozsnyai, F., & Ladik, J. (1970). Calculation of effects of hydration and divalent metal ions on DNA base pairs. Bulletin of the American Physical Society, 15, 325.

    Google Scholar 

  • Rulíšek, L., & Šponer, J. (2003). Outer-shell and inner-shell coordination of phosphate group to hydrated metal ions (Mg2+, Cu,2+Zn2+, Cd2+) in the presence and absence of nucleobase. The role of nonelectrostatic effects. The Journal of Physical Chemistry B, 107, 1913.

    Google Scholar 

  • Russo, N., Toscano, M., & Grand, A. (2001). Bond energies and attachments sites of sodium and potassium cations to ONA and RNA nucleic acid bases in the gas phase. Journal of the American Chemical Society, 123, 10272.

    Article  CAS  Google Scholar 

  • Saenger, W. (1983). Principles of nucleic acid structure. New York: Springer.

    Google Scholar 

  • Schmidt, K. S., Reedijk, J., Weisz, K., Basilio Janke, E. M., Sponer, J. E., Sponer, J. & Lippert, B. (2002). Loss of Hoogsteen pairing ability upon N1 adenine platinum binding. Inorganic Chemistry, 41, 2855.

    Article  CAS  Google Scholar 

  • Schreiber, M., & Gonzalez, L. (2007). Structure and bonding of Ag(I)-DNA base complexes and Ag(I)-adenine-cytosine mispairs: An ab initio study. Journal of Computational Chemistry, 28, 2299.

    Article  CAS  Google Scholar 

  • Schreiber, M., & Gonzalez, L. (2007). The role of Ag(I) ions in the electronic spectroscopy of adenine-cytosine mispairs A MS-CASPT2 theoretical study. Journal of Photochemistry and Photobiology A: Chemistry, 190, 301.

    Article  CAS  Google Scholar 

  • Setnicka, V., Novy, J., Bohm, S., Sreenivasachary, N., Urbanova, M., & Volka, K. (2008). Molecular structure of guanine-quartet supramolecular assemblies in a gel-state based on a DFT calculation of infrared and vibrational circular dichroism spectra. Langmuir, 24, 7520.

    Article  CAS  Google Scholar 

  • Sigel, H. (1993). Interactions of metal ions with nucleotides and nucleic acids and their constituents. Chemical Society Reviews, 22(4), 255.

    Article  CAS  Google Scholar 

  • Sigel, R. K. O., & Lippert, B. (1999). PtII coordination to guanine-N7: Enhancement of the stability of the Watson–Crick base pair with cytosine. Chemical Communications, 21(1999), 2167.

    Article  Google Scholar 

  • Šponer, J., & Spackova, N. (2007). Molecular dynamics simulations and their application to four-stranded DNA. Methods, 43, 278.

    Article  Google Scholar 

  • Šponer, J., Burda, J. V., Mejzlik, P., Leszczynski, J., & Hobza, P. (1997). Hydrogen-bonded trimers of DNA bases and their interaction with metal cations: Ab initio quantum-chemical and empirical potential study. Journal of Biomolecular Structure and Dynamics, 14, 613.

    Article  Google Scholar 

  • Šponer, J., Burda, J. V., Sabat, M., Leszczynski, J., & Hobza, P. (1998). Interaction between the guanine-cytosine Watson-Crick DNA base pair and hydrated group IIa (Mg2+, Ca2+, Sr2+, Ba2+) and group IIb (Zn2+, Cd2+, Hg2+) metal cations. The Journal of Physical Chemistry A, 102, 5951.

    Google Scholar 

  • Šponer, J., Burda, J., Leszczynski, J., & Hobza, P. (1999). Interactions of hydrated IIa and IIb group metal cations with thioguanine-cytosine DNA base pair: Ab initio and density functional theory investigation of polarization effects, differences among cations, and flexibility of the cation hydration shell. Journal of Biomolecular Structure and Dynamics, 17, 631.

    Google Scholar 

  • Šponer, J., Sabat, M., Burda, J. V., Leszczynski, J., & Hobza, P. (1999). Interaction of the adenine-thymine Watson-Crick and adenine-adenine reverse-Hoogsteen DNA base pairs with hydrated group IIa (Mg2+, Ca2+, Sr2+, Ba2+) and IIb (Zn2+, Cd2+, Hg2+) metal cations: Absence of the base pair stabilization by metal-induced polarization effects. The Journal of Physical Chemistry B, 103, 2528.

    Article  Google Scholar 

  • Šponer, J., Sabat, M., Burda, J. V., Leszczynski, J., Hobza, P., & Lippert, B. (1999). Metal ions in non-complementary DNA base pairs: An ab initio study of Cu(I), Ag(I), and Au(I) complexes with the cytosine-adenine base pair. Journal of Biological Inorganic Chemistry, 4, 537.

    Article  Google Scholar 

  • Šponer, J., Sponer, J. E., Gorb, L., Leszczynski, J., & Lippert, B. (1999). Metal-stabilized rare tautomers and mispairs of DNA bases: N6-metalated adenine and N4-metalated cytosine, theoretical and experimental views. The Journal of Physical Chemistry A, 103, 11406.

    Article  Google Scholar 

  • Šponer, J., Sabat, M., Gorb, L., Leszczynski, J., Lippert, B., & Hobza, P. (2000). The effect of metal binding to the N7 site of purine nucleotides on their structure, energy, and involvement in base pairing. The Journal of Physical Chemistry B, 104, 7535.

    Article  Google Scholar 

  • Šponer, J., Šponer, J. E., & Leszczynski, J. (2000). Cation – pi and amino-acceptor interactions between hydrated metal cations and DNA bases. A quantum-chemical view. Journal of Biomolecular Structure and Dynamics, 17, 1087.

    Google Scholar 

  • Šponer, J. E., Leszczynski, J., Glahe, F., Lippert, B., & Šponer, J. (2001). Protonation of platinated adenine nucleobases. Gas phase vs condensed phase picture. Inorganic Chemistry, 40, 3269.

    Google Scholar 

  • Sychrovsky, V., Sponer, J., & Hobza, P. (2004). Theoretical calculation of the NMR spin-spin coupling constants and the NMR shifts allow distinguishability between the specific direct and the water-mediated binding of a divalent metal cation to guanine. Journal of the American Chemical Society, 126, 663.

    Article  CAS  Google Scholar 

  • Tanaka, Y., Kojima, C., Morita, E. H., Kasai, Y., Yamasaki, K., Ono, A., Kainosho, M., & Taira, K. (2002). Identification of the metal Ion binding site on an RNA motif from hammerhead ribozymes using 15N NMR spectroscopy. Journal of the American Chemical Society, 124, 4595.

    Article  CAS  Google Scholar 

  • van der Wijst, T., Guerra, C. F., Swart, M., Bickelhaupt, F. M., & Lippert, B. (2009). Rare tautomers of 1-Methyluracil and 1-Methylthymine: Tuning relative stabilities through coordination to Pt-II complexes. Chemistry – A European Journal, 15, 209.

    Google Scholar 

  • Varnali, T., & Tozumcalgan, D. (1995). Interaction of divalent metal-cations and nucleotides – A computational study. The Journal of Structural Chemistry, 6, 343.

    Article  CAS  Google Scholar 

  • Zeizinger, M., Burda, J. V., & Leszczynski, J. (2004). The influence of a sugar-phosphate backbone on the cisplatin-bridged BpB′ models of DNA purine bases. Quantum chemical calculations of Pt(II) bonding characteristics. Physical Chemistry Chemical Physics, 6, 3585.

    Google Scholar 

  • Zhang, Y., & Huang, K. X. (2007). The influence of the hydrated metal cations binding to adenine-N7 or adenine-N3 on the hydrogen bonding in adenine-thymine base pair: A comparative study. Journal of Molecular Structure: Theochem, 822, 57.

    Article  CAS  Google Scholar 

  • Zilberberg, I. L., Avdeev, V. I., & Zhidomirov, G. M. (1997). Effect of cisplatin binding on guanine in nucleic acid: An ab initio study. Journal of Molecular Structure (Theochem), 418, 73–81.

    Article  CAS  Google Scholar 

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Acknowledgments

The study was supported by projects MSM 0021620835, Grant Agency of the Czech Republic (GAČR) No P205/10/0228 (JVB) and GAČR No. 203/09/1476 (JS). The work in the USA was supported by the NSF CREST Grant No. 9805465. The authors thank the Meta-Centers in Prague (Charles University and Czech Technical University), Brno (Masaryk University), and Pilsen (University of West Bohemia) for the generous support of the computational resources.

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Authors and Affiliations

  1. Charles University in Prague, Ke Karlovu 3, 12116, Prague 2, Czech Republic

    Jaroslav V Burda

  2. Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic

    Jiřı́ Šponer

  3. Interdisciplinary Nanotoxicity Center, Department of Chemistry and Biochemistry, Jackson State University, 1400 J. R. Lynch Street, P.O. Box 17910, 39217, Jackson, Mississippi, USA

    Jerzy Leszczynski

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  1. Jaroslav V Burda
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  1. Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS, 39217, USA

    Jerzy Leszczynski

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Burda, J., Šponer, J., Leszczynski, J. (2012). Metal Interactions with Nucleobases, Base Pairs, and Oligomer Sequences; Computational Approach. In: Leszczynski, J. (eds) Handbook of Computational Chemistry. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-0711-5_36

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