Skip to main content
SpringerLink
Log in
Book cover

Handbook of Computational Chemistry pp 1827–1874Cite as

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

  • Reference work entry
  • First Online:

Abstract

This chapter concerns some of the computational studies devoted to interactions of metal cations with nucleobases, nucleotides, and short oligonucleotides considered as DNA/RNA models. Our topic is fairly complex, therefore the results obtained using mainly ab initio and DFT methods are discussed. The first part focuses on the interactions of isolated bases with metal cations either in bare, hydrated, or ligated forms. We begin with interactions of naked cations with nucleobases in gas phase. Subsequently, solvation effects using polarizable continuum models are analyzed together with a comparison to explicitly hydrated ions. In the second part, adducts of various metals with base pairs and oligomeric models of DNA/RNA are discussed. Separate sections are devoted to complexes of promising anticancer drugs. Stacked bases and larger systems (quadruplexes) studied by semiempirical and QM/MM methods are mentioned in the last part.

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   1,099.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD   1,399.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Bibliography

  • 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(6), 1047–1052.

    CAS  Google Scholar 

  • Alberto, M. E., Butera, V., & Russo, N. (2011). Which one among the Pt-containing anticancer drugs more easily forms monoadducts with G and A DNA bases? A comparative study among oxaliplatin, nedaplatin, and carboplatin. Inorganic Chemistry, 50(15), 6965–6971. doi:10.1021/ic200148n.

    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. Journal of Physical Chemistry A, 110, 6139–6144.

    CAS  Google Scholar 

  • Andrushchenko, V., & Bour, P. (2009). Infrared absorption detection of metal ion-deoxyguanosine monophosphate binding: Experimental and theoretical study. Journal of Physical Chemistry B, 113(1), 283–291. doi:10.1021/jp8058678.

    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, 757–769.

    CAS  Google Scholar 

  • Aquino, A. J. A., Tunega, D., Haberhauer, G., Gerzabek, M. H., & Lischka, H. (2008). Acid–base properties of a goethite surface model: A theoretical view. Geochimica et Cosmochimica Acta, 72, 3587–3602.

    CAS  Google Scholar 

  • Arpalahti, J., & Lippert, B. (1990). Coordination of aquated cis-platinum(II) diamines to purine nucleosides. Kinetics of complex formation. Inorganic Chemistry, 29, 104–109.

    CAS  Google Scholar 

  • Bagchi, S., Mandal, D., Ghosh, D., & Das, A. K. (2012). Density functional theory study of interaction, bonding and affinity of group IIb transition metal cations with nucleic acid bases. Chemical Physics, 400, 108–117. doi:10.1016/j.chemphys.2012.03.003.

    CAS  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, 4495–4503.

    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(46), 14082–14092.

    CAS  Google Scholar 

  • Banas, P., Jurecka, P., Walter, N. G., Šponer, J., & Otyepka, M. (2009). Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM methods. Methods, 49, 202–216.

    CAS  Google Scholar 

  • Bancroft, D. P., Lepre, C. A., & Lippard, S. J. (1990). Platinum-195 NMR kinetic and mechanistic studies of cis- and trans-diamminedichloroplatinum(II) binding to DNA. Journal of the American Chemical Society, 112, 6860–6867.

    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 & Dynamics, 21(3), 447–458.

    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, 684–688.

    CAS  Google Scholar 

  • Benda, L., Straka, M., Tanaka, Y., & Sychrovsky, V. (2011). On the role of mercury in the non-covalent stabilisation of consecutive U-HgII-U metal-mediated nucleic acid base pairs: Metallophilic attraction enters the world of nucleic acids. Physical Chemistry Chemical Physics, 13(1), 100–103. doi:10.1039/C0CP01534B.

    CAS  Google Scholar 

  • Benda, L., Straka, M., Sychrovský, V., Bouř, P., & Tanaka, Y. (2012). Detection of mercury–TpT dinucleotide binding by Raman spectra: A computational study. The Journal of Physical Chemistry. A, 116(32), 8313–8320. doi:10.1021/jp3045077.

    CAS  Google Scholar 

  • Benedikt, U., Schneider, W. B., & Auer, A. A. (2013). Modelling electrified interfaces in quantum chemistry: Constant charge vs. constant potential. Physical Chemistry Chemical Physics, 15, 2712–2724.

    CAS  Google Scholar 

  • Besker, N., Coletti, C., Marrone, A., & Re, N. (2007). Binding of antitumor ruthenium complexes to DNA and proteins: A theoretical approach. Journal of Physical Chemistry B, 111(33), 9955–9964. doi:10.1021/jp072182q.

    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, 553–566.

    CAS  Google Scholar 

  • Burda, J. V., & Gu, J. (2008). A computational study on DNA bases interactions with dinuclear tetraacetato-diaqua-dirhodium(II, II) complex. Journal of Inorganic Biochemistry, 102, 53–62.

    CAS  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(22), 7162–7172.

    CAS  Google Scholar 

  • Burda, J. V., Šponer, 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(17), 7250–7255.

    CAS  Google Scholar 

  • Burda, J. V., Šponer, 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. Journal of Physical Chemistry B, 101(46), 9670–9677.

    CAS  Google Scholar 

  • Burda, J. V., Šponer, 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(2), 178–188.

    CAS  Google Scholar 

  • Burda, J. V., Šponer, 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(19), 4404–4411.

    CAS  Google Scholar 

  • Burda, J. V., Šponer, J., Hrabáková, 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. Journal of Physical Chemistry B, 107(22), 5349–5356.

    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(1–3), 183–193. doi:10.1016/j.theochem.2004.06.013.

    CAS  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, 362–369.

    CAS  Google Scholar 

  • Burda, J. V., Murray, J. S., Gutierrez-Oliva, S., Politzer, P., & Toro-Labbe, A. (2015). Journal of Chemical Theory and Computation. Submitted.

    Google Scholar 

  • Ceron-Carrasco, J. P., & Jacquemin, D. (2011). Influence of Mg2+ on the guanine-cytosine tautomeric equilibrium: Simulations of the induced intermolecular proton transfer. Chemphyschem, 12(14), 2615–2623. doi:10.1002/cphc.201100264.

    CAS  Google Scholar 

  • Ceron-Carrasco, J. P., Jacquemin, D., & Cauet, E. (2012a). Cisplatin cytotoxicity: A theoretical study of induced mutations. Physical Chemistry Chemical Physics, 14(36), 12457–12464. doi:10.1039/C2CP40515F.

    Google Scholar 

  • Ceron-Carrasco, J. P., Requena, A., & Jacquemin, D. (2012b). Impact of DFT functionals on the predicted magnesium-DNA interaction: An ONIOM study. Theoretical Chemistry Accounts, 131(3). doi:10.1007/s00214-012-1188-9.

    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.

    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, 1105–1118.

    CAS  Google Scholar 

  • Chval, Z., Kabelac, M., & Burda, J. V. (2013). Mechanism of the cis- Pt(1R,2R-DACH)(H2O)(2) (2+) intrastrand binding to the double-stranded (pGpG)center dot(CpC) dinucleotide in aqueous solution: A computational DFT study. Inorganic Chemistry, 52(10), 5801–5813. doi:10.1021/ic302654s.

    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(29), 6811–6821.

    CAS  Google Scholar 

  • Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, J., Kenneth, M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., James Caldwell, J. W., & Kollman, P. A. (1995). A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. Journal of the American Chemical Society, 117, 5179–5197.

    CAS  Google Scholar 

  • Deeth, R. J. (2001). The ligand field molecular mechanics model and the stereoelectronic effects of d and s electrons. Coordination Chemistry Reviews, 212(1), 11–34. doi:10.1016/S0010-8545(00)00354-4.

    CAS  Google Scholar 

  • Deeth, R. J., Anastasi, A., Diedrich, C., & Randell, K. (2009). Molecular modelling for transition metal complexes: Dealing with d-electron effects. Coordination Chemistry Reviews, 253(5–6), 795–816. doi:10.1016/j.ccr.2008.06.018.

    CAS  Google Scholar 

  • Del Bene, J. E. (1984). Moleculat orbital study of the Li+ complexes of the DNA bases. Journal of Physical Chemistry, 88, 5927–5931.

    Google Scholar 

  • Del Bene, J. E. (1985). Molecular orbital theory of the hydrogen bond. Journal of Molecular Structure, 124, 201–212.

    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(17), 1974–1977. doi:10.1002/anie.200250462.

    CAS  Google Scholar 

  • Draper, D. E., Grilley, D., & Soto, A. M. (2005). Ions and RNA folding. Annual Review of Biophysics and Biomolecular Structure, 34, 221–243.

    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, 180–184.

    CAS  Google Scholar 

  • Egli, M., Williams, L. D., Fredericks, C. A., & Rich, A. (1991). DNA-nogalamycin interactions. Biochemistry, 30, 1364.

    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 & Dynamics, 13(1), 69–86.

    CAS  Google Scholar 

  • Fortino, M., Marino, T., & Russo, N. (2015). Theoretical study of silver-ion-mediated base pairs: The case of C–Ag–C and C–Ag–A systems. The Journal of Physical Chemistry. A, 119(21), 5153–5157. doi:10.1021/jp5096739.

    CAS  Google Scholar 

  • Frank Eckert, A. K. (2006). Accurate prediction of basicity in aqueous solution with COSMO-RS. Journal of Computational Chemistry, 27(1), 11–19.

    Google Scholar 

  • Fuentes-Cabrera, M., Sumpter, B. G., & Šponer, J. E. (2007). Theoretical study on the structure, stability, and electronic properties of the guanine–Zn–cytosine base pair in M-DNA. Journal of Physical Chemistry B, 111, 870–875.

    CAS  Google Scholar 

  • Futera, Z., & Burda, J. V. (2014). Reaction mechanism of Ru(II) piano-stool complexes: Umbrella sampling QM/MM MD study. Journal of Computational Chemistry, 35, 1446–1456.

    CAS  Google Scholar 

  • Futera, Z., Klenko, J., Šponer, J. E., Šponer, J., & Burda, J. V. (2009a). Interactions of the “Piano-stool” [Ruthenium(II)(g6-arene)(en)Cl]1 complexes with water and nucleobases; ab initio and DFT study. Journal of Computational Chemistry, 30, 1758–1770.

    CAS  Google Scholar 

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

    CAS  Google Scholar 

  • Futera, Z., Klenko, J., Šponer, J. E., Šponer, J., & Burda, J. V. (2009c). Interactions of the “Piano-stool” ruthenium(II)(eta(6)-arene)(en)Cl (+) complexes with water and nucleobases; A initio and DFT study. Journal of Computational Chemistry, 30(12), 1758–1770. doi:10.1002/jcc.21179.

    CAS  Google Scholar 

  • Futera, Z., Platts, J. A., & Burda, J. V. (2012). Binding of piano-stool Ru(II) complexes to DNA; QM/MM study. Journal of Computational Chemistry, 33, 2092–2101.

    CAS  Google Scholar 

  • Gkionis, K., Mutter, S. T., & Platts, J. A. (2013). QM/MM description of platinum-DNA interactions: Comparison of binding and DNA distortion of five drugs. RSC Advances, 3(12), 4066–4073. doi:10.1039/C3RA23041D>.

    CAS  Google Scholar 

  • Gkionis, K., Kruse, H., Platts, J. A., Mládek, A., Koča, J., & Šponer, J. (2014). Ion binding to quadruplex DNA stems. Comparison of MM and QM descriptions reveals sizable polarization effects not included in contemporary simulations. Journal of Chemical Theory and Computation, 10(3), 1326–1340. doi:10.1021/ct4009969.

    CAS  Google Scholar 

  • Gresh, N., Šponer, J. E., Špačková, 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, 8669–8681.

    CAS  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. Journal of Physical Chemistry A, 104(26), 6308–6313.

    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(48), 15383–15390.

    CAS  Google Scholar 

  • Hud, N. V., Schultze, P., & Feigon, J. (1998). Ammonium ion as an NMR probe for monovalent cation coordination sites of DNA quadruplexes. Journal of the American Chemical Society, 120, 6403–6408.

    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, 3590–3594.

    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. Journal of Physical Chemistry B, 110, 14515–14523.

    Google Scholar 

  • Klamt, A., & Schuurmann, G. (1993). Cosmo – A new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient. Journal of the Chemical Society, Perkin Transactions, 2(5), 799–805.

    Google Scholar 

  • Korth, M., Pitoňák, M., Řezáč, J., & Hobza, P. (2010). A transferable H-bonding correction for semiempirical quantum-chemical methods. Journal of Chemical Theory and Computation, 6(1), 344–352. doi:10.1021/ct900541n.

    CAS  Google Scholar 

  • Kosenkov, D., Gorb, L., Shishkin, O. V., Šponer, J., & Leszczynski, J. (2008). Tautomeric equilibrium, stability, and hydrogen bonding in 2’-deoxyguanosine monophosphate complexed with Mg2+. Journal of Physical Chemistry B, 112, 150–158.

    CAS  Google Scholar 

  • Kratochvílová, I., Golan, M., Vala, M., Špérová, M., Weiter, M., Páv, O., Šebera, J., Rosenberg, I., Sychrovský, V., Tanaka, Y., & Bickelhaupt, F. M. (2014). Theoretical and experimental study of charge transfer through DNA: Impact of mercury mediated T-Hg-T base pair. The Journal of Physical Chemistry B, 118(20), 5374–5381. doi:10.1021/jp501986a.

    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, 295–305.

    Google Scholar 

  • Marenich, A. V., Cramer, C. J., & Truhlar, D. G. (2009). Universal solvation model based on solute electron density and a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions. Journal of Physical Chemistry B, 113, 6378–6396.

    CAS  Google Scholar 

  • Margiotta, N., Petruzzella, E., Platts, J. A., Mutter, S. T., Deeth, R. J., Ranaldo, R., Papadia, P., Marzilli, P. A., Marzilli, L. G., Hoeschele, J. D., & Natile, G. (2015). DNA fragment conformations in adducts with Kiteplatin. Dalton Transactions, 44(8), 3544–3556. doi:10.1039/C4DT01796J.

    CAS  Google Scholar 

  • Marino, T. (2014). DFT investigation of the mismatched base pairs (T-Hg-T)3, (U-Hg-U)3, d(T-Hg-T)2, and d(U-Hg-U)2. Journal of Molecular Modeling, 20(6), 1–5. doi:10.1007/s00894-014-2303-8.

    CAS  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(4), 347–354.

    CAS  Google Scholar 

  • Marino, T., Mazzuca, D., Toscano, M., Russo, N., & Grand, A. (2007). Gas phase interaction of zinc ion with purine and pyrimidine DNA and RNA bases. International Journal of Quantum Chemistry, 107, 311–320.

    CAS  Google Scholar 

  • Marino, T., Mazzuca, D., Russo, N., Toscano, M., & Grand, A. (2010). On the interaction of rubidium and cesium mono-, strontium and barium bi-cations with DNA and RNA bases. A theoretical study. International Journal of Quantum Chemistry, 110(1), 138–147. doi:10.1002/qua.22076.

    CAS  Google Scholar 

  • Marino, T., Russo, N., Toscano, M., & Pavelka, M. (2012). Theoretical investigation on DNA/RNA base pairs mediated by copper, silver, and gold cations. Dalton Transactions, 41(6), 1816–1823. doi:10.1039/C1DT11028D.

    CAS  Google Scholar 

  • Martínez, J. M., Pappalardo, R. R., & Marcos, E. S. (1997). Study of the Ag+ hydration by means of a semicontinuum quantum-chemical solvation model. Journal of Physical Chemistry A, 101, 4444–4448.

    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, 203–213.

    CAS  Google Scholar 

  • Megger, D. A., Fonseca Guerra, C., Bickelhaupt, F. M., & Müller, J. (2011a). Silver(I)-mediated Hoogsteen-type base pairs. Journal of Inorganic Biochemistry, 105(11), 1398–1404. doi:10.1016/j.jinorgbio.2011.07.005.

    CAS  Google Scholar 

  • Megger, D. A., Fonseca Guerra, C., Hoffmann, J., Brutschy, B., Bickelhaupt, F. M., & Müller, J. (2011b). Contiguous metal-mediated base pairs comprising two AgI ions. Chemistry - A European Journal, 17(23), 6533–6544. doi:10.1002/chem.201002944.

    CAS  Google Scholar 

  • Mennucci, B., Cammi, R., & Tomasi, J. (1998). Excited states and solvatochromic shifts within a nonequilibrium solvation approach: A new formulation of the integral equation formalism method at the self-consistent field, configuration interaction, and multiconfiguration self-consistent field level. Journal of Chemical Physics, 109(7), 2798–2807.

    CAS  Google Scholar 

  • Meyer, M., & Sühnel, J. (2008). Density functional study of adenine tetrads with N6 − H6 · · · N3 hydrogen bonds. The Journal of Physical Chemistry. A, 112(18), 4336–4341. doi:10.1021/jp710242k.

    CAS  Google Scholar 

  • Meyer, M., Steinke, T., Brandl, M., & Suhnel, J. (2001). Density functional study of guanine and uracil quartets and of guanine quartet/metal ion complexes. Journal of Computational Chemistry, 22(1), 109–124.

    CAS  Google Scholar 

  • Meyer, M., Hocquet, A., & Sühnel, J. (2005). Interaction of sodium and potassium ions with sandwiched cytosine-, guanine-, thymine-, and uracil-base tetrads. Journal of Computational Chemistry, 26(4), 352–364. doi:10.1002/jcc.20176.

    CAS  Google Scholar 

  • Meyer, M., Steinke, T., & Sühnel, J. (2007). Density functional study of isoguanine tetrad and pentad sandwich complexes with alkali metal ions. Journal of Molecular Modeling, 13(2), 335–345. doi:10.1007/s00894-006-0148-5.

    CAS  Google Scholar 

  • Miertus, S., Scrocco, E., & Tomasi, J. (1981). Electrostatic interaction of a solute with a continuum. A direct utilizaion of AB initio molecular potentials for the prevision of solvent effects. Chemical Physics, 55(1), 117–129.

    CAS  Google Scholar 

  • Mlynsky, V., Walter, N. G., Šponer, J., Otyepka, M., & Banas, P. (2015). The role of an active site Mg2+ in HDV ribozyme self-cleavage: Insights from QM/MM calculations. Physical Chemistry Chemical Physics, 17(1), 670–679. doi:10.1039/C4CP03857F.

    CAS  Google Scholar 

  • Morari, C., Bogdan, D., & Muntean, C. M. (2012). Binding effects of Mn2+ and Zn2+ ions on the vibrational properties of guanine-cytosine base pairs in the Watson-Crick and Hoogsteen configurations. Journal of Molecular Modeling, 18(11), 4781–4786. doi:10.1007/s00894-012-1480-6.

    CAS  Google Scholar 

  • Morari, C., Muntean, C. M., Tripon, C., Buimaga-Iarinca, L., & Calborean, A. (2014). DFT investigation of the vibrational properties of GC Watson-Crick and Hoogsteen base pairs in the presence of Mg2+, Ca2+, and Cu2+ ions. Journal of Molecular Modeling, 20(4). doi:10.1007/s00894-014-2220-x.

    Google Scholar 

  • Mukhopadhyay, A., Aguilar, B. H., Tolokh, I. S., & Onufriev, A. V. (2014). Introducing charge hydration asymmetry into the generalized born model. Journal of Chemical Theory and Computation, 10, 1788–1794.

    CAS  Google Scholar 

  • Mutter, S., Margiotta, N., Papadia, P., & Platts, J. (2015). Computational evidence for structural consequences of kiteplatin damage on DNA. JBIC, Journal of Biological Inorganic Chemistry, 20(1), 35–48. doi:10.1007/s00775-014-1207-5.

    CAS  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. Journal of Physical Chemistry A, 108(2), 333–341. doi:10.1021/jp036573q.

    CAS  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. Journal of Physical Chemistry A, 111(39), 9823–9829. doi:10.1021/jp073858k.

    CAS  Google Scholar 

  • Noguera, M., Bertran, J., & Sodupe, M. (2008). Cu2+/+ cation coordination to adenine-thymine base pair. Effects on intermolecular proton-transfer processes. Journal of Physical Chemistry B, 112(15), 4817–4825. doi:10.1021/jp711982g.

    CAS  Google Scholar 

  • Oliva, R., & Cavallo, L. (2009). Frequency and effect of the binding of Mg2+, Mn2+, and Co2+ ions on the guanine base in Watson-Crick and reverse Watson-Crick base pairs. Journal of Physical Chemistry B, 113(47), 15670–15678. doi:10.1021/jp906847p.

    CAS  Google Scholar 

  • Parr, R. G., & Pearson, R. G. (1983). Absolute hardness: Companion parameter to absolute electronegativity. Journal of the American Chemical Society, 105(26), 7512–7516.

    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, 193–204. doi:10.1016/j.chemphys.2004.11.034.

    CAS  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. Journal of Physical Chemistry A, 110, 4795–4809.

    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. Journal of Physical Chemistry A, 112(2), 256–267. doi:10.1021/jp074891+.

    CAS  Google Scholar 

  • Petrov, A. S., Lamm, G., & Pack, G. R. (2005). Calculation of the binding free energy for magnesium – RNA interactions. Biopolymers, 77(3), 137–154.

    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(4), 717–725.

    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 & Dynamics, 11, 1035–1040.

    CAS  Google Scholar 

  • Raber, J., Zhu, C., & Eriksson, L. A. (2005). Theoretical study of cisplatin binding to DNA: The importance of initial complex stabilisation. Journal of Physical Chemistry, 109, 11006–11015.

    CAS  Google Scholar 

  • Reshetnikov, R. V., Šponer, J., Rassokhina, O. I., Kopylov, A. M., Tsvetkov, P. O., Makarov, A. A., & Golovin, A. V. (2011). Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process. Nucleic Acids Research, 39(22), 9789–9802. doi:10.1093/nar/gkr639.

    CAS  Google Scholar 

  • Řezáč, J., Fanfrlík, J., Salahub, D., & Hobza, P. (2009). Semiempirical quantum chemical PM6 method augmented by dispersion and H-bonding correction terms reliably describes carious types of noncovalent complexes. Journal of Chemical Theory and Computation, 5(7), 1749–1760. doi:10.1021/ct9000922.

    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(4972), 698–699.

    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, 385–391.

    CAS  Google Scholar 

  • Roux, B., Yu, H. A., & Karplus, M. (1990). Molecular basis for the born model of ion solvation. Journal of Physical Chemistry, 94, 4683–4688.

    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(3), 325.

    Google Scholar 

  • Rulisek, 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. Journal of Physical Chemistry B, 107(8), 1913–1923. doi:10.1021/jp027058f.

    CAS  Google Scholar 

  • Russo, N., & Toscano, M., A. G. (2001). Lithium affinity for DNA and RNA nucleobases. The role of theoretical information in the elucidation of the mass spectrometry data. Journal of Physical Chemistry B, 105, 4735–4741.

    CAS  Google Scholar 

  • Russo, N., Toscano, M., & Grand, A. (2003). Gas-phase absolute Ca2+ and Mg2+ affinity for nucleic acid bases. A theoretical determination. Journal of Physical Chemistry A, 107(51), 11533–11538. doi:10.1021/jp0358681.

    CAS  Google Scholar 

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

    Google Scholar 

  • Santangelo, M. G., Antoni, P. M., Spingler, B., & Jeschke, G. (2010). Can copper(II) mediate Hoogsteen base-pairing in a left-handed DNA duplex? A pulse EPR study. ChemPhysChem, 11, 599–606.

    CAS  Google Scholar 

  • Schmidt, K. S., Reedijk, J., Weisz, K., Basilio Janke, E. M., Šponer, J. E., Šponer, J., & Lippert, B. (2002). Loss of Hoogsteen pairing ability upon N1 adenine platinum binding. Inorganic Chemistry, 41, 2855–2863.

    CAS  Google Scholar 

  • Schreiber, M., & Gonzalez, L. (2007a). Structure and bonding of Ag(I)-DNA base complexes and Ag(I)-adenine-cytosine mispairs: An ab initio study. Journal of Computational Chemistry, 28, 2299–2308. doi:10.1002/jcc.20743.

    CAS  Google Scholar 

  • Schreiber, M., & Gonzalez, L. (2007b). 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(2–3), 301–309. doi:10.1016/j.jphotochem.2007.01.035.

    CAS  Google Scholar 

  • Šebera, J., Burda, J. V., Straka, M., Ono, A., Kojima, C., Tanaka, Y., & Sychrovsky, V. (2013a). Formation of a thymine-Hg II -thymine metal-mediated DNA base pair: Proposal and theoretical calculation of the reaction pathway. Chemistry - A European Journal, 19, 9884–9894.

    Google Scholar 

  • Šebera, J., Burda, J., Straka, M., Ono, A., Kojima, C., Tanaka, Y., & Sychrovský, V. (2013b). Formation of a thymine-HgII-thymine metal-mediated DNA base pair: Proposal and theoretical calculation of the reaction pathway. Chemistry - A European Journal, 19(30), 9884–9894. doi:10.1002/chem.201300460.

    Google Scholar 

  • Šebesta, F., & Burda, J. V. (2016). Reduction process of tetraplatin in the presence of deoxyguanosine monophosphate (dGMP): A computational DFT study. Chemistry - A European Journal, 22, 1037–1047.

    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(14), 7520–7527. doi:10.1021/la800611h.

    CAS  Google Scholar 

  • Sigel, H. (1993). Interactions of metal ions with nucleotides and nucleic acids and their constituents. Chemical Society Reviews, 22, 255–267.

    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, 2167.

    Google Scholar 

  • Šponer, J., & Špackova, N. (2007). Molecular dynamics simulations and their application to four-stranded DNA. Methods, 43, 278–284.

    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 & Dynamics, 14(5), 613–628.

    Google Scholar 

  • Šponer, J., Burda, J. V., Sabat, M., Leszczynski, J., & Hobza, P. (1998a). 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. Journal of Physical Chemistry A, 102(29), 5951–5957.

    Google Scholar 

  • Šponer, J., Sabat, M., Burda, J. V., Doody, A. M., Leszczynski, J., & Hobza, P. (1998b). Stabilization of the purine center dot purine center dot pyrimidine DNA base triplets by divalent metal cations. Journal of Biomolecular Structure & Dynamics, 16(1), 139–143.

    Google Scholar 

  • Šponer, J., Sabat, M., Burda, J., Leszczynski, J., Hobza, P., & Lippert, B. (1999a). Metal ions in non-complementary DNA base pairs: An ab initio study of Cu(I), Ag(I), and Au(I) complexes with cytosine-adenine base pair. Journal of Biological Inorganic Chemistry, 4, 537–545.

    Google Scholar 

  • Šponer, J., Burda, J. V., Leszczynski, J., & Hobza, P. (1999b). 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 & Dynamics, 17(1), 61–77.

    Google Scholar 

  • Šponer, J., Šponer, J. E., Gorb, L., Leszczynski, J., & Lippert, B. (1999c). Metal-stabilized rare tautomers and mispairs of DNA bases: N6-metalated adenine and N4-metalated cytosine, theoretical and experimental views. Journal of Physical Chemistry A, 103, 11406–11413.

    Google Scholar 

  • Šponer, J., Sabat, M., Burda, J. V., Leszczynski, J., & Hobza, P. (1999d). 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. Journal of Physical Chemistry B, 103(13), 2528–2534.

    Google Scholar 

  • Šponer, J., Sabat, M., Burda, J. V., Leszczynski, J., Hobza, P., & Lippert, B. (1999e). 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(5), 537–545.

    Google Scholar 

  • Šponer, J., Šponer, J. E., & Leszczynski, J. (2000a). Cation – Pi and amino-acceptor interactions between hydrated metal cations and DNA bases. A quantum-chemical view. Journal of Biomolecular Structure and Dynamics, 17(6), 1087–1096.

    Google Scholar 

  • Šponer, J., Sabat, M., Gorb, L., Leszczynski, J., Lippert, B., & Hobza, P. (2000b). The effect of metal binding to the N7 site of purine nucleotides on their structure, energy, and involvement in base pairing. Journal of Physical Chemistry B, 104(31), 7535–7544. doi:10.1021/jp001711m.

    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, 3269–3278.

    Google Scholar 

  • Šponer, J., Mládek, A., Špačková, N., Cang, X., Cheatham, T. E., & Grimme, S. (2013). Relative stability of different DNA guanine quadruplex stem topologies derived using large-scale quantum-chemical computations. Journal of the American Chemical Society, 135(26), 9785–9796. doi:10.1021/ja402525c.

    Google Scholar 

  • Sychrovsky, V., Šponer, 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(2), 663–672.

    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, 4595–4601.

    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(1), 209–218. doi:10.1002/chem.200801476.

    Google Scholar 

  • Varnali, T., & Tozumcalgan, D. (1995). Interaction of divalent metal-cations and nucleotides – A computational study. Structural Chemistry, 6(4–5), 343–348.

    CAS  Google Scholar 

  • Wang, F. Y., Habtemariam, A., van der Geer, E. P. L., Fernandez, R., Melchart, M., Deeth, R. J., Aird, R., Guichard, S., Fabbiani, F. P. A., Lozano-Casal, P., Oswald, I. D. H., Jodrell, D. I., Parsons, S., & Sadler, P. J. (2005). Controlling ligand substitution reactions of organometallic complexes: Tuning cancer cell cytotoxicity. PNAS, 102(51), 18269–18274.

    CAS  Google Scholar 

  • Wu, Y. B., Bhattacharyya, D., King, C. L., Baskerville-Abraham, I., Huh, S. H., Boysen, G., Swenberg, J. A., Temple, B., Campbell, S. L., & Chaney, S. G. (2007). Solution structures of a DNA dodecamer duplex with and without a cisplatin 1,2-d(GG) intrastrand cross-link: Comparison with the same DNA duplex containing an oxaliplatin 1,2-d(GG) intrastrand cross-link. Biochemistry, 46(22), 6477–6487.

    CAS  Google Scholar 

  • Yamaguchi, H., Šebera, J., Kondo, J., Oda, S., Komuro, T., Kawamura, T., Daraku, T., Kondo, Y., Okamoto, I., Ono, A., Burda, J. V., Kojima, C., Sychrovský, V., & Tanaka, Y. (2014). The structure of metallo-DNA with consecutive T-HgII-T base-pairs ex-plains positive reaction entropy for the metallo-base-pair formation. Nucleic Acids Research, 42, 4094–4099.

    CAS  Google Scholar 

  • Yurenko, Y. P., Novotny, J., Sklenar, V., & Marek, R. (2014). Exploring non-covalent interactions in guanine- and xanthine-based model DNA quadruplex structures: A comprehensive quantum chemical approach. Physical Chemistry Chemical Physics, 16(5), 2072–2084. doi:10.1039/C3CP53875C.

    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(10), 3585–3590.

    CAS  Google Scholar 

  • Zhang, Y., & Huang, K. X. (2007). On the interactions of hydrated metal cations (Mg2+, Mn2+, Ni2+, Zn2+) with guanine-cytosine Watson-Crick and guanine-guanine reverse-Hoogsteen DNA base pairs. Journal of Molecular Structure (THEOCHEM), 812(1–3), 51–62. doi:10.1016/j.theochem.2007.02.009.

    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.

    CAS  Google Scholar 

Download references

Acknowledgments

The study was supported by projects Grant Agency of the Czech Republic (GAČR) No. 16-06240S. The authors thank the Meta-Centers in Prague (Charles University and Czech Technical University), Brno (Masaryk University), Pilsen (University of West Bohemia) for the generous support of the computational resources.

Author information

Authors and Affiliations

  1. Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 3, 12116, Prague 2, Czech Republic

    Jaroslav V. Burda & Filip Šebesta

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

    Jiří Šponer

Authors
  1. Jaroslav V. Burda
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jiří Šponer
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Filip Šebesta
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jaroslav V. Burda .

Editor information

Editors and Affiliations

  1. Department of Chemistry and Biochemistry, Interdisciplinary Center for Nanotoxicity, Jackson State University, Jackson, Mississippi, USA

    Jerzy Leszczynski

  2. Faculty of Chemistry, Nicolaus Copernicus University, Toruń, Poland

    Anna Kaczmarek-Kedziera

  3. Laboratory of Environmental Chemometrics, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland

    Tomasz Puzyn

  4. Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece

    Manthos G. Papadopoulos

  5. Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece

    Heribert Reis

  6. US Army Engineer Research and Development Center, Vicksburg, Mississippi, USA

    Manoj K. Shukla

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer International Publishing Switzerland

About this entry

Cite this entry

Burda, J.V., Šponer, J., Šebesta, F. (2017). Metal Interactions with Nucleobases, Base Pairs, and Oligomer Sequences; Computational Approach. In: Leszczynski, J., Kaczmarek-Kedziera, A., Puzyn, T., G. Papadopoulos, M., Reis, H., K. Shukla, M. (eds) Handbook of Computational Chemistry. Springer, Cham. https://doi.org/10.1007/978-3-319-27282-5_36

Download citation

Publish with us

Policies and ethics

Search

Navigation