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Volumn , Issue , 2006, Pages 389-410

Interaction of metal cations with nucleic acids and their building units: A comprehensive view from quantum chemical calculations

Author keywords

DFT; DNA; metals; nucleic acids; quantum chemistry; RNA

Indexed keywords


EID: 84889960886     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-4020-4851-3_15     Document Type: Chapter
Times cited : (9)

References (50)
  • 1
    • 33845376625 scopus 로고
    • New perspectives on the essential trace-elements
    • Frieden, E. J. (1985). New perspectives on the essential trace-elements. J. Chem. Ed. 62, 917-923.
    • (1985) J. Chem. Ed. , vol.62 , pp. 917-923
    • Frieden, E.J.1
  • 4
    • 3042609925 scopus 로고    scopus 로고
    • Nteractions of hydrated divalent metal cations with nucleic acid bases. how to relate the gas phase data to solution situation and binding selectivity in nucleic acids
    • Šponer, J. E., Sychrovský, V., Hobza, P., and Šponer, J. (2004). Interactions of hydrated divalent metal cations with nucleic acid bases. How to relate the gas phase data to solution situation and binding selectivity in nucleic acids. Phys. Chem. Chem. Phys. 6, 2772-2780.
    • (2004) Phys. Chem. Chem. Phys. , vol.6 , pp. 2772-2780
    • Šponer, J.E.1    Sychrovský, V.2    Hobza, P.3    Šponer, J.4
  • 7
    • 0346456864 scopus 로고    scopus 로고
    • 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
    • Sychrovský, V., Šponer, J. and 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. J. Am. Chem. Soc. 126, 663-672.
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 663-672
    • Sychrovský, V.1    Šponer, J.2    Hobza, P.3
  • 8
    • 0033581166 scopus 로고    scopus 로고
    • Manganese as a replacement for magnesium and zinc: Functional comparison of the divalent ions
    • Bock, C. W., Katz, A. K., Markham, G. D. and Glusker, J. P. (1999). Manganese as a replacement for magnesium and zinc: Functional comparison of the divalent ions. J. Am. Chem. Soc. 121, 7360-7372.
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 7360-7372
    • Bock, C.W.1    Katz, A.K.2    Markham, G.D.3    Glusker, J.P.4
  • 9
    • 84889986890 scopus 로고    scopus 로고
    • Metal cation-nucleic acids interactions
    • (online edition), (von Ragué Schleyer, P., Schaefer, III, H. F., Schreiner, P. R., Jorgensen, W. L., Thiel, W. and Glen, R. C., eds), John Wiley & Sons, Chichester, doi:10.1002/0470845015.cn0094
    • Bertran, J., Sodupe, M., Šponer, J. and Šponer, J. E. (2005). Metal cation-nucleic acids interactions. In: Encyclopedia of Computational Chemistry (online edition), (von Ragué Schleyer, P., Schaefer, III, H. F., Schreiner, P. R., Jorgensen, W. L., Thiel, W. and Glen, R. C., eds), John Wiley & Sons, Chichester, doi:10.1002/0470845015.cn0094.
    • (2005) Encyclopedia of Computational Chemistry
    • Bertran, J.1    Sodupe, M.2    Šponer, J.3    Šponer, J.E.4
  • 10
    • 0025216553 scopus 로고
    • Tereochemistry of phosphate-lewis acid interactions-implications for nucleic-acid structure and recognition
    • Alexander, R. S., Kanyo, Z. F., Chirlian, L. E. and Christianson, D. W. (1990). Stereochemistry of phosphate-Lewis acid interactions-implications for nucleic-acid structure and recognition. J. Am. Chem. Soc. 112, 933-937.
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 933-937
    • Alexander, R.S.1    Kanyo, Z.F.2    Chirlian, L.E.3    Christianson, D.W.4
  • 11
    • 0030443476 scopus 로고    scopus 로고
    • Geometry of the phosphate group and its interactions with metal cations in crystals and ab initio calculations
    • Schneider, B., Kabelác, M. and Hobza, P. (1996). Geometry of the phosphate group and its interactions with metal cations in crystals and ab initio calculations. J. Am. Chem. Soc. 118, 12207-12217
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 12207-12217
    • Schneider, B.1    Kabelác, M.2    Hobza, P.3
  • 12
    • 0001659148 scopus 로고    scopus 로고
    • Theoretical study of complexation of phosphodiester linkage with alkali and alkaline-earth cations
    • Murashov, V. V. and J. Leszczynski (1999). Theoretical study of complexation of phosphodiester linkage with alkali and alkaline-earth cations. J. Phys. Chem. B 103, 8391-8397.
    • (1999) J. Phys. Chem. B , vol.103 , pp. 8391-8397
    • Murashov, V.V.1    Leszczynski, J.2
  • 14
    • 0036601149 scopus 로고    scopus 로고
    • The role of metal ions in rna catalysis
    • Fedor, M. J. (2002). The role of metal ions in RNA catalysis. Curr. Opin. Struct. Biol. 12, 289-295
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 289-295
    • Fedor, M.J.1
  • 15
    • 0034249870 scopus 로고    scopus 로고
    • The effect of metal binding to the n7 site of purine nucleotides on their structure, energy, and involvement in base pairing
    • Šponer, J., Sabat. M., Gorb, L., Leszczynski, J., Lippert, B. and Hobza, P. (2000). The effect of metal binding to the N7 site of purine nucleotides on their structure, energy, and involvement in base pairing. J. Phys. Chem. B 104, 7535-7544.
    • (2000) J. Phys. Chem. B , vol.104 , pp. 7535-7544
    • Šponer, J.1    Sabat, M.2    Gorb, L.3    Leszczynski, J.4    Lippert, B.5    Hobza, P.6
  • 16
    • 0043289936 scopus 로고    scopus 로고
    • Theoretical study of binding of hydrated zn(ii) and mg(ii) cations to 5'-guanosine monophosphate. toward polarizable molecular mechanics for dna and rna
    • Gresh, N, Šponer, J. E., Špacková, N. and Šponer, J. (2003). Theoretical study of binding of hydrated Zn(II) and Mg(II) cations to 5'-guanosine monophosphate. Toward polarizable molecular mechanics for DNA and RNA. J. Phys. Chem. B 107, 8669-8681.
    • (2003) J. Phys. Chem. B , vol.107 , pp. 8669-8681
    • Gresh, N.1    Šponer, J.E.2    Špacková, N.3    Šponer, J.4
  • 17
    • 0037468432 scopus 로고    scopus 로고
    • +) in the presence and absence of nucleobase. The role of nonelectrostatic effects
    • +) in the presence and absence of nucleobase. The role of nonelectrostatic effects. J. Phys. Chem. B 107, 1913-1923.
    • (2003) J. Phys. Chem. B , vol.107 , pp. 1913-1923
    • Rulíšek, L.1    Šponer, J.2
  • 20
    • 0035963771 scopus 로고    scopus 로고
    • + cation with bases, base pairs, and nucleotides. electron topology, natural bond orbital, electrostatic and vibrational study
    • + cation with bases, base pairs, and nucleotides. Electron topology, natural bond orbital, electrostatic and vibrational study. J. Phys. Chem. B 105, 6051-6060.
    • (2001) J. Phys. Chem. B , vol.105 , pp. 6051-6060
    • Munoz, J.1    Šponer, J.2    Hobza, P.3    Orozco, M.4    Luque, F.J.5
  • 22
    • 0035796190 scopus 로고    scopus 로고
    • Protonation of platinated adenine nucleobases. gas phase vs condensed phase picture
    • Šponer, J. E., Leszczynski, J., Glahe, F., Lippert, B. and Šponer, J. (2001). Protonation of platinated adenine nucleobases. Gas phase vs condensed phase picture. Inorg. Chem. 40, 3269-3278
    • (2001) Inorg. Chem. , vol.40 , pp. 3269-3278
    • Šponer, J.E.1    Leszczynski, J.2    Glahe, F.3    Lippert, B.4    Šponer, J.5
  • 23
    • 0000245686 scopus 로고    scopus 로고
    • Metal-stabilized rare tautomers and mispairs of dna bases: N6-metalated adenine and n4-metalated cytosine. theoretical and experimental views
    • Šponer, J., Šponer, J. E., Gorb, L., Leszczynski, J. and Lippert, B. (1999). Metal-stabilized rare tautomers and mispairs of DNA bases: N6-metalated adenine and N4-metalated cytosine. Theoretical and experimental views. J. Phys. Chem. A 103, 11406-11413.
    • (1999) J. Phys. Chem. A , vol.103 , pp. 11406-11413
    • Šponer, J.1    Šponer, J.E.2    Gorb, L.3    Leszczynski, J.4    Lippert, B.5
  • 24
    • 0034018494 scopus 로고    scopus 로고
    • He interactions of square platinum(ii) complexes with guanine and adenine: A quantum-chemical ab initio study of metalated tautomeric forms
    • Burda, J. V., Šponer, J. and Leszczynski, J. (2000). The interactions of square platinum(II) complexes with guanine and adenine: A quantum-chemical ab initio study of metalated tautomeric forms. J. Biol. Inorg. Chem. 5, 178-188
    • (2000) J. Biol. Inorg. Chem. , vol.5 , pp. 178-188
    • Burda, J.V.1    Šponer, J.2    Leszczynski, J.3
  • 26
    • 0035723011 scopus 로고    scopus 로고
    • He influence of square planar platinum complexes on dna base pairing. an ab initio dft study
    • Burda, J. V., Šponer, J. and Leszczynski, J. (2001). The influence of square planar platinum complexes on DNA base pairing. An ab initio DFT study. Phys. Chem. Chem. Phys. 3, 4404-4411.
    • (2001) Phys. Chem. Chem. Phys. , vol.3 , pp. 4404-4411
    • Burda, J.V.1    Šponer, J.2    Leszczynski, J.3
  • 27
    • 0037833728 scopus 로고    scopus 로고
    • 7 guanine modifications on the strength of watson-crick base pairing and guanine n1 acidity: Comparison of gas-phase and condensed-phase trends
    • 7 guanine modifications on the strength of Watson-Crick base pairing and guanine N1 acidity: Comparison of gas-phase and condensed-phase trends. J. Phys. Chem. B 107, 5349-5356.
    • (2003) J. Phys. Chem. B , vol.107 , pp. 5349-5356
    • Burda, J.V.1    Šponer, J.2    Hrabáková, J.3    Zeizinger, M.4    Leszczynski, J.5
  • 28
    • 0034126663 scopus 로고    scopus 로고
    • Effects of n7-methylation, n7-platination, and c8-hydroxylation of guanine on h-bond formation with cytosine: Platinum coordination strengthens the watson-crick pair
    • Siegel, R. K. O., Freisinger, E. and Lippert, B. (2000). Effects of N7-methylation, N7-platination, and C8-hydroxylation of guanine on H-bond formation with cytosine: Platinum coordination strengthens the Watson-Crick pair. J. Biol. Inorg. Chem. 5, 287-299.
    • (2000) J. Biol. Inorg. Chem. , vol.5 , pp. 287-299
    • Siegel, R.K.O.1    Freisinger, E.2    Lippert, B.3
  • 30
    • 20344379193 scopus 로고    scopus 로고
    • Hydration process as an activation of trans-and cisplatin complexes in anticancer treatment. dft and ab initio computational study of thermodynamic and kinetic parameters
    • Burda, J. V., Zeizinger, M. and Leszczynski, J. (2005). Hydration process as an activation of trans-and cisplatin complexes in anticancer treatment. DFT and ab initio computational study of thermodynamic and kinetic parameters. J. Comput. Chem. 26, 907-914.
    • (2005) J. Comput. Chem. , vol.26 , pp. 907-914
    • Burda, J.V.1    Zeizinger, M.2    Leszczynski, J.3
  • 31
    • 1542331447 scopus 로고    scopus 로고
    • The solvent effect on the aquation processes of the cis- dichloro(ethylenediammine)platinum(ii) using continuum solvation models
    • Costa, L. A. S., Rocha, W. R., De Almeida, W. B. and Dos Santos, H. F. (2004). The solvent effect on the aquation processes of the cis- dichloro(ethylenediammine)platinum(II) using continuum solvation models. Chem. Phys. Lett. 387, 182-187.
    • (2004) Chem. Phys. Lett. , vol.387 , pp. 182-187
    • Costa, L.A.S.1    Rocha, W.R.2    De Almeida, W.B.3    Dos Santos, F.H.4
  • 32
    • 0035861989 scopus 로고    scopus 로고
    • Unrestrained 5 ns molecular dynamics simulation of a cisplatin-dna 1, 2-gg adduct provides a rationale for the nmr features and reveals increased conformational flexibility at the platinum binding site
    • Elizondo-Riojas, M. A. and Kozelka, J. (2001). Unrestrained 5 ns molecular dynamics simulation of a cisplatin-DNA 1, 2-GG adduct provides a rationale for the NMR features and reveals increased conformational flexibility at the platinum binding site. J. Mol. Biol., 314, 1227-1243.
    • (2001) J. Mol. Biol. , vol.314 , pp. 1227-1243
    • Elizondo-Riojas, M.A.1    Kozelka, J.2
  • 33
    • 0242582476 scopus 로고    scopus 로고
    • Theoretical study of cisplatin binding to purine bases: Why does cisplatin prefer guanine over adenine?
    • Baik, M.-H., Friesner, R. A. and Lippard, S. J. (2003). Theoretical study of cisplatin binding to purine bases: Why does cisplatin prefer guanine over adenine? J. Am. Chem. Soc. 125, 14082-14092.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 14082-14092
    • Baik, M.-H.1    Friesner, R.A.2    Lippard, S.J.3
  • 34
    • 0347594104 scopus 로고    scopus 로고
    • 3) binding to purines and co: Does ji-back-donation play a role?
    • 3) binding to purines and CO: Does ji-back-donation play a role? Inorg. Chem. 42, 8615-8617.
    • (2003) Inorg. Chem. , vol.42 , pp. 8615-8617
    • Baik, M.-H.1    Friesner, R.A.2    Lippard, S.J.3
  • 35
    • 0242322061 scopus 로고    scopus 로고
    • How strong can the bend be on a dna helix from cisplatin? dft and mp2 quantum chemical calculations of cisplatin-bridged dna purine bases
    • Burda, J. V. and 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. Inorg. Chem. 42, 7162-7172.
    • (2003) Inorg. Chem. , vol.42 , pp. 7162-7172
    • Burda, J.V.1    Leszczynski, J.2
  • 36
    • 0037157085 scopus 로고    scopus 로고
    • On the competition of the purine bases, functionalities of peptide side chains, and protecting agents for the coordination sites of dicationic cisplatin derivatives
    • Deubel, D. V. (2002). On the competition of the purine bases, functionalities of peptide side chains, and protecting agents for the coordination sites of dicationic cisplatin derivatives. J. Am. Chem. Soc. 124, 5834-5842.
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 5834-5842
    • Deubel, D.V.1
  • 37
    • 2442511188 scopus 로고    scopus 로고
    • Factors governing the kinetic competition of nitrogen and sulfur ligands in cisplatin binding to biological targets
    • Deubel, D. V. (2004). Factors governing the kinetic competition of nitrogen and sulfur ligands in cisplatin binding to biological targets. J. Am. Chem. Soc. 126, 5999-6004.
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 5999-6004
    • Deubel, D.V.1
  • 38
    • 18544364930 scopus 로고    scopus 로고
    • Loss of ammine from platinum(ii) complexes: Implications for cisplatin inactivation, storage and resistance
    • Lau, J. K.-C. and Deubel, D. V. (2005). Loss of ammine from platinum(II) complexes: Implications for cisplatin inactivation, storage and resistance. Chem.-Eur. J. 11, 2849-2855.
    • (2005) Chem.-Eur. J. , vol.11 , pp. 2849-2855
    • Lau, J.K.-C.1    Deubel, D.V.2
  • 39
    • 0037165749 scopus 로고    scopus 로고
    • Theoretical study on the stability of n-glycosyl bonds: Why does n7-platination not promote depurination?
    • Baik, M.-H, Friesner, R. A. and Lippard, S. J. (2002). Theoretical study on the stability of N-glycosyl bonds: Why does N7-platination not promote depurination? J. Am. Chem. Soc. 124, 4495-4503
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 4495-4503
    • Baik, M.-H.1    Friesner, R.A.2    Lippard, S.J.3
  • 40
    • 0033913014 scopus 로고    scopus 로고
    • Cation-n and amino-acceptor interactions between hydrated metal cations and dna bases. A quantum chemical view
    • Šponer, J., Šponer, J. E. and Leszczynski, J. (2000). Cation-n and amino-acceptor interactions between hydrated metal cations and DNA bases. A quantum chemical view. J. Biomol. Struct. Dyn. 17, 1087-1096.
    • (2000) J. Biomol. Struct. Dyn. , vol.17 , pp. 1087-1096
    • Šponer, J.1    Šponer, J.E.2    Leszczynski, J.3
  • 42
    • 10044224233 scopus 로고    scopus 로고
    • Calculation of the binding free energy for magnesium-rna interactions
    • Petrov, A. S., Lamm, G and Pack, G R. (2005). Calculation of the binding free energy for magnesium-RNA interactions. Biopolymers, 77, 137-154.
    • (2005) Biopolymers , vol.77 , pp. 137-154
    • Petrov, A.S.1    Lamm, G.2    Pack, G.R.3
  • 43
    • 0025197061 scopus 로고
    • as of ionizable groups in proteins-atomic detail from a continuum electrostatic model
    • as of ionizable groups in proteins-atomic detail from a continuum electrostatic model. Biochemistry, 29, 10219-10225.
    • (1990) Biochemistry , vol.29 , pp. 10219-10225
    • Bashford, D.1    Karplus, M.2
  • 44
    • 14244271476 scopus 로고    scopus 로고
    • Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise
    • Cheatham, T. E. and Young, M. A. (2000). Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise. Biopolymers, 56, 232-256.
    • (2000) Biopolymers , vol.56 , pp. 232-256
    • Cheatham, T.E.1    Young, M.A.2
  • 45
    • 1242347628 scopus 로고    scopus 로고
    • Structure recognition properties, and flexibility of the dna-rna hybrid
    • Orozco, M., Perez, A., Noy, A. and Luque, F. J. (2003). Structure, recognition properties, and flexibility of the DNA-RNA hybrid. Chem. Soc. Rev., 32, 350-364.
    • (2003) Chem. Soc. Rev. , vol.32 , pp. 350-364
    • Orozco, M.1    Perez, A.2    Noy, A.3    Luque, F.J.4
  • 46
    • 0037764044 scopus 로고    scopus 로고
    • Non-watson-crick basepairing and hydration in rna motifs: Molecular dynamics of 5s rrna loop e
    • Reblová, K., Špacková, N, Štefl, R., Csaszar, K., Koca, J., Leontis, N. B., Šponer, J. (2003). Non-Watson-Crick basepairing and hydration in RNA motifs: Molecular dynamics of 5S rRNA loop E. Biophys. J., 84, 3564-3582.
    • (2003) Biophys. J. , vol.84 , pp. 3564-3582
    • Reblová, K.1    Špacková, N.2    Štefl, R.3    Csaszar, K.4    Koca, J.5    Leontis, N.B.6    Šponer, J.7
  • 48
    • 12844258405 scopus 로고    scopus 로고
    • Ong-residency hydration, cation binding, and dynamics of loop e/helix iv rrna-l25 protein complex
    • Reblová, K., Špacková, N, Koca, J., Leontis, N. B., Šponer, J. (2004). Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex. Biophys. J., 87, 3397-3412.
    • (2004) Biophys. J. , vol.87 , pp. 3397-3412
    • Reblová, K.1    Špacková, N.2    Koca, J.3    Leontis, N.B.4    Šponer, J.5
  • 49
    • 0042823487 scopus 로고    scopus 로고
    • Formation pathways of a guanine-quadruplex dna revealed by molecular dynamics and thermodynamic analysis of the substates
    • Štefl, R., Cheatham, T. E., Špacková, N, Fadrná, E., Berger, I., Koca, J., Šponer, J. (2003). Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates. Biophys. J., 85, 1787-1804.
    • (2003) Biophys. J. , vol.85 , pp. 1787-1804
    • Štefl, R.1    Cheatham, T.E.2    Špacková, N.3    Fadrná, E.4    Berger, I.5    Koca, J.6    Šponer, J.7
  • 50
    • 17944388579 scopus 로고    scopus 로고
    • Olecular dynamics simulations of rna kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets
    • Reblová, K, Špacková, N, Šponer, J. E., Koca, J., Šponer, J. (2003). Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets. Nucleic Acids Res., 31, 6942-6952.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 6942-6952
    • Reblová, K.1    Špacková, N.2    Šponer, J.E.3    Koca, J.4    Šponer, J.5


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