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Volumn 32, Issue 14, 2004, Pages 4269-4280

DNA and its counterions: A molecular dynamics study

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; CYTOSINE; DNA; DNA BASE; GUANINE; OLIGOMER; PHOSPHATE; POTASSIUM ION; SODIUM ION; THYMINE; MONOVALENT CATION; POTASSIUM; SODIUM;

EID: 4043179941     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh765     Document Type: Article
Times cited : (220)

References (50)
  • 2
    • 0019387686 scopus 로고
    • Structure of a B-DNA dodecamer: Influence of base sequence on helix structure
    • Dickerson,R.E. and Drew,H.R. (1981) Structure of a B-DNA dodecamer: influence of base sequence on helix structure. J. Mol. Biol., 149, 761-786.
    • (1981) J. Mol. Biol. , vol.149 , pp. 761-786
    • Dickerson, R.E.1    Drew, H.R.2
  • 3
    • 0023513912 scopus 로고
    • The structure of an oligo(dA)·oligo(dT) tract and its biological implications
    • Nelson,H.C., Finch,J.T., Luisi,B.F. and Klug,A. (1987) The structure of an oligo(dA)·oligo(dT) tract and its biological implications. Nature, 330, 221-226.
    • (1987) Nature , vol.330 , pp. 221-226
    • Nelson, H.C.1    Finch, J.T.2    Luisi, B.F.3    Klug, A.4
  • 4
    • 0019843568 scopus 로고
    • Structure of a B-DNA dodecamer. III. Geometry of hydration
    • Drew,H.R. and Dickerson,R.E. (1981) Structure of a B-DNA dodecamer. III. Geometry of hydration. J. Mol. Biol., 151, 535-556.
    • (1981) J. Mol. Biol. , vol.151 , pp. 535-556
    • Drew, H.R.1    Dickerson, R.E.2
  • 5
    • 0020692923 scopus 로고
    • Ordered water structure around a B-DNA dodecamer. A quantitative study
    • Kopka,M.L., Fratini,A.V., Drew,H.R. and Dickerson,R.E. (1983) Ordered water structure around a B-DNA dodecamer. A quantitative study. J. Mol. Biol., 163, 129-146.
    • (1983) J. Mol. Biol. , vol.163 , pp. 129-146
    • Kopka, M.L.1    Fratini, A.V.2    Drew, H.R.3    Dickerson, R.E.4
  • 6
    • 0032387836 scopus 로고    scopus 로고
    • Structure of the potassium form of CGCGAATTCGCG: DNA deformation by electrostatic collapse around inorganic cations
    • Shui,X., Sines,C.C., McFail-Isom,L., VanDerveer,D. and Williams,L.D. (1998) Structure of the potassium form of CGCGAATTCGCG: DNA deformation by electrostatic collapse around inorganic cations. Biochemistry, 37, 16877-16887.
    • (1998) Biochemistry , vol.37 , pp. 16877-16887
    • Shui, X.1    Sines, C.C.2    McFail-Isom, L.3    VanDerveer, D.4    Williams, L.D.5
  • 7
    • 0032499635 scopus 로고    scopus 로고
    • The B-DNA dodecamer at high resolution reveals a spine of water on sodium
    • Shui,X., McFail-Isom,L., Hu,G.G. and Williams,L.D. (1998) The B-DNA dodecamer at high resolution reveals a spine of water on sodium. Biochemistry, 37, 8341-8355.
    • (1998) Biochemistry , vol.37 , pp. 8341-8355
    • Shui, X.1    McFail-Isom, L.2    Hu, G.G.3    Williams, L.D.4
  • 8
    • 0033585580 scopus 로고    scopus 로고
    • The Dickerson-Drew B-DNA dodecamer revisited at atomic resolution
    • Tereshko,V., Minasov,G. and Egli,M. (1999) The Dickerson-Drew B-DNA dodecamer revisited at atomic resolution. J. Am. Chem. Soc., 121, 470-471.
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 470-471
    • Tereshko, V.1    Minasov, G.2    Egli, M.3
  • 9
    • 0033600794 scopus 로고    scopus 로고
    • Absence of minor groove monovalent cations in the crosslinked dodecamer CGCGAATTCGCG
    • Chiu,T.K., Kaczor-Grzeskowiak,M. and Dickerson,R.E. (1999) Absence of minor groove monovalent cations in the crosslinked dodecamer CGCGAATTCGCG. J. Mol. Biol., 292, 589-608.
    • (1999) J. Mol. Biol. , vol.292 , pp. 589-608
    • Chiu, T.K.1    Kaczor-Grzeskowiak, M.2    Dickerson, R.E.3
  • 10
    • 0033594498 scopus 로고    scopus 로고
    • A 'hydrat-ion' spine in a B-DNA minor groove
    • Tereshko,V., Minasov,G. and Egli,M. (1999) A 'hydrat-ion' spine in a B-DNA minor groove. J. Am. Chem. Soc., 121, 3590-3595.
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 3590-3595
    • Tereshko, V.1    Minasov, G.2    Egli, M.3
  • 13
    • 0033605083 scopus 로고    scopus 로고
    • Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending
    • Hud,N.V., Sklenar,V. and Feigon,J. (1999) Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending. J. Mol. Biol., 286, 651-660.
    • (1999) J. Mol. Biol. , vol.286 , pp. 651-660
    • Hud, N.V.1    Sklenar, V.2    Feigon, J.3
  • 14
    • 0034681195 scopus 로고    scopus 로고
    • Sequence-specific binding of counterions to B-DNA
    • Denisov,V.P. and Halle,B. (2000) Sequence-specific binding of counterions to B-DNA. Proc. Natl Acad. Sci. USA, 97, 629-633.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 629-633
    • Denisov, V.P.1    Halle, B.2
  • 15
    • 14244271476 scopus 로고    scopus 로고
    • Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise
    • Cheatham,T.E.,III and Young,M.A. (2001) Molecular dynamics simulation of nucleic acids: successes, limitations, and promise. Biopolymers, 56, 232-256.
    • (2001) Biopolymers , vol.56 , pp. 232-256
    • Cheatham III, T.E.1    Young, M.A.2
  • 16
    • 0031047279 scopus 로고    scopus 로고
    • Intrusion of counterions into the spine of hydration in the minor groove of B-DNA: Fractional occupancy of electronegative pockets
    • Young,M.A., Jarayam,B. and Beveridge,D.L. (1997) Intrusion of counterions into the spine of hydration in the minor groove of B-DNA: fractional occupancy of electronegative pockets. J. Am. Chem. Soc., 119, 59-69.
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 59-69
    • Young, M.A.1    Jarayam, B.2    Beveridge, D.L.3
  • 17
    • 0034671291 scopus 로고    scopus 로고
    • DNA structure: What's in charge?
    • McConnell,K.J. and Beveridge,D.L. (2000) DNA structure: what's in charge? J. Mol. Biol., 304, 803-820.
    • (2000) J. Mol. Biol. , vol.304 , pp. 803-820
    • McConnell, K.J.1    Beveridge, D.L.2
  • 18
    • 0034327565 scopus 로고    scopus 로고
    • Flexible structure of DNA: Ion dependence of minor-groove structure and dynamics
    • Hamelberg,D., McFail-Isom,L., Williams,L.D. and Wilson,W.D. (2000) Flexible structure of DNA: ion dependence of minor-groove structure and dynamics. J. Am. Chem. Soc., 122, 10513-10520.
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 10513-10520
    • Hamelberg, D.1    McFail-Isom, L.2    Williams, L.D.3    Wilson, W.D.4
  • 19
    • 0037385644 scopus 로고    scopus 로고
    • Molecular dynamics simulations of A·T-rich oligomers: Sequence-specific binding of Na+ in the minor groove of B-DNA
    • Mocci,F. and Saba,G. (2003) Molecular dynamics simulations of A·T-rich oligomers: sequence-specific binding of Na+ in the minor groove of B-DNA. Biopolymers, 68, 471-485.
    • (2003) Biopolymers , vol.68 , pp. 471-485
    • Mocci, F.1    Saba, G.2
  • 20
    • 0032851951 scopus 로고    scopus 로고
    • Sodium and chlorine ions as part of the DNA solvation shell
    • Feig,M. and Pettitt,B.M. (1999) Sodium and chlorine ions as part of the DNA solvation shell. Biophys. J., 77, 1769-1781.
    • (1999) Biophys. J. , vol.77 , pp. 1769-1781
    • Feig, M.1    Pettitt, B.M.2
  • 21
    • 0036106375 scopus 로고    scopus 로고
    • On the competition between water, sodium ions, and spermine in binding to DNA: A molecular dynamics computer simulation study
    • Korolev,N., Lyubartsev,A.P., Laaksonen,A. and Nordenskiold,L. (2002) On the competition between water, sodium ions, and spermine in binding to DNA: a molecular dynamics computer simulation study. Biophys. J., 82, 2860-2875.
    • (2002) Biophys. J. , vol.82 , pp. 2860-2875
    • Korolev, N.1    Lyubartsev, A.P.2    Laaksonen, A.3    Nordenskiold, L.4
  • 22
    • 0034725528 scopus 로고    scopus 로고
    • Water and ion binding around RNA and DNA (C,G) oligomers
    • Auffinger,P. and Westhof,E. (2000) Water and ion binding around RNA and DNA (C,G) oligomers. J. Mol. Biol., 300, 1113-1131.
    • (2000) J. Mol. Biol. , vol.300 , pp. 1113-1131
    • Auffinger, P.1    Westhof, E.2
  • 23
    • 0035793219 scopus 로고    scopus 로고
    • Water and ion binding around r(UpA)12 and d(TpA)12 oligomers. Comparison with RNA and DNA (CpG)12 duplexes
    • Auffinger,P. and Westhof,E. (2001) Water and ion binding around r(UpA)12 and d(TpA)12 oligomers. Comparison with RNA and DNA (CpG)12 duplexes. J. Mol. Biol., 305, 1057-1072.
    • (2001) J. Mol. Biol. , vol.305 , pp. 1057-1072
    • Auffinger, P.1    Westhof, E.2
  • 24
    • 0037342509 scopus 로고    scopus 로고
    • DNA polymorphism: A comparison of force fields for nucleic acids
    • Reddy,S.Y., Leclerc,F. and Karplus,M. (2003) DNA polymorphism: a comparison of force fields for nucleic acids. Biophys. J., 84, 1421-1449.
    • (2003) Biophys. J. , vol.84 , pp. 1421-1449
    • Reddy, S.Y.1    Leclerc, F.2    Karplus, M.3
  • 25
    • 0037178070 scopus 로고    scopus 로고
    • Base flipping in DNA: Pathways and energetics studied with molecular dynamics simulations
    • Várnai,P. and Lavery,R. (2002) Base flipping in DNA: pathways and energetics studied with molecular dynamics simulations. J. Am. Chem. Soc., 124, 7272-7273.
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 7272-7273
    • Várnai, P.1    Lavery, R.2
  • 27
    • 0001398008 scopus 로고    scopus 로고
    • How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
    • Wang,J., Cieplak,P. and Kollman,P.A. (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem., 21, 1049-1074.
    • (2000) J. Comput. Chem. , vol.21 , pp. 1049-1074
    • Wang, J.1    Cieplak, P.2    Kollman, P.A.3
  • 28
    • 1842738520 scopus 로고    scopus 로고
    • Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: Diffusion, free energy of hydration, and structural properties
    • Patra,M. and Karttunen,M. (2004) Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: diffusion, free energy of hydration, and structural properties. J. Comput. Chem., 25, 678-689.
    • (2004) J. Comput. Chem. , vol.25 , pp. 678-689
    • Patra, M.1    Karttunen, M.2
  • 29
    • 2942547665 scopus 로고    scopus 로고
    • Simulation and modeling of nucleic acid structure, dynamics and interactions
    • Cheatham,T.E.,III (2004) Simulation and modeling of nucleic acid structure, dynamics and interactions. Curr. Opin. Struct. Biol., 14, 360-367.
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , pp. 360-367
    • Cheatham III, T.E.1
  • 30
    • 1642525904 scopus 로고    scopus 로고
    • Influence of artificial periodicity and ionic strength in MD simulations of charged biomolecules employing lattice-sum methods
    • Kastenholtz,M.A. and Hünenberger,H.P. (2004) Influence of artificial periodicity and ionic strength in MD simulations of charged biomolecules employing lattice-sum methods. J. Phys. Chem. B, 108, 774-788.
    • (2004) J. Phys. Chem. B. , vol.108 , pp. 774-788
    • Kastenholtz, M.A.1    Hünenberger, H.P.2
  • 32
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert,J.P., Ciccotti,G. and Berendsen,H.J.C. (1977) Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J. Comp. Phys., 23, 327-341.
    • (1977) J. Comp. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 33
    • 33846823909 scopus 로고
    • Particle mesh ewald: An N-log(N) methods for Ewald sums in large systems
    • Darden,T., York,D. and Pedersen,L. (1993) Particle mesh ewald: an N-log(N) methods for Ewald sums in large systems. J. Chem. Phys., 98, 10089-10092.
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 34
    • 0027304152 scopus 로고
    • Hydration of proteins. A comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations
    • Brunne,R.M., Liepinsh,E., Otting,G., Wuthrich,K. and van Gunsteren.W.F. (1993) Hydration of proteins. A comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations. J. Mol. Biol., 231, 1040-1048.
    • (1993) J. Mol. Biol. , vol.231 , pp. 1040-1048
    • Brunne, R.M.1    Liepinsh, E.2    Otting, G.3    Wuthrich, K.4    van Gunsteren, W.F.5
  • 35
    • 0024539180 scopus 로고
    • Defining the structure of irregular nucleic acids: Convention and principles
    • Lavery,R. and Sklenar,H. (1989) Defining the structure of irregular nucleic acids: convention and principles. J. Biomol. Struct. Dyn., 6, 655-667.
    • (1989) J. Biomol. Struct. Dyn. , vol.6 , pp. 655-667
    • Lavery, R.1    Sklenar, H.2
  • 36
    • 0028184697 scopus 로고
    • Measuring the geometry of DNA grooves
    • Stofer,E. and Lavery,R. (1994) Measuring the geometry of DNA grooves. Biopolymers, 34, 337-346.
    • (1994) Biopolymers , vol.34 , pp. 337-346
    • Stofer, E.1    Lavery, R.2
  • 37
    • 0025283002 scopus 로고
    • Electrostatic interactions in macromolecules: Theory and applications
    • Sharp,K.A. and Honig,B. (1990) Electrostatic interactions in macromolecules: theory and applications. Annu. Rev. Biophys. Chem., 19, 301-332.
    • (1990) Annu. Rev. Biophys. Chem. , vol.19 , pp. 301-332
    • Sharp, K.A.1    Honig, B.2
  • 38
    • 0031807764 scopus 로고    scopus 로고
    • Diffusion of solvent around biomolecular solutes: A molecular dynamics simulation study
    • Makarov,V.A., Feig,M., Andrews,B.K. and Pettitt,B.M. (1998) Diffusion of solvent around biomolecular solutes: a molecular dynamics simulation study. Biophys. J., 75, 150-158.
    • (1998) Biophys. J. , vol.75 , pp. 150-158
    • Makarov, V.A.1    Feig, M.2    Andrews, B.K.3    Pettitt, B.M.4
  • 39
  • 40
    • 0001324374 scopus 로고    scopus 로고
    • Solvent structure, dynamics, and ion mobility in aqueous solutions at 25°C
    • Koneshan,S., Rasaiah,J.C., Lynden-Bell,R.M. and Lee,S.H. (1998) Solvent structure, dynamics, and ion mobility in aqueous solutions at 25°C. J. Phys. Chem. B, 102, 4193-4204.
    • (1998) J. Phys. Chem. B. , vol.102 , pp. 4193-4204
    • Koneshan, S.1    Rasaiah, J.C.2    Lynden-Bell, R.M.3    Lee, S.H.4
  • 42
    • 17944388579 scopus 로고    scopus 로고
    • Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets
    • Reblova,K., Spackova,N., Sponer,J.E., Koca,J. and Sponer,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
    • Reblova, K.1    Spackova, N.2    Sponer, J.E.3    Koca, J.4    Sponer, J.5
  • 43
    • 0037764044 scopus 로고    scopus 로고
    • Non-Watson-Crick basepairing and hydration in RNA motifs: Molecular dynamics of 5S rRNA loop E
    • Reblova,K., Spackova,N., Stefl,R., Csaszar,K., Koca,J., Leontis,N.B. and Sponer,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
    • Reblova, K.1    Spackova, N.2    Stefl, R.3    Csaszar, K.4    Koca, J.5    Leontis, N.B.6    Sponer, J.7
  • 44
    • 0042823487 scopus 로고    scopus 로고
    • Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates
    • Stefl,R., Cheatham,T.E.,III, Spackova,N., Fadrna,E., Berger,I., Koca,J. and Sponer,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
    • Stefl, R.1    Cheatham III, T.E.2    Spackova, N.3    Fadrna, E.4    Berger, I.5    Koca, J.6    Sponer, J.7
  • 45
    • 0034836422 scopus 로고    scopus 로고
    • Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations
    • Spackova,N., Berger,I. and Sponer,J. (2001) Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations. J. Am. Chem. Soc., 123, 3295-3307.
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 3295-3307
    • Spackova, N.1    Berger, I.2    Sponer, J.3
  • 46
    • 0036569686 scopus 로고    scopus 로고
    • Bending of DNA by asymmetric charge neutralization: All-atom energy simulations
    • Kosikov,K.M., Gorin,A.A., Lu,X.-J., Olson,W.K. and Manning,G.S. (2002) Bending of DNA by asymmetric charge neutralization: all-atom energy simulations. J. Am. Chem. Soc., 124, 4838-4847.
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 4838-4847
    • Kosikov, K.M.1    Gorin, A.A.2    Lu, X.-J.3    Olson, W.K.4    Manning, G.S.5
  • 47
    • 0038713237 scopus 로고    scopus 로고
    • A unified model for the origin of DNA sequence-directed curvature
    • Hud,N.V. and Plavec,J. (2003) A unified model for the origin of DNA sequence-directed curvature. Biopolymers, 69, 144-159.
    • (2003) Biopolymers , vol.69 , pp. 144-159
    • Hud, N.V.1    Plavec, J.2
  • 48
    • 0025778738 scopus 로고
    • Are time-averaged restraints necessary for nuclear magnetic resonance refinement? A model study for DNA
    • Pearlman,D.A. and Kollman,P.A. (1991) Are time-averaged restraints necessary for nuclear magnetic resonance refinement? A model study for DNA. J. Mol. Biol., 220, 457-479.
    • (1991) J. Mol. Biol. , vol.220 , pp. 457-479
    • Pearlman, D.A.1    Kollman, P.A.2
  • 49
    • 0027432486 scopus 로고
    • Molecular dynamics with weighted time-averaged restraints for a DNA octamer. Dynamic interpretation of nuclear magnetic resonance data
    • Schmitz,U., Ulyanov,N.B., Kumar,A. and James,T.L. (1993) Molecular dynamics with weighted time-averaged restraints for a DNA octamer. Dynamic interpretation of nuclear magnetic resonance data. J. Mol. Biol., 234, 373-389.
    • (1993) J. Mol. Biol. , vol.234 , pp. 373-389
    • Schmitz, U.1    Ulyanov, N.B.2    Kumar, A.3    James, T.L.4


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