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Volumn 25, Issue , 1996, Pages 367-394

Modeling DNA in aqueous solutions: Theoretical and computer simulation studies on the ion atmosphere of DNA

Author keywords

counterion condensation; dynamics; energetics; Poisson Boltzmann studies; structure

Indexed keywords

DNA; ION; POLYELECTROLYTE;

EID: 0030007604     PISSN: 10568700     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.bb.25.060196.002055     Document Type: Review
Times cited : (118)

References (171)
  • 1
    • 0001200075 scopus 로고
    • End effects in electrostatic potentials of cylinders: Models for DNA fragments
    • Allison SA. 1994. End effects in electrostatic potentials of cylinders: models for DNA fragments. J. Phys. Chem. 98:12091
    • (1994) J. Phys. Chem. , vol.98 , pp. 12091
    • Allison, S.A.1
  • 3
    • 0025308916 scopus 로고
    • Ionic distributions around DNA and other cylindrical polyions: Theoretical descriptions and physical implications
    • Anderson CF, Record MT Jr. 1990. Ionic distributions around DNA and other cylindrical polyions: theoretical descriptions and physical implications. Annu. Rev. Biophys. Biophys. Chem. 19:423
    • (1990) Annu. Rev. Biophys. Biophys. Chem. , vol.19 , pp. 423
    • Anderson, C.F.1    Record Jr., M.T.2
  • 4
    • 0000144150 scopus 로고
    • Salt dependence of oligoion-polyion binding: A thermodynamic description based on preferential interaction coefficients
    • 3a. Anderson C, Record MT. 1993. Salt dependence of oligoion-polyion binding: a thermodynamic description based on preferential interaction coefficients. J. Phys. Chem. 97:7116
    • (1993) J. Phys. Chem. , vol.97 , pp. 7116
    • Anderson, C.1    Record, M.T.2
  • 5
    • 0000836584 scopus 로고
    • Ionic atmosphere of rod-like polyelectrolytes. A hypernetted chain study
    • Bacquet R, Rossky PJ. 1984. Ionic atmosphere of rod-like polyelectrolytes. A hypernetted chain study. J. Phys. Chem. 88:2660
    • (1984) J. Phys. Chem. , vol.88 , pp. 2660
    • Bacquet, R.1    Rossky, P.J.2
  • 6
    • 0000533571 scopus 로고
    • Ionic distributions and competitive association in DNA/mixed salt solutions
    • Bacquet RJ, Rossky PJ. 1988. Ionic distributions and competitive association in DNA/mixed salt solutions. J. Phys. Chem. 92:3604
    • (1988) J. Phys. Chem. , vol.92 , pp. 3604
    • Bacquet, R.J.1    Rossky, P.J.2
  • 7
    • 36749121933 scopus 로고
    • Theory of twisting and bending of chain macromolecules: Analysis of the fluorescence depolarization of DNA
    • Barkley MD, Zimm BH. 1979. Theory of twisting and bending of chain macromolecules: analysis of the fluorescence depolarization of DNA. J. Chem. Phys. 70:2991
    • (1979) J. Chem. Phys. , vol.70 , pp. 2991
    • Barkley, M.D.1    Zimm, B.H.2
  • 8
    • 0000339209 scopus 로고
    • Electrostatic effects in biological molecules
    • Bashford D. 1991. Electrostatic effects in biological molecules. Curr. Opin. Struct. Biol. 1:175
    • (1991) Curr. Opin. Struct. Biol. , vol.1 , pp. 175
    • Bashford, D.1
  • 11
    • 0026742978 scopus 로고
    • The Nucleic Acid Database: A comprehensive relational database of three dimensional structures of nucleic acids
    • Berman HM, Olson WK, Beveridge DL, Westbrook J, Gelbin A, et al. 1992. The Nucleic Acid Database: a comprehensive relational database of three dimensional structures of nucleic acids. Biophys. J. 63:751
    • (1992) Biophys. J. , vol.63 , pp. 751
    • Berman, H.M.1    Olson, W.K.2    Beveridge, D.L.3    Westbrook, J.4    Gelbin, A.5
  • 13
    • 0024578173 scopus 로고
    • Free energy via molecular simulation: Applications to chemical and biomolecular systems
    • Beveridge DL, Dicapua FM. 1989. Free energy via molecular simulation: applications to chemical and biomolecular systems. Annu. Rev. Biophys. Biophys. Chem. 18:431
    • (1989) Annu. Rev. Biophys. Biophys. Chem. , vol.18 , pp. 431
    • Beveridge, D.L.1    Dicapua, F.M.2
  • 18
    • 0000806644 scopus 로고
    • Sodium-23 nuclear magnetic resonance studies of cation-deoxyribonucleic acid interactions
    • Bleam ML, Anderson CF, Record MT Jr. 1983. Sodium-23 nuclear magnetic resonance studies of cation-deoxyribonucleic acid interactions. Biochemistry 22:5418
    • (1983) Biochemistry , vol.22 , pp. 5418
    • Bleam, M.L.1    Anderson, C.F.2    Record Jr., M.T.3
  • 19
    • 0026253815 scopus 로고
    • Condensation of DNA by multivalent cations: Considerations on mechanism
    • Bloomfield VA. 1991. Condensation of DNA by multivalent cations: considerations on mechanism. Biopolymers 31:1471
    • (1991) Biopolymers , vol.31 , pp. 1471
    • Bloomfield, V.A.1
  • 20
    • 0028030641 scopus 로고
    • Conformational transitions of duplex and triplex nucleic acid helices: Thermodynamic analysis of the effects of salt concentration on stability using preferential interaction coefficients
    • 18a. Bond JP, Anderson CF, Record MT. 1994. Conformational transitions of duplex and triplex nucleic acid helices: thermodynamic analysis of the effects of salt concentration on stability using preferential interaction coefficients. Biophys. J. 67:825
    • (1994) Biophys. J. , vol.67 , pp. 825
    • Bond, J.P.1    Anderson, C.F.2    Record, M.T.3
  • 21
    • 0025924787 scopus 로고
    • 1H NMR study of the base-pairing reaction of d(GGAATTCC): Salt effects on the equilibria and kinetics of strand association
    • 1H NMR study of the base-pairing reaction of d(GGAATTCC): salt effects on the equilibria and kinetics of strand association. Biochemistry 30: 754
    • (1991) Biochemistry , vol.30 , pp. 754
    • Braunlin, W.H.1    Bloomfield, V.A.2
  • 22
    • 0000583619 scopus 로고
    • Evidence for the stochastic nature of base pair opening in DNA. A Brownian dynamics simulation
    • Briki F, Ramstein J, Lavery R, Genest D. 1991. Evidence for the stochastic nature of base pair opening in DNA. A Brownian dynamics simulation. J. Am. Chem. Soc. 113:2490
    • (1991) J. Am. Chem. Soc. , vol.113 , pp. 2490
    • Briki, F.1    Ramstein, J.2    Lavery, R.3    Genest, D.4
  • 23
    • 0023140814 scopus 로고
    • Crystallographic R factor refinement by molecular dynamics
    • Bruenger A, Kuriyan J, Karplus M. 1987. Crystallographic R factor refinement by molecular dynamics. Science 235:458
    • (1987) Science , vol.235 , pp. 458
    • Bruenger, A.1    Kuriyan, J.2    Karplus, M.3
  • 24
    • 0027554810 scopus 로고
    • A model for the dynemicin-A cleavage of DNA using molecular dynamics simulation
    • Cardozo MG, Hopfinger AJ. 1993. A model for the dynemicin-A cleavage of DNA using molecular dynamics simulation. Biopolymers 33:377
    • (1993) Biopolymers , vol.33 , pp. 377
    • Cardozo, M.G.1    Hopfinger, A.J.2
  • 25
    • 0001373924 scopus 로고
    • Measurements of monovalent and divalent counterion distributions around persistence length DNA fragments in solution
    • Chang S-L, Chen S-H, Rill RL, Lin JS. 1990. Measurements of monovalent and divalent counterion distributions around persistence length DNA fragments in solution. J. Phys. Chem. 94:8025
    • (1990) J. Phys. Chem. , vol.94 , pp. 8025
    • Chang, S.-L.1    Chen, S.-H.2    Rill, R.L.3    Lin, J.S.4
  • 26
    • 0029170114 scopus 로고
    • Molecular dynamics simulations on solvated biomolecular systems: The particle mesh Ewald method leads to stable trajectories of DNA, RNA and proteins
    • Cheatham TE III, Miller JL, Fox T, Darden TA, Kollman PA. 1995. Molecular dynamics simulations on solvated biomolecular systems: The particle mesh Ewald method leads to stable trajectories of DNA, RNA and proteins. J. Am. Chem. Soc. 117:4193
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 4193
    • Cheatham III, T.E.1    Miller, J.L.2    Fox, T.3    Darden, T.A.4    Kollman, P.A.5
  • 28
    • 0028184699 scopus 로고
    • Kinetics of supercoiling studied by Brownian dynamics simulation
    • Chirico G, Langowski J. 1994. Kinetics of supercoiling studied by Brownian dynamics simulation. Biopolymers 34:415
    • (1994) Biopolymers , vol.34 , pp. 415
    • Chirico, G.1    Langowski, J.2
  • 29
    • 0025308014 scopus 로고
    • Free energy calculation of base specificity of drug-DNA interactions: Application to daunomycin and acridine intercalation into DNA
    • Cieplak P, Rao SN, Grootenhuis PDJ, Kollman PA. 1990. Free energy calculation of base specificity of drug-DNA interactions: application to daunomycin and acridine intercalation into DNA. Biopolymers 29: 717
    • (1990) Biopolymers , vol.29 , pp. 717
    • Cieplak, P.1    Rao, S.N.2    Grootenhuis, P.D.J.3    Kollman, P.A.4
  • 30
    • 0024116002 scopus 로고
    • Ions around DNA: Monte Carlo estimates of distribution with improved electrostatic potentials
    • Conrad J, Troll M, Zimm BH. 1988. Ions around DNA: Monte Carlo estimates of distribution with improved electrostatic potentials. Biopolymers 27:1711
    • (1988) Biopolymers , vol.27 , pp. 1711
    • Conrad, J.1    Troll, M.2    Zimm, B.H.3
  • 31
    • 0029011701 scopus 로고
    • A second generation force field for the simulation of proteins, nucleic acids and organic molecules
    • 28a. Cornell WD, Cieplak P, Bayly CI, Gould IA, et al. 1995. A second generation force field for the simulation of proteins, nucleic acids and organic molecules. J. Am. Chem. Soc. 117: 5179
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 5179
    • Cornell, W.D.1    Cieplak, P.2    Bayly, C.I.3    Gould, I.A.4
  • 32
    • 33645085472 scopus 로고
    • Modified Poisson-Boltzmann theory applied to linear polyelectrolyte solutions
    • Das T, Bratko D, Bhuiyan LB, Outhwaite CW. 1995. Modified Poisson-Boltzmann theory applied to linear polyelectrolyte solutions. J. Phys. Chem. 99:410
    • (1995) J. Phys. Chem. , vol.99 , pp. 410
    • Das, T.1    Bratko, D.2    Bhuiyan, L.B.3    Outhwaite, C.W.4
  • 33
    • 4243463817 scopus 로고
    • Electrostatics in biomolecular structure and dynamics
    • Davis ME, McCammon JA. 1990. Electrostatics in biomolecular structure and dynamics. Chem. Rev. 90: 509
    • (1990) Chem. Rev. , vol.90 , pp. 509
    • Davis, M.E.1    McCammon, J.A.2
  • 34
    • 0019843568 scopus 로고
    • Structure of a B-DNA dodecamer. III. Geometry of hydration
    • Drew HR, Dickerson RE. 1981. Structure of a B-DNA dodecamer. III. Geometry of hydration. J. Mol. Biol. 151:535
    • (1981) J. Mol. Biol. , vol.151 , pp. 535
    • Drew, H.R.1    Dickerson, R.E.2
  • 35
    • 0027367276 scopus 로고
    • Brownian dynamics simulations of probe and self-diffusion in concentrated protein and DNA solutions
    • 31a. Dwyer JD, Bloomfield VA. 1993. Brownian dynamics simulations of probe and self-diffusion in concentrated protein and DNA solutions. Biophys. J. 65:1810
    • (1993) Biophys. J. , vol.65 , pp. 1810
    • Dwyer, J.D.1    Bloomfield, V.A.2
  • 36
    • 0027395303 scopus 로고
    • Theoretical predictions of DNA hairpin-loop conformations. Correlations with thermodynamic and spectroscopic data
    • Erie DA, Suri AK, Breslauer KJ, Jones RA, Olson WK. 1993. Theoretical predictions of DNA hairpin-loop conformations. Correlations with thermodynamic and spectroscopic data. Biochemistry 32:436
    • (1993) Biochemistry , vol.32 , pp. 436
    • Erie, D.A.1    Suri, A.K.2    Breslauer, K.J.3    Jones, R.A.4    Olson, W.K.5
  • 37
    • 0025672928 scopus 로고
    • Approach to the limit of counterion condensation
    • Fenley MO, Manning GS, Olson WK. 1990. Approach to the limit of counterion condensation. Biopolymers 30:1191
    • (1990) Biopolymers , vol.30 , pp. 1191
    • Fenley, M.O.1    Manning, G.S.2    Olson, W.K.3
  • 40
    • 0000246675 scopus 로고
    • Molecular dynamics studies of the behaviour of water molecules and small ions in concentrated solutions of polymeric B-DNA
    • Forester TR, McDonald IR. 1991. Molecular dynamics studies of the behaviour of water molecules and small ions in concentrated solutions of polymeric B-DNA. Mol. Phys. 72: 643
    • (1991) Mol. Phys. , vol.72 , pp. 643
    • Forester, T.R.1    McDonald, I.R.2
  • 42
    • 0026816545 scopus 로고
    • The electrostatic contribution to DNA base-stacking interactions
    • Friedman R, Honig B. 1992. The electrostatic contribution to DNA base-stacking interactions. Biopolymers 32:145
    • (1992) Biopolymers , vol.32 , pp. 145
    • Friedman, R.1    Honig, B.2
  • 44
    • 84986467024 scopus 로고
    • Efficient conformational space sampling for nucleosides using internal coordinate Monte Carlo simulations and a modified furanose description
    • Gabb HA, Lavery R, Prevost C. 1995. Efficient conformational space sampling for nucleosides using internal coordinate Monte Carlo simulations and a modified furanose description. J. Comp. Chem. 16:667
    • (1995) J. Comp. Chem. , vol.16 , pp. 667
    • Gabb, H.A.1    Lavery, R.2    Prevost, C.3
  • 45
    • 0025231445 scopus 로고
    • Netropsin binding to poly[d(ic)] poly-[d(IC)] and poly[d(GC)] poly-[d(GC)]: A computer simulation
    • Gago F, Richards WG. 1990. Netropsin binding to poly[d(ic)] poly-[d(IC)] and poly[d(GC)] poly-[d(GC)]: a computer simulation. Mol. Pharmacol. 37:341
    • (1990) Mol. Pharmacol. , vol.37 , pp. 341
    • Gago, F.1    Richards, W.G.2
  • 46
    • 0343757149 scopus 로고
    • Harmonic vibrations and thermodynamic stability of a DNA oligomer in monovalent salt solution
    • Garcia AE, Soumpasis DM. 1989. Harmonic vibrations and thermodynamic stability of a DNA oligomer in monovalent salt solution. Proc. Natl. Acad. Sci. USA 86:3160
    • (1989) Proc. Natl. Acad. Sci. USA , vol.86 , pp. 3160
    • Garcia, A.E.1    Soumpasis, D.M.2
  • 47
    • 0347920629 scopus 로고
    • Simulations of the counterion and solvent distribution functions around two simple models of a polyelectrolyte
    • Gordon HL, Goldman S. 1992. Simulations of the counterion and solvent distribution functions around two simple models of a polyelectrolyte. J. Phys. Chem. 96:1921
    • (1992) J. Phys. Chem. , vol.96 , pp. 1921
    • Gordon, H.L.1    Goldman, S.2
  • 48
    • 0001828023 scopus 로고
    • Interactions of polyelectrolytes with simple electrolytes. I. Theory for electrostatic potential and Donnan equilibrium for a cylindrical rod model: The effect of site-binding in chemical physics of ionic solutions
    • ed. BE Conway, RG Barradas, New York: Wiley & Sons
    • Gross LM, Strauss UP. 1966. Interactions of polyelectrolytes with simple electrolytes. I. Theory for electrostatic potential and Donnan equilibrium for a cylindrical rod model: the effect of site-binding in chemical physics of ionic solutions. In Chemical Physics of Ionic Solutions ed. BE Conway, RG Barradas, pp. 361-89. New York: Wiley & Sons
    • (1966) Chemical Physics of Ionic Solutions , pp. 361-389
    • Gross, L.M.1    Strauss, U.P.2
  • 49
    • 0026656556 scopus 로고
    • A simple explanation of the electrostatics of the B to Z transition of DNA
    • Gueron M, Demaret J-P. 1992. A simple explanation of the electrostatics of the B to Z transition of DNA. Proc. Natl. Acad. Sci. USA 89:5740
    • (1992) Proc. Natl. Acad. Sci. USA , vol.89 , pp. 5740
    • Gueron, M.1    Demaret, J.-P.2
  • 50
    • 84985698666 scopus 로고
    • Polyelectrolyte theory. I. Counterion accumulation site binding and their insensitivity to polyelectrolyte shape in solutions containing finite salt concentrations
    • Gueron M, Weisbuch G. 1980. Polyelectrolyte theory. I. Counterion accumulation site binding and their insensitivity to polyelectrolyte shape in solutions containing finite salt concentrations. Biopolymers 19:353
    • (1980) Biopolymers , vol.19 , pp. 353
    • Gueron, M.1    Weisbuch, G.2
  • 51
    • 0001097403 scopus 로고
    • Distribution and dynamics of mobile ions in systems of ordered B-DNA
    • Guldbrand LE, Forester TR, Lynden-Bell RM. 1989. Distribution and dynamics of mobile ions in systems of ordered B-DNA. Mol. Phys. 67:473
    • (1989) Mol. Phys. , vol.67 , pp. 473
    • Guldbrand, L.E.1    Forester, T.R.2    Lynden-Bell, R.M.3
  • 52
    • 0024519351 scopus 로고
    • Treatment of electrostatic effects in macromolecular modeling
    • Harvey S. 1989. Treatment of electrostatic effects in macromolecular modeling. Proteins 5:78
    • (1989) Proteins , vol.5 , pp. 78
    • Harvey, S.1
  • 53
    • 0026563459 scopus 로고
    • Physico chemical properties of 〉- vs (S)-methylphosphonate substitution on antisense DNA hybridization determined by free energy perturbation and molecular dynamics
    • Hausheer FH, Rao BG, Saxe JD, Singh UC. 1992. Physico chemical properties of 〉- vs (S)-methylphosphonate substitution on antisense DNA hybridization determined by free energy perturbation and molecular dynamics. J. Am. Chem. Soc. 114: 3201
    • (1992) J. Am. Chem. Soc. , vol.114 , pp. 3201
    • Hausheer, F.H.1    Rao, B.G.2    Saxe, J.D.3    Singh, U.C.4
  • 54
    • 21944448053 scopus 로고
    • Electrostatic potentials near the surface of DNA: Comparing theory and experiment
    • Hecht JL, Honig B, Shin Y-K, Hubbell WL. 1995. Electrostatic potentials near the surface of DNA: comparing theory and experiment. J. Phys. Chem. 99:7782
    • (1995) J. Phys. Chem. , vol.99 , pp. 7782
    • Hecht, J.L.1    Honig, B.2    Shin, Y.-K.3    Hubbell, W.L.4
  • 55
    • 84990406847 scopus 로고
    • Dielectric effects in biopolymers: The theory of ionic saturation revisited
    • Hingerty BE, Ritchie RH, Ferrell TL, Turner JE. 1985. Dielectric effects in biopolymers: the theory of ionic saturation revisited. Biopolymers 24:427
    • (1985) Biopolymers , vol.24 , pp. 427
    • Hingerty, B.E.1    Ritchie, R.H.2    Ferrell, T.L.3    Turner, J.E.4
  • 56
    • 0347696834 scopus 로고
    • Salt induced conformational changes in DNA: Analysis using the polymer RISM theory
    • Hirata F, Levy RM. 1989. Salt induced conformational changes in DNA: analysis using the polymer RISM theory. J. Phys. Chem. 93:479
    • (1989) J. Phys. Chem. , vol.93 , pp. 479
    • Hirata, F.1    Levy, R.M.2
  • 57
    • 0028092707 scopus 로고
    • Protein electrostatics - Rapid multigrid-based Newton algorithm for solution of the full nonlinear Poisson-Boltzmann equation
    • 51a. Holst M, Kozack R, Saied F. 1994. Protein electrostatics - rapid multigrid-based Newton algorithm for solution of the full nonlinear Poisson-Boltzmann equation. J. Biomol. Struct. Dyn. 11:1437
    • (1994) J. Biomol. Struct. Dyn. , vol.11 , pp. 1437
    • Holst, M.1    Kozack, R.2    Saied, F.3
  • 58
    • 0000525721 scopus 로고
    • Multigrid solution of the Poisson-Boltzmann equation
    • 51b. Holst M, Saied F. 1993. Multigrid solution of the Poisson-Boltzmann equation. J. Comp. Chem. 14:105
    • (1993) J. Comp. Chem. , vol.14 , pp. 105
    • Holst, M.1    Saied, F.2
  • 59
    • 0029016182 scopus 로고
    • Classical electrostatics in biology and chemistry
    • Honig B, Nicholls A. 1995. Classical electrostatics in biology and chemistry. Science 268:1144
    • (1995) Science , vol.268 , pp. 1144
    • Honig, B.1    Nicholls, A.2
  • 61
    • 0343648651 scopus 로고
    • Free energy of an arbitrary charge distribution imbedded in coaxial cylindrical dielectric continua: Application to conformational preferences of DNA in aqueous solutions
    • and references therein
    • Jayaram B, Beveridge DL. 1990. Free energy of an arbitrary charge distribution imbedded in coaxial cylindrical dielectric continua: application to conformational preferences of DNA in aqueous solutions. J. Phys. Chem. 94:4666 (and references therein)
    • (1990) J. Phys. Chem. , vol.94 , pp. 4666
    • Jayaram, B.1    Beveridge, D.L.2
  • 62
    • 33751499778 scopus 로고
    • Grand canonical Monte Carlo simulations on aqueous solutions of NaCl and NaDNA: Excess chemical potentials and sources of nonideality in electrolyte and polyelectrolyte solutions
    • Jayaram B, Beveridge DL. 1991. Grand canonical Monte Carlo simulations on aqueous solutions of NaCl and NaDNA: excess chemical potentials and sources of nonideality in electrolyte and polyelectrolyte solutions. J. Phys. Chem. 95:2506
    • (1991) J. Phys. Chem. , vol.95 , pp. 2506
    • Jayaram, B.1    Beveridge, D.L.2
  • 63
    • 1442299978 scopus 로고
    • Energetic and kinetic aspects of macromolecular association: A computational study of repressor-operator complexation
    • THEOCHEM. In press
    • Jayaram B, Das A, Aneja N. 1995. Energetic and kinetic aspects of macromolecular association: a computational study of repressor-operator complexation. J. Mol. Struct. (THEOCHEM). In press
    • (1995) J. Mol. Struct.
    • Jayaram, B.1    Das, A.2    Aneja, N.3
  • 64
    • 0001739390 scopus 로고
    • A theoretical study of polyelectrolyte effects in protein-DNA interactions: Monte Carlo free energy simulations on the ion atmosphere contribution to the thermodynamics of λ repressor-operator complex formation
    • Jayaram B, DiCapua FM, Beveridge DL. 1991. A theoretical study of polyelectrolyte effects in protein-DNA interactions: Monte Carlo free energy simulations on the ion atmosphere contribution to the thermodynamics of λ repressor-operator complex formation. J. Am. Chem. Soc. 113:5211
    • (1991) J. Am. Chem. Soc. , vol.113 , pp. 5211
    • Jayaram, B.1    DiCapua, F.M.2    Beveridge, D.L.3
  • 65
    • 0024580271 scopus 로고
    • The electrostatic potential of B-DNA
    • Jayaram B, Sharp K, Honig B. 1989. The electrostatic potential of B-DNA. Biopolymers 28:975
    • (1989) Biopolymers , vol.28 , pp. 975
    • Jayaram, B.1    Sharp, K.2    Honig, B.3
  • 66
    • 0025444642 scopus 로고
    • Monte Carlo simulation studies on the structure of the counterion atmosphere of B-DNA. Variations on the primitive dielectric model
    • Jayaram B, Swaminathan S, Beveridge DL, Sharp K, Honig B. 1990. Monte Carlo simulation studies on the structure of the counterion atmosphere of B-DNA. Variations on the primitive dielectric model. Macromolecules 23:3156
    • (1990) Macromolecules , vol.23 , pp. 3156
    • Jayaram, B.1    Swaminathan, S.2    Beveridge, D.L.3    Sharp, K.4    Honig, B.5
  • 67
    • 0026029516 scopus 로고
    • Zinc ion-DNA polymer interactions
    • Jia X, Marzilli LG. 1991. Zinc ion-DNA polymer interactions. Biopolymers 31:23
    • (1991) Biopolymers , vol.31 , pp. 23
    • Jia, X.1    Marzilli, L.G.2
  • 68
    • 0027435626 scopus 로고
    • Comparative spectroscopic, calorimetric and computational studies of nucleic acid complexes with 2′,5″- versus 3′,5″-phosphodiester linkages
    • Jin R, Chapman WH, Srinivasan R, Olson WK, Breslow RD, Breslauer KJ. 1993. Comparative spectroscopic, calorimetric and computational studies of nucleic acid complexes with 2′,5″- versus 3′,5″-phosphodiester linkages. Proc. Natl. Acad. Sci. USA 90:10568
    • (1993) Proc. Natl. Acad. Sci. USA , vol.90 , pp. 10568
    • Jin, R.1    Chapman, W.H.2    Srinivasan, R.3    Olson, W.K.4    Breslow, R.D.5    Breslauer, K.J.6
  • 70
    • 0022799313 scopus 로고
    • Manganese-deoxyribonucleic acid binding modes: Nuclear magnetic relaxation dispersion results
    • Kennedy SD, Bryant RG. 1986. Manganese-deoxyribonucleic acid binding modes: nuclear magnetic relaxation dispersion results. Biophys. J. 50:669
    • (1986) Biophys. J. , vol.50 , pp. 669
    • Kennedy, S.D.1    Bryant, R.G.2
  • 71
    • 0025778131 scopus 로고
    • Computation of ionic distribution around charged biomolecular structures: Results for right handed and left handed DNA
    • Klement R, Soumpasis DM, Jovin TM. 1991. Computation of ionic distribution around charged biomolecular structures: results for right handed and left handed DNA. Proc. Natl. Acad. Sci. USA 88:4631
    • (1991) Proc. Natl. Acad. Sci. USA , vol.88 , pp. 4631
    • Klement, R.1    Soumpasis, D.M.2    Jovin, T.M.3
  • 72
    • 0025264106 scopus 로고
    • Inclusion of ionic interactions in force field calculations of charged biomolecules - DNA structural transitions
    • Klement R, Soumpasis DM, Kitzing EV, Jovin TM. 1990. Inclusion of ionic interactions in force field calculations of charged biomolecules - DNA structural transitions. Biopolymers 29:1089
    • (1990) Biopolymers , vol.29 , pp. 1089
    • Klement, R.1    Soumpasis, D.M.2    Kitzing, E.V.3    Jovin, T.M.4
  • 73
    • 0020856901 scopus 로고
    • Calculations of the spatial distribution of charge density in the environment of DNA
    • Klein BJ, Pack GR. 1983. Calculations of the spatial distribution of charge density in the environment of DNA. Biopolymers 22:2331
    • (1983) Biopolymers , vol.22 , pp. 2331
    • Klein, B.J.1    Pack, G.R.2
  • 74
    • 0024295009 scopus 로고
    • Dynamics of repressor-operator recognition: The trilo-encooed tetracycline resistance control
    • Kleinschmidt C, Tovar K, Hillen W, Porschke D. 1988. Dynamics of repressor-operator recognition: the trilo-encooed tetracycline resistance control. Biochemistry 27:1094
    • (1988) Biochemistry , vol.27 , pp. 1094
    • Kleinschmidt, C.1    Tovar, K.2    Hillen, W.3    Porschke, D.4
  • 75
    • 7044239742 scopus 로고
    • Free energy calculations: Applications to chemical and biochemical phenomena
    • Kollman P. 1993. Free energy calculations: applications to chemical and biochemical phenomena. Chem. Rev. 93:2395
    • (1993) Chem. Rev. , vol.93 , pp. 2395
    • Kollman, P.1
  • 76
    • 0025292904 scopus 로고
    • Langevin modes of macromolecules: Application to crambin and DNA hexamers
    • Kottalam J, Case DA. 1990. Langevin modes of macromolecules: application to crambin and DNA hexamers. Biopolymers 29:1409
    • (1990) Biopolymers , vol.29 , pp. 1409
    • Kottalam, J.1    Case, D.A.2
  • 78
    • 0028128015 scopus 로고
    • Monte Carlo and Poisson-Boltzmann calculations of the fraction of counterions bound to DNA
    • Lamm G, Wong L, Pack GR. 1994. Monte Carlo and Poisson-Boltzmann calculations of the fraction of counterions bound to DNA. Biopolymers 34:227
    • (1994) Biopolymers , vol.34 , pp. 227
    • Lamm, G.1    Wong, L.2    Pack, G.R.3
  • 79
    • 0028261555 scopus 로고
    • Modelling DNA conformational mechanics
    • Lavery R, Hartmann B. 1994. Modelling DNA conformational mechanics. Biophys. Chem. 50:33
    • (1994) Biophys. Chem. , vol.50 , pp. 33
    • Lavery, R.1    Hartmann, B.2
  • 80
    • 0022008114 scopus 로고
    • The dependence of the surface electrostatic potential of B-DNA on environmental factors
    • 72a. Lavery R, Pullman B. 1985. The dependence of the surface electrostatic potential of B-DNA on environmental factors. J. Biomol. Struct. Dyn. 2: 1021
    • (1985) J. Biomol. Struct. Dyn. , vol.2 , pp. 1021
    • Lavery, R.1    Pullman, B.2
  • 81
    • 0021383374 scopus 로고
    • Monte Carlo determination of the distribution of ions about a cylindrical polyelectrolyte
    • Le Bret M, Zimm BH. 1984. Monte Carlo determination of the distribution of ions about a cylindrical polyelectrolyte. Biopolymers 23:271
    • (1984) Biopolymers , vol.23 , pp. 271
    • Le Bret, M.1    Zimm, B.H.2
  • 82
    • 0020262664 scopus 로고
    • Computer simulation of DNA double helix dynamics
    • Levitt M. 1983. Computer simulation of DNA double helix dynamics. Cold Spring Harbor Symp. Quant. Biol. 47:251
    • (1983) Cold Spring Harbor Symp. Quant. Biol. , vol.47 , pp. 251
    • Levitt, M.1
  • 83
    • 0022573212 scopus 로고
    • Kinetics of protein-nucleic acid interactions: Use of salt effects to prove mechanisms of interaction
    • Lohman TM. 1986. Kinetics of protein-nucleic acid interactions: use of salt effects to prove mechanisms of interaction. CRC Crit. Rev. Biochem. 19:191
    • (1986) CRC Crit. Rev. Biochem. , vol.19 , pp. 191
    • Lohman, T.M.1
  • 84
    • 0001660190 scopus 로고
    • Theoretical studies of DNA during orthogonal field alternating gel electrophoresis
    • Madden TL, Deutsch JM. 1991. Theoretical studies of DNA during orthogonal field alternating gel electrophoresis. J. Chem. Phys. 94:1584
    • (1991) J. Chem. Phys. , vol.94 , pp. 1584
    • Madden, T.L.1    Deutsch, J.M.2
  • 86
    • 0017895903 scopus 로고
    • The molecular theory of polyelectrolyte solutions with application to the electrostatic properties of polynucleotides
    • Manning GS. 1978. The molecular theory of polyelectrolyte solutions with application to the electrostatic properties of polynucleotides. Q. Rev. Biophys. 11:179
    • (1978) Q. Rev. Biophys. , vol.11 , pp. 179
    • Manning, G.S.1
  • 87
    • 0000541402 scopus 로고
    • Counterion binding in polyelectrolyte theory
    • Manning GS. 1979. Counterion binding in polyelectrolyte theory. Acc. Chem. Res. 12:443
    • (1979) Acc. Chem. Res. , vol.12 , pp. 443
    • Manning, G.S.1
  • 88
    • 0021936282 scopus 로고
    • Netropsin binding to poly d(AT)-poly d(AT) and to poly dA-poly dT: A comparative thermodynamic study
    • Marky LA, Curry J, Breslauer KJ. 1985. Netropsin binding to poly d(AT)-poly d(AT) and to poly dA-poly dT: a comparative thermodynamic study. Prog. Clin. Biol. Res. 172:155
    • (1985) Prog. Clin. Biol. Res. , vol.172 , pp. 155
    • Marky, L.A.1    Curry, J.2    Breslauer, K.J.3
  • 89
    • 0021752280 scopus 로고
    • Differential electrostatic stabilization of A, B and Z forms of DNA
    • Matthew JB, Richards FM. 1984. Differential electrostatic stabilization of A, B and Z forms of DNA. Biopolymers 23:2743
    • (1984) Biopolymers , vol.23 , pp. 2743
    • Matthew, J.B.1    Richards, F.M.2
  • 90
    • 0026253724 scopus 로고
    • Distance dependent dielectric constants and their application to double helical DNA
    • Mazur J, Jernigan RL. 1991. Distance dependent dielectric constants and their application to double helical DNA. Biopolymers 31:1615
    • (1991) Biopolymers , vol.31 , pp. 1615
    • Mazur, J.1    Jernigan, R.L.2
  • 94
    • 0000001012 scopus 로고
    • Monte Carlo studies of counterion-DNA interactions. Comparison of the radial distribution of counterions with predictions of other polyelectrolyte theories
    • Mills P, Anderson CF, Record MT Jr. 1985. Monte Carlo studies of counterion-DNA interactions. Comparison of the radial distribution of counterions with predictions of other polyelectrolyte theories. J. Phys. Chem. 89:3984
    • (1985) J. Phys. Chem. , vol.89 , pp. 3984
    • Mills, P.1    Anderson, C.F.2    Record Jr., M.T.3
  • 96
    • 0000883906 scopus 로고
    • Grand canonical Monte Carlo calculations of thermodynamic coefficients for a primitive model of DNA-salt solutions
    • Mills P, Anderson CF, Record MT Jr. 1986. Grand canonical Monte Carlo calculations of thermodynamic coefficients for a primitive model of DNA-salt solutions. J. Phys. Chem. 90:6541
    • (1986) J. Phys. Chem. , vol.90 , pp. 6541
    • Mills, P.1    Anderson, C.F.2    Record Jr., M.T.3
  • 98
    • 0028239626 scopus 로고
    • Salt effects on protein-DNA interactions: The lambda cI repressor and Eco RI endonuclease
    • Misra V, Hecht J, Sharp K, Friedman R, Honig B. 1994. Salt effects on protein-DNA interactions: the lambda cI repressor and Eco RI endonuclease. J. Mol. Biol. 238:264
    • (1994) J. Mol. Biol. , vol.238 , pp. 264
    • Misra, V.1    Hecht, J.2    Sharp, K.3    Friedman, R.4    Honig, B.5
  • 99
    • 0028246710 scopus 로고
    • Salt effects on ligand-DNA binding: Minor groove antibiotics
    • Misra V, Sharp K, Friedman R, Honig B. 1994. Salt effects on ligand-DNA binding: minor groove antibiotics. J. Mol. Biol. 238:245
    • (1994) J. Mol. Biol. , vol.238 , pp. 245
    • Misra, V.1    Sharp, K.2    Friedman, R.3    Honig, B.4
  • 100
    • 0001008705 scopus 로고
    • Molecular dynamics simulation of ions and water around triplex DNA
    • Mohan V, Smith PE, Pettitt BM. 1993. Molecular dynamics simulation of ions and water around triplex DNA. J. Phys. Chem. 97:12984
    • (1993) J. Phys. Chem. , vol.97 , pp. 12984
    • Mohan, V.1    Smith, P.E.2    Pettitt, B.M.3
  • 101
    • 33845378291 scopus 로고
    • Ionic distributions near polyelectrolytes. A comparison of theoretical approaches
    • Murthy CS, Bacquet RJ, Rossky PJ. 1985. Ionic distributions near polyelectrolytes. A comparison of theoretical approaches. J. Phys. Chem. 89: 701
    • (1985) J. Phys. Chem. , vol.89 , pp. 701
    • Murthy, C.S.1    Bacquet, R.J.2    Rossky, P.J.3
  • 102
    • 0026337344 scopus 로고
    • Molecular modeling to study DNA intercalation by antitumor drugs in methods in enzymology
    • Neidle S, Jenkins TC. 1991. Molecular modeling to study DNA intercalation by antitumor drugs in methods in enzymology. Methods Enzymol. 203: 433
    • (1991) Methods Enzymol. , vol.203 , pp. 433
    • Neidle, S.1    Jenkins, T.C.2
  • 103
    • 84988103838 scopus 로고
    • Energy functions from energy minimization and dynamics of nucleic acids
    • Nilsson L, Karplus M. 1984. Energy functions from energy minimization and dynamics of nucleic acids. J. Comput. Chem. 1:591
    • (1984) J. Comput. Chem. , vol.1 , pp. 591
    • Nilsson, L.1    Karplus, M.2
  • 104
    • 0028285106 scopus 로고
    • Monte Carlo simulations on potentiometric titration of cylindrical polyelectrolytes: Introduction of a method and its application to model systems without added salt
    • Nishio T. 1994. Monte Carlo simulations on potentiometric titration of cylindrical polyelectrolytes: introduction of a method and its application to model systems without added salt. Biophys. Chem. 49:201
    • (1994) Biophys. Chem. , vol.49 , pp. 201
    • Nishio, T.1
  • 105
    • 0021760642 scopus 로고
    • 23Na NMR relaxation study of the effects of conformation and base composition on the interactions of counterions with double-helical DNA
    • 23Na NMR relaxation study of the effects of conformation and base composition on the interactions of counterions with double-helical DNA. Biochemistry 23:4309
    • (1984) Biochemistry , vol.23 , pp. 4309
    • Nordenskiold, L.1    Chang, D.K.2    Anderson, C.F.3    Record Jr., M.T.4
  • 106
    • 0027209697 scopus 로고
    • Multigrid solution of the nonlinear Poisson-Boltzmann equation and calculation of titration curves
    • 97a. Oberoi H, Allewell N. 1993. Multigrid solution of the nonlinear Poisson-Boltzmann equation and calculation of titration curves. Biophys. J. 65:48
    • (1993) Biophys. J. , vol.65 , pp. 48
    • Oberoi, H.1    Allewell, N.2
  • 107
    • 0000014960 scopus 로고
    • Monte Carlo description of oligoelectrolyte properties of DNA oligomers
    • 97b. Olmsted MC, Anderson CF, Record MT. 1989. Monte Carlo description of oligoelectrolyte properties of DNA oligomers. Proc. Natl. Acad. Sci. 86:7766
    • (1989) Proc. Natl. Acad. Sci. , vol.86 , pp. 7766
    • Olmsted, M.C.1    Anderson, C.F.2    Record, M.T.3
  • 108
    • 0026253640 scopus 로고
    • Importance of oligoelectrolyte end effects for the thermodynamics of conformational transitions of nucleic acid oligomers: A grand canonical Monte Carlo analysis
    • Olmsted MC, Anderson CF, Record MT Jr. 1991. Importance of oligoelectrolyte end effects for the thermodynamics of conformational transitions of nucleic acid oligomers: a grand canonical Monte Carlo analysis. Biopolymers 31:1593
    • (1991) Biopolymers , vol.31 , pp. 1593
    • Olmsted, M.C.1    Anderson, C.F.2    Record Jr., M.T.3
  • 109
    • 0028887796 scopus 로고
    • Grand Canonical Monte Carlo molecular and thermodynamic predictions of ion effects on binding of an oligocation to the center of DNA oligomers
    • 98a. Olmsted MC, Bond J, Anderson CF, Record MT. 1995. Grand Canonical Monte Carlo molecular and thermodynamic predictions of ion effects on binding of an oligocation to the center of DNA oligomers. Biophys. J. 68:634
    • (1995) Biophys. J. , vol.68 , pp. 634
    • Olmsted, M.C.1    Bond, J.2    Anderson, C.F.3    Record, M.T.4
  • 110
    • 8944255827 scopus 로고
    • Excess counterion accumulation around branched nucleic acids
    • 98b. Olmsted MC, Hagerman PJ. 1995. Excess counterion accumulation around branched nucleic acids. J. Mol. Biol. 238:455
    • (1995) J. Mol. Biol. , vol.238 , pp. 455
    • Olmsted, M.C.1    Hagerman, P.J.2
  • 111
    • 0026339117 scopus 로고
    • Computer simulation of DNA supercoiling
    • Olson WK, Zhang P. 1991. Computer simulation of DNA supercoiling. Methods Enzymol. 203:403
    • (1991) Methods Enzymol. , vol.203 , pp. 403
    • Olson, W.K.1    Zhang, P.2
  • 112
    • 0001575672 scopus 로고
    • A simple theory for thermodynamic properties of polyelectrolyte solutions
    • Oosawa F. 1957. A simple theory for thermodynamic properties of polyelectrolyte solutions. J. Polym. Soc. Jpn. 23:421
    • (1957) J. Polym. Soc. Jpn. , vol.23 , pp. 421
    • Oosawa, F.1
  • 113
    • 0025086442 scopus 로고
    • Molecular mechanics modelling of drug-DNA structures: The effects of differing dielectric treatment on helix parameters and comparison with a fully solvated structural model
    • Orozco M, Laughton CA, Herzyk P, Neidle S. 1990. Molecular mechanics modelling of drug-DNA structures: the effects of differing dielectric treatment on helix parameters and comparison with a fully solvated structural model. J. Biomol. Struct. Dyn. 8:359
    • (1990) J. Biomol. Struct. Dyn. , vol.8 , pp. 359
    • Orozco, M.1    Laughton, C.A.2    Herzyk, P.3    Neidle, S.4
  • 115
    • 84990707598 scopus 로고
    • Counterion condensation theory revisited: Limits on its application
    • 102a. Pack GR. 1993. Counterion condensation theory revisited: limits on its application. Int. J. Quantum Chem. 20:213-30
    • (1993) Int. J. Quantum Chem. , vol.20 , pp. 213-230
    • Pack, G.R.1
  • 116
    • 0027379329 scopus 로고
    • The effect of a variable dielectric coefficient and finite ion size on Poisson-Boltzmann calculations of DNA-electrolyte systems
    • Pack GR, Garrett GA, Wong L, Lamm G. 1993. The effect of a variable dielectric coefficient and finite ion size on Poisson-Boltzmann calculations of DNA-electrolyte systems. Biophys. J. 65:1363
    • (1993) Biophys. J. , vol.65 , pp. 1363
    • Pack, G.R.1    Garrett, G.A.2    Wong, L.3    Lamm, G.4
  • 118
    • 0001426265 scopus 로고
    • Ion-ion correlations in polyelectrolyte solutions: Hard sphere counterions
    • Penford R, Jonsson B, Nordholm S. 1993. Ion-ion correlations in polyelectrolyte solutions: hard sphere counterions. J. Chem. Phys. 99:497
    • (1993) J. Chem. Phys. , vol.99 , pp. 497
    • Penford, R.1    Jonsson, B.2    Nordholm, S.3
  • 119
    • 0019598899 scopus 로고
    • Molecular electrostatic potential of the nucleic acids
    • Pullman A, Pullman B. 1981. Molecular electrostatic potential of the nucleic acids. Q. Rev. Biophys. 14:289
    • (1981) Q. Rev. Biophys. , vol.14 , pp. 289
    • Pullman, A.1    Pullman, B.2
  • 120
    • 0020953988 scopus 로고
    • Electrostatics of polymorphic DNA
    • Pullman B. 1983. Electrostatics of polymorphic DNA. J. Biomol. Struct. Dyn. 1:773
    • (1983) J. Biomol. Struct. Dyn. , vol.1 , pp. 773
    • Pullman, B.1
  • 121
    • 0028334940 scopus 로고
    • Counterion condensation in DNA systems: The cylindrical Poisson-Boltzmann model revisited
    • Rajasekaran E, Jayaram B. 1994. Counterion condensation in DNA systems: the cylindrical Poisson-Boltzmann model revisited. Biopolymers 34:443
    • (1994) Biopolymers , vol.34 , pp. 443
    • Rajasekaran, E.1    Jayaram, B.2
  • 122
    • 0000777707 scopus 로고
    • Energetic coupling between DNA bending and base-pair opening
    • Ramstein J, Lavery R. 1988. Energetic coupling between DNA bending and base-pair opening. Proc. Natl. Acad. Sci. USA 85:7231
    • (1988) Proc. Natl. Acad. Sci. USA , vol.85 , pp. 7231
    • Ramstein, J.1    Lavery, R.2
  • 123
    • 84986522875 scopus 로고
    • New method for the computation of ionic distribution of round rod-like polyelectrolytes with the helical distribution of charges. I. General approach and a nonlinearized Poisson-Boltzmann equation
    • Rashin AA, Malinsky J. 1991. New method for the computation of ionic distribution of round rod-like polyelectrolytes with the helical distribution of charges. I. General approach and a nonlinearized Poisson-Boltzmann equation. J. Comp. Chem. 12: 981
    • (1991) J. Comp. Chem. , vol.12 , pp. 981
    • Rashin, A.A.1    Malinsky, J.2
  • 126
    • 0026869974 scopus 로고
    • Theory of delocalized ionic binding to polynucleotides: Structural and excluded volume effects
    • 112a. Ray J, Manning GS. 1992. Theory of delocalized ionic binding to polynucleotides: structural and excluded volume effects. Biopolymers 32: 541-549
    • (1992) Biopolymers , vol.32 , pp. 541-549
    • Ray, J.1    Manning, G.S.2
  • 127
    • 0017820499 scopus 로고
    • Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: The role of ion association and release, screening and ion effects on water activity
    • Record MT Jr, Anderson CF, Lohman T. 1978. Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the role of ion association and release, screening and ion effects on water activity. Q. Rev. Biophys. 11:103
    • (1978) Q. Rev. Biophys. , vol.11 , pp. 103
    • Record Jr., M.T.1    Anderson, C.F.2    Lohman, T.3
  • 129
    • 2542606126 scopus 로고
    • Counterion spin relaxation in DNA solutions: A stochastic dynamics simulation study
    • Reddy MR, Rossky PJ, Murthy CS. 1987. Counterion spin relaxation in DNA solutions: a stochastic dynamics simulation study. J. Phys. Chem. 91:4923
    • (1987) J. Phys. Chem. , vol.91 , pp. 4923
    • Reddy, M.R.1    Rossky, P.J.2    Murthy, C.S.3
  • 130
    • 0001369897 scopus 로고
    • Monte Carlo study of titration of linear polyelectrolyte effects
    • Reed CE, Reed WF. 1991. Monte Carlo study of titration of linear polyelectrolyte effects. J. Chem. Phys. 96: 1609
    • (1991) J. Chem. Phys. , vol.96 , pp. 1609
    • Reed, C.E.1    Reed, W.F.2
  • 131
    • 0001574661 scopus 로고
    • Entropy volume correlation with hydration changes in DNA-ligand interactions
    • Rentzeperis D, Marky LA, Kupke DW. 1992. Entropy volume correlation with hydration changes in DNA-ligand interactions. J. Phys. Chem. 96:9612
    • (1992) J. Phys. Chem. , vol.96 , pp. 9612
    • Rentzeperis, D.1    Marky, L.A.2    Kupke, D.W.3
  • 133
    • 0000127073 scopus 로고
    • Sequence-specific recognition of double helical nucleic acids by proteins
    • Seeman NC, Rosenberg JM, Rich A. 1976. Sequence-specific recognition of double helical nucleic acids by proteins. Proc. Natl. Acad. Sci. USA 73:804
    • (1976) Proc. Natl. Acad. Sci. USA , vol.73 , pp. 804
    • Seeman, N.C.1    Rosenberg, J.M.2    Rich, A.3
  • 135
    • 0027377079 scopus 로고
    • Molecular dynamics investigations of DNA triple helical models: Unique features of the Watson-Crick duplex
    • Sekharudu CY, Yathindra N, Sundaralingam M. 1993. Molecular dynamics investigations of DNA triple helical models: unique features of the Watson-Crick duplex. J. Biomol. Struct. Dyn. 11:225
    • (1993) J. Biomol. Struct. Dyn. , vol.11 , pp. 225
    • Sekharudu, C.Y.1    Yathindra, N.2    Sundaralingam, M.3
  • 136
    • 0025741694 scopus 로고
    • Comparison of operator-specific and nonspecific DNA binding of the λ cI repressor: [KCl] and pH effects
    • Senear DF, Batey R. 1991. Comparison of operator-specific and nonspecific DNA binding of the λ cI repressor: [KCl] and pH effects. Biochemistry 30:6677
    • (1991) Biochemistry , vol.30 , pp. 6677
    • Senear, D.F.1    Batey, R.2
  • 137
    • 0028215767 scopus 로고
    • Electrostatic interactions in macromolecules
    • Sharp K. 1994. Electrostatic interactions in macromolecules. Curr. Opin. Struct. Biol. 4:234
    • (1994) Curr. Opin. Struct. Biol. , vol.4 , pp. 234
    • Sharp, K.1
  • 138
    • 0029068766 scopus 로고
    • Polyelectrolyte electrostatics: Salt dependence, entropic and enthalpic contributions to free energy in the non-linear Poisson-Boltzmann model
    • In press
    • 122a. Sharp K. 1995. Polyelectrolyte electrostatics: salt dependence, entropic and enthalpic contributions to free energy in the non-linear Poisson-Boltzmann model. Biopolymers. In press
    • (1995) Biopolymers.
    • Sharp, K.1
  • 139
    • 0029038105 scopus 로고
    • Salt effects on polyelectrolyte-ligand binding: Comparison of Poisson Boltzmann and limiting law counterion binding models
    • In press
    • 122b. Sharp K, Friedman R, Misra V, Hecht J, Honig B. 1995. Salt effects on polyelectrolyte-ligand binding: comparison of Poisson Boltzmann and limiting law counterion binding models. Biopolymers. In press
    • (1995) Biopolymers
    • Sharp, K.1    Friedman, R.2    Misra, V.3    Hecht, J.4    Honig, B.5
  • 140
    • 0025283002 scopus 로고
    • Electrostatic interactions in macromolecules: Theory and applications
    • Sharp K, Honig B. 1990. Electrostatic interactions in macromolecules: theory and applications. Annu. Rev. Biophys. Biophys. Chem. 19:301
    • (1990) Annu. Rev. Biophys. Biophys. Chem. , vol.19 , pp. 301
    • Sharp, K.1    Honig, B.2
  • 142
    • 0001555216 scopus 로고
    • A molecular dynamics simulation of double helical B-DNA including counterions and water
    • Siebel GL, Singh UC, Kollman PA. 1985. A molecular dynamics simulation of double helical B-DNA including counterions and water. Proc. Natl. Acad. Sci. USA 82:6537
    • (1985) Proc. Natl. Acad. Sci. USA , vol.82 , pp. 6537
    • Siebel, G.L.1    Singh, U.C.2    Kollman, P.A.3
  • 143
    • 0007158350 scopus 로고
    • Contributions of the polyion and counterions to the internal and free energies of polyelectrolyte solutions
    • Skerjanc J. 1990. Contributions of the polyion and counterions to the internal and free energies of polyelectrolyte solutions. J. Chem. Phys. 93: 6731
    • (1990) J. Chem. Phys. , vol.93 , pp. 6731
    • Skerjanc, J.1
  • 144
    • 0026253887 scopus 로고
    • + on the persistence length and excluded volume of T7 bacteriophage DNA
    • + on the persistence length and excluded volume of T7 bacteriophage DNA. Biopolymers 31:1559
    • (1991) Biopolymers , vol.31 , pp. 1559
    • Sobel, E.S.1    Harpst, J.A.2
  • 145
    • 0007646582 scopus 로고
    • Statistical mechanics of the B-Z transition of DNA: Contribution of diffuse ionic interactions
    • Soumpasis DM. 1984. Statistical mechanics of the B-Z transition of DNA: contribution of diffuse ionic interactions. Proc. Natl. Acad. Sci. USA 81:5116
    • (1984) Proc. Natl. Acad. Sci. USA , vol.81 , pp. 5116
    • Soumpasis, D.M.1
  • 146
    • 0001370674 scopus 로고
    • Theory for second virial coefficients of short DNA
    • Stigter D, Dill KA. 1993. Theory for second virial coefficients of short DNA. J. Phys. Chem. 97:12995
    • (1993) J. Phys. Chem. , vol.97 , pp. 12995
    • Stigter, D.1    Dill, K.A.2
  • 147
    • 0024121512 scopus 로고
    • Theoretical considerations on the "spine of hydration" in the minor groove of d(CGC GA at TCG CG) d (GC GC T-TAAGCGC): Monte Carlo computer simulations
    • Subramanian P, Ravishanker G, Beveridge DL. 1988. Theoretical considerations on the "spine of hydration" in the minor groove of d(CGC GA AT TCG CG) d (GC GC T-TAAGCGC): Monte Carlo computer simulations. Proc. Natl. Acad. Sci. USA 85:1836
    • (1988) Proc. Natl. Acad. Sci. USA , vol.85 , pp. 1836
    • Subramanian, P.1    Ravishanker, G.2    Beveridge, D.L.3
  • 148
    • 0006613264 scopus 로고
    • Molecular dynamics simulation of a deoxynucleoside-drug intercalation complex: DCpG/ proflayin
    • Swaminathan S, Beveridge DL, Berman HM. 1990. Molecular dynamics simulation of a deoxynucleoside-drug intercalation complex: dCpG/ proflayin. J. Phys. Chem. 94:4660
    • (1990) J. Phys. Chem. , vol.94 , pp. 4660
    • Swaminathan, S.1    Beveridge, D.L.2    Berman, H.M.3
  • 149
    • 0000930430 scopus 로고
    • Molecular dynamics of B-DNA including counterions and water: A 140 psec trajectory for d(CGCGAATTCGCG) based on the GROMOS force field
    • Swaminathan S, Ravishanker G, Beveridge DL. 1991. Molecular dynamics of B-DNA including counterions and water: a 140 psec trajectory for d(CGCGAATTCGCG) based on the GROMOS force field. J. Am. Chem. Soc. 113:5027
    • (1991) J. Am. Chem. Soc. , vol.113 , pp. 5027
    • Swaminathan, S.1    Ravishanker, G.2    Beveridge, D.L.3
  • 150
    • 0023449766 scopus 로고
    • Hydration structure and dynamics of B-and Z-DNA in the presence of counterions via molecular dynamics simulations
    • Swamy KN, Clementi E. 1987. Hydration structure and dynamics of B-and Z-DNA in the presence of counterions via molecular dynamics simulations. Biopolymers 26:1901
    • (1987) Biopolymers , vol.26 , pp. 1901
    • Swamy, K.N.1    Clementi, E.2
  • 151
    • 0025355712 scopus 로고
    • Application of the method of phage T4 DNA ligase-catalyzed ring-closure to the study of DNA structure. II. NaCl dependence of DNA flexibility and helical repeat
    • Taylor WH, Hagerman PJ. 1990. Application of the method of phage T4 DNA ligase-catalyzed ring-closure to the study of DNA structure. II. NaCl dependence of DNA flexibility and helical repeat. J. Mol. Biol. 212:363
    • (1990) J. Mol. Biol. , vol.212 , pp. 363
    • Taylor, W.H.1    Hagerman, P.J.2
  • 152
    • 11744256643 scopus 로고
    • Molecular interactions in solution: An overview of methods based on continuous distributions of the solvent
    • Tomasi J, Persico M. 1994. Molecular interactions in solution: an overview of methods based on continuous distributions of the solvent. Chem. Rev. 94:2027
    • (1994) Chem. Rev. , vol.94 , pp. 2027
    • Tomasi, J.1    Persico, M.2
  • 153
    • 33845376356 scopus 로고
    • Electrostatic effects on ion distribution around aqueous macromolecules
    • Troll MT, Roitman D, Conrad J, Zimm BH. 1986. Electrostatic effects on ion distribution around aqueous macromolecules. Macromolecules 19:1186
    • (1986) Macromolecules , vol.19 , pp. 1186
    • Troll, M.T.1    Roitman, D.2    Conrad, J.3    Zimm, B.H.4
  • 154
  • 155
    • 0001449615 scopus 로고
    • Flexible polyelectrolyte in ionic solution: A Monte Carlo study
    • Valleau JP. 1989. Flexible polyelectrolyte in ionic solution: a Monte Carlo study. Chem. Phys. 129:163
    • (1989) Chem. Phys. , vol.129 , pp. 163
    • Valleau, J.P.1
  • 156
    • 2142813682 scopus 로고
    • Computer simulation of molecular dynamics: Methodology, applications and perspectives in chemistry
    • van Gunsteren WF, Berendsen HJC. 1990. Computer simulation of molecular dynamics: methodology, applications and perspectives in chemistry. Angew. Chem. Int. Ed. Engl. 29: 992
    • (1990) Angew. Chem. Int. Ed. Engl. , vol.29 , pp. 992
    • Gunsteren, W.F.1    Berendsen, H.J.C.2
  • 157
    • 36549096819 scopus 로고
    • A grand canonical Monte Carlo simulation study of polyelectrolyte solutions
    • Vlachy V, Haymet ADJ. 1986. A grand canonical Monte Carlo simulation study of polyelectrolyte solutions. J. Chem. Phys. 84:5874
    • (1986) J. Chem. Phys. , vol.84 , pp. 5874
    • Vlachy, V.1    Haymet, A.D.J.2
  • 159
    • 0026713204 scopus 로고
    • Modeling DNA structures: Molecular mechanics and molecular dynamics
    • von Kitzing E. 1992. Modeling DNA structures: molecular mechanics and molecular dynamics. Methods Enzymol. 211:449
    • (1992) Methods Enzymol. , vol.211 , pp. 449
    • Kitzing, E.1
  • 162
    • 0026511587 scopus 로고
    • Towards a dynamical structure of duplex DNA in solution: Comparison of theoretical and experimental NOE intensities of d(CGCGAATTCGCG)
    • Whitka JM, Swaminathan S, Srinivasan J, Beveridge DL, Bolton PH. 1992. Towards a dynamical structure of duplex DNA in solution: comparison of theoretical and experimental NOE intensities of d(CGCGAATTCGCG). Science 255:597
    • (1992) Science , vol.255 , pp. 597
    • Whitka, J.M.1    Swaminathan, S.2    Srinivasan, J.3    Beveridge, D.L.4    Bolton, P.H.5
  • 163
    • 0024328777 scopus 로고
    • Laser temperature-jump, spectroscopic, and thermodynamic study of salt effects on duplex formation by dGCATGC
    • Williams AP, Longfellow CE, Freier SM, Kierzek R, Turner DH. 1989. Laser temperature-jump, spectroscopic, and thermodynamic study of salt effects on duplex formation by dGCATGC. Biochemistry 28:4283
    • (1989) Biochemistry , vol.28 , pp. 4283
    • Williams, A.P.1    Longfellow, C.E.2    Freier, S.M.3    Kierzek, R.4    Turner, D.H.5
  • 164
    • 0019887628 scopus 로고
    • Diffusion driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor-operator interactions: Kinetic measurements and conclusions
    • Winter RB, Berg OG, von Hippel PH. 1981. Diffusion driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor-operator interactions: kinetic measurements and conclusions. Biochemistry 20:6929
    • (1981) Biochemistry , vol.20 , pp. 6929
    • Winter, R.B.1    Berg, O.G.2    Von Hippel, P.H.3
  • 165
    • 8944229901 scopus 로고    scopus 로고
    • Counterions may intrude into the spine of hydration in the minor groove of the B DNA double helix: The "AT pocket."
    • Submitted
    • 146a. Young M, Jayaram B, Beveridge DL. 1996. Counterions may intrude into the spine of hydration in the minor groove of the B DNA double helix: the "AT pocket." J. Am. Chem. Soc. Submitted
    • (1996) J. Am. Chem. Soc.
    • Young, M.1    Jayaram, B.2    Beveridge, D.L.3
  • 166
    • 8944240556 scopus 로고    scopus 로고
    • Nanosecond molecular dynamics trajectories for a B DNA oligonucleotide and explicit water and counterions based on the AMBER force field
    • Submitted
    • 146b. Young MA, Ravishanker G, Beveridge DL. 1996. Nanosecond molecular dynamics trajectories for a B DNA oligonucleotide and explicit water and counterions based on the AMBER force field. Biophys. J. Submitted
    • (1996) Biophys. J.
    • Young, M.A.1    Ravishanker, G.2    Beveridge, D.L.3
  • 167
    • 0029110156 scopus 로고
    • Toward the accurate modeling of DNA: The importance of long-range electrostatics
    • York DM, Yang W, Lee H, Darden T, Pedersen LG. 1995. Toward the accurate modeling of DNA: the importance of long-range electrostatics. J. Am. Chem. Soc. 117:5001
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 5001
    • York, D.M.1    Yang, W.2    Lee, H.3    Darden, T.4    Pedersen, L.G.5
  • 168
    • 0026619551 scopus 로고
    • Poisson-Boltzmann analysis of the lambda repressor-operator interaction
    • Zacharias M, Luty BA, Davis ME, McCammon JA. 1992. Poisson-Boltzmann analysis of the lambda repressor-operator interaction. Biophys. J. 63:1280
    • (1992) Biophys. J. , vol.63 , pp. 1280
    • Zacharias, M.1    Luty, B.A.2    Davis, M.E.3    McCammon, J.A.4
  • 170
    • 36449007981 scopus 로고
    • Lakes-straits model of field inversion gel electrophoresis of DNA
    • Zimm BH. 1991. Lakes-straits model of field inversion gel electrophoresis of DNA. J. Chem. Phys. 94:2187
    • (1991) J. Chem. Phys. , vol.94 , pp. 2187
    • Zimm, B.H.1
  • 171
    • 0020954109 scopus 로고
    • Counterion condensation and system dimensionality
    • Zimm BH, LeBret M. 1983. Counterion condensation and system dimensionality. J. Biomol. Struct. Dyn. 1: 461
    • (1983) J. Biomol. Struct. Dyn. , vol.1 , pp. 461
    • Zimm, B.H.1    LeBret, M.2


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