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Volumn 72, Issue 1, 1997, Pages 291-300

Proton equilibria in the minor groove of DNA

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID ANALYSIS; ARTICLE; CALCULATION; DNA ADDUCT; DNA DETERMINATION; DNA STRUCTURE;

EID: 0031030755     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(97)78668-5     Document Type: Article
Times cited : (23)

References (38)
  • 1
    • 0028305457 scopus 로고
    • Prediction of pH-dependent properties of proteins
    • Antosiewicz, J., J. A. McCammon, and M. K. Gilson. 1994. Prediction of pH-dependent properties of proteins. J. Mol. Biol. 238:415-436.
    • (1994) J. Mol. Biol. , vol.238 , pp. 415-436
    • Antosiewicz, J.1    McCammon, J.A.2    Gilson, M.K.3
  • 2
    • 0026612756 scopus 로고
    • Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin
    • Bashtford, D., and K. Gerwert. 1992. Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin. J. Mol Biol. 224: 473-486.
    • (1992) J. Mol Biol. , vol.224 , pp. 473-486
    • Bashtford, D.1    Gerwert, K.2
  • 3
    • 0025197061 scopus 로고
    • pKa's of ionizable groups in proteins: Atomic detail from a continuum electrostatic model
    • Bashford, D., and M. Karplus. 1990. pKa's 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
  • 4
    • 0019883889 scopus 로고
    • Circular dichroism spectral properties of covalent complexes of deoxyribonucleic acid and n-butylamine
    • Chen, C., R. Kilkuskie, and S. Hanlon. 1981. Circular dichroism spectral properties of covalent complexes of deoxyribonucleic acid and n-butylamine. Biochemistry. 20:4987-4995.
    • (1981) Biochemistry , vol.20 , pp. 4987-4995
    • Chen, C.1    Kilkuskie, R.2    Hanlon, S.3
  • 5
    • 0021113918 scopus 로고
    • Conformational characteristics of deoxyribonucleic acid-butylamine complexes with C-type circular dichroism spectra. 1. An X-ray fiber diffraction study
    • Chen, C. Y., B. H. Pheiffer, S. B. Zimmerman, and S. Hanlon. 1983. Conformational characteristics of deoxyribonucleic acid-butylamine complexes with C-type circular dichroism spectra. 1. An X-ray fiber diffraction study. Biochemistry. 22:4746-4751.
    • (1983) Biochemistry , vol.22 , pp. 4746-4751
    • Chen, C.Y.1    Pheiffer, B.H.2    Zimmerman, S.B.3    Hanlon, S.4
  • 6
    • 0023657146 scopus 로고
    • Covalent attachment of an alkylamine prevents the B to Z transition in poly(dG-dC)
    • Chen, C., S. Ringquist, and S. Hanlon. 1987. Covalent attachment of an alkylamine prevents the B to Z transition in poly(dG-dC). Biochemistry. 26:8213-8221.
    • (1987) Biochemistry , vol.26 , pp. 8213-8221
    • Chen, C.1    Ringquist, S.2    Hanlon, S.3
  • 8
    • 0021113910 scopus 로고
    • Conformational characteristics of deoxyribonucleic acid-butylamine complexes with C-type circular dichroism spectra. 2. A Raman spectroscopic study
    • Fish, S. R., C. Y. Chen, G.-J. Thomas Jr., and S. Hanlon. 1983. Conformational characteristics of deoxyribonucleic acid-butylamine complexes with C-type circular dichroism spectra. 2. A Raman spectroscopic study. Biochemistry. 22:4751-4756.
    • (1983) Biochemistry , vol.22 , pp. 4751-4756
    • Fish, S.R.1    Chen, C.Y.2    Thomas G.-J., Jr.3    Hanlon, S.4
  • 9
    • 84985698666 scopus 로고
    • Polyelectrolyte theory. I. Counterion accumulation, site-binding, and their insensitivity to polyelectrolyte shape in solutions containing finite salt concentrations
    • Guéron, M., and G. Weisbuch. 1980. Polyelectrolyte theory. I. Counterion accumulation, site-binding, and their insensitivity to polyelectrolyte shape in solutions containing finite salt concentrations. Biopolymers. 19:353-382.
    • (1980) Biopolymers , vol.19 , pp. 353-382
    • Guéron, M.1    Weisbuch, G.2
  • 10
    • 0011961957 scopus 로고
    • The distribution and dynamics of small ions in simulations of ordered polyelectrolyte solutions
    • Guldbrand, L. 1989. The distribution and dynamics of small ions in simulations of ordered polyelectrolyte solutions. Mol. Physiol. 67: 217-237.
    • (1989) Mol. Physiol. , vol.67 , pp. 217-237
    • Guldbrand, L.1
  • 12
    • 0024580271 scopus 로고
    • The electrostatic potential of B-DNA
    • Jayaram, B., K. A. Sharp, and B. Honig. 1989. The electrostatic potential of B-DNA. Biopolymers. 28:975-993.
    • (1989) Biopolymers , vol.28 , pp. 975-993
    • Jayaram, B.1    Sharp, K.A.2    Honig, B.3
  • 13
    • 0024286079 scopus 로고
    • Effects of charge modification on the helical period of duplex DNA
    • Kilkuskie, R., N. Wood, S. Ringquist, R. Shinn, and S. Hanlon. 1988. Effects of charge modification on the helical period of duplex DNA. Biochemistry. 27:4377-4386.
    • (1988) Biochemistry , vol.27 , pp. 4377-4386
    • Kilkuskie, R.1    Wood, N.2    Ringquist, S.3    Shinn, R.4    Hanlon, S.5
  • 14
    • 0020856901 scopus 로고
    • Calculations of the spatial distribution of charge density in the environment of DNA
    • Klein, B. J., and G. R. Pack. 1983. Calculations of the spatial distribution of charge density in the environment of DNA. Biopolymers. 22: 2331-2352.
    • (1983) Biopolymers , vol.22 , pp. 2331-2352
    • Klein, B.J.1    Pack, G.R.2
  • 15
    • 0025244380 scopus 로고
    • Acidic domains around nucleic acids
    • Lamm, G., and G. R. Pack. 1990. Acidic domains around nucleic acids. Proc. Natl. Acad. Sci. USA. 87:9033-9036.
    • (1990) Proc. Natl. Acad. Sci. USA , vol.87 , pp. 9033-9036
    • Lamm, G.1    Pack, G.R.2
  • 16
    • 0028128015 scopus 로고
    • Monte Carlo and Poisson-Boltzmann calculations of the fraction of counterions bound to DNA
    • Lamm, G., L. Wong, and G. R. Pack. 1994. Monte Carlo and Poisson-Boltzmann calculations of the fraction of counterions bound to DNA. Biopolymers. 34:227-237.
    • (1994) Biopolymers , vol.34 , pp. 227-237
    • Lamm, G.1    Wong, L.2    Pack, G.R.3
  • 17
    • 0029866083 scopus 로고    scopus 로고
    • DNA-mediated acid catalysis: Calculations of the rates of DNA-catalyzed hydrolyses of diol epoxides
    • Lamm, G., L. Wong, and G. R. Pack. 1996. DNA-mediated acid catalysis: calculations of the rates of DNA-catalyzed hydrolyses of diol epoxides. J. Am. Chem. Soc. 118:3325-3331.
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 3325-3331
    • Lamm, G.1    Wong, L.2    Pack, G.R.3
  • 18
    • 84990422191 scopus 로고
    • Distribution of counterions around a cylindrical polyelectrolyte and Manning's condensation theory
    • LeBret, M., and B. H. Zimm. 1984a. Distribution of counterions around a cylindrical polyelectrolyte and Manning's condensation theory. Biopolymers. 23:287-312.
    • (1984) Biopolymers , vol.23 , pp. 287-312
    • LeBret, M.1    Zimm, B.H.2
  • 19
    • 0021383374 scopus 로고
    • Monte Carlo determination of the distribution of ions about a cylindrical polyelectrolyte
    • LeBret, M., and B. H. Zimm. 1984b. Monte Carlo determination of the distribution of ions about a cylindrical polyelectrolyte. Biopolymers. 23:271-285.
    • (1984) Biopolymers , vol.23 , pp. 271-285
    • LeBret, M.1    Zimm, B.H.2
  • 20
    • 0024602840 scopus 로고
    • Base and conformational specificity of an amine modification of DNA
    • Maibenco, D., P. Tang, R. Shinn, and S. Hanlon. 1989. Base and conformational specificity of an amine modification of DNA. Biopolymers. 28:549-571.
    • (1989) Biopolymers , vol.28 , pp. 549-571
    • Maibenco, D.1    Tang, P.2    Shinn, R.3    Hanlon, S.4
  • 21
    • 0017895903 scopus 로고
    • The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides
    • Manning, G. S. 1978. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Q. Rev. Biophys. 2:179-246.
    • (1978) Q. Rev. Biophys. , vol.2 , pp. 179-246
    • Manning, G.S.1
  • 22
    • 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., C. F. Anderson, and M. T. Record, Jr. 1985. Monte Carlo studies of counterion-DNA interactions. Comparison of the radial distribution of counterions with predictions of other polyelectrolyte theories. J. Chem. Phys. 89:3984-3994.
    • (1985) J. Chem. Phys. , vol.89 , pp. 3984-3994
    • Mills, P.1    Anderson, C.F.2    Record M.T., Jr.3
  • 23
    • 0029047968 scopus 로고
    • On the magnitude of the electrostatic contribution to ligand-DNA interactions
    • Misra, V. K., and B. Honig. 1995. On the magnitude of the electrostatic contribution to ligand-DNA interactions. Proc. Natl. Acad. Sci. USA. 92:4691-4695.
    • (1995) Proc. Natl. Acad. Sci. USA , vol.92 , pp. 4691-4695
    • Misra, V.K.1    Honig, B.2
  • 24
    • 33845378291 scopus 로고
    • Ionic distributions near polyelectrolytes. A comparison of theoretical approaches
    • Murthy, C. S., R. J. Bacquet, and P. J. Rossky. 1985. Ionic distributions near polyelectrolytes. A comparison of theoretical approaches. J. Phys. Chem. 89:701-710.
    • (1985) J. Phys. Chem. , vol.89 , pp. 701-710
    • Murthy, C.S.1    Bacquet, R.J.2    Rossky, P.J.3
  • 25
    • 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. 23:4309-4317.
    • (1984) Biochemistry , vol.23 , pp. 4309-4317
    • Nordenskiöld, L.1    Chang, D.K.2    Anderson, C.F.3    Record M.T., Jr.4
  • 26
    • 0027209697 scopus 로고
    • Multigrid solution of the nonlinear Poisson-Boltzmann equation and calculation of titration curves
    • Oberoi, H., and N. M. Allewell. 1993. Multigrid solution of the nonlinear Poisson-Boltzmann equation and calculation of titration curves. Biophys. J. 65:48-55.
    • (1993) Biophys. J. , vol.65 , pp. 48-55
    • Oberoi, H.1    Allewell, N.M.2
  • 27
    • 0027379329 scopus 로고
    • The effect of a variable dielectric coefficient and finite ion size on Poisson-Boltzmann calculations of DNA-electrolyte systems
    • Pack, G. R., G. A. Garrett, L. Wong, and G. Lamm. 1993. The effect of a variable dielectric coefficient and finite ion size on Poisson-Boltzmann calculations of DNA-electrolyte systems. Biophys. J. 65:1363-1370.
    • (1993) Biophys. J. , vol.65 , pp. 1363-1370
    • Pack, G.R.1    Garrett, G.A.2    Wong, L.3    Lamm, G.4
  • 28
    • 0021667810 scopus 로고
    • Generalized Poisson-Boltzmann calculation of the distribution of electrolyte ions around the B- and Z-conformers of DNA
    • Pack, G. R., and B. J. Klein. 1984. Generalized Poisson-Boltzmann calculation of the distribution of electrolyte ions around the B-and Z-conformers of DNA. Biopolymers. 23:2801-2823.
    • (1984) Biopolymers , vol.23 , pp. 2801-2823
    • Pack, G.R.1    Klein, B.J.2
  • 29
    • 0343783562 scopus 로고
    • The structure of the electrolyte environment of DNA
    • D. L. Beveridge and R. Lavery, editors. Adenine Press, New York
    • Pack, G. R., G. Lamm, L. Wong, and D. Clifton. 1990. The structure of the electrolyte environment of DNA. In Theoretical Biochemistry and Molecular Biophysics, Vol. 1. D. L. Beveridge and R. Lavery, editors. Adenine Press, New York. 237-246.
    • (1990) Theoretical Biochemistry and Molecular Biophysics , vol.1 , pp. 237-246
    • Pack, G.R.1    Lamm, G.2    Wong, L.3    Clifton, D.4
  • 30
    • 0022776991 scopus 로고
    • Calculations on the effect of methylation on the electrostatic stability of the B- and Z-conformers of DNA
    • Pack, G. R., C. V. Prasad, J. S. Salafsky, and L. Wong. 1986a. Calculations on the effect of methylation on the electrostatic stability of the B-and Z-conformers of DNA. Biopolymers. 25:1697-1715.
    • (1986) Biopolymers , vol.25 , pp. 1697-1715
    • Pack, G.R.1    Prasad, C.V.2    Salafsky, J.S.3    Wong, L.4
  • 31
    • 0030542296 scopus 로고    scopus 로고
    • Electrostatic effects on the rates of DNA-catalyzed reactions
    • Pack, G. R., and L. Wong. 1996. Electrostatic effects on the rates of DNA-catalyzed reactions. Chem. Phys. 204:279-288.
    • (1996) Chem. Phys. , vol.204 , pp. 279-288
    • Pack, G.R.1    Wong, L.2
  • 32
    • 84990634556 scopus 로고
    • Model systems for DNA and its environment: Suitability and accuracy in theoretical calculations
    • Pack, G. R., L. Wong, and G. Lamm. 1989. Model systems for DNA and its environment: suitability and accuracy in theoretical calculations. Int. J. Quant. Chem. 16:1-15.
    • (1989) Int. J. Quant. Chem. , vol.16 , pp. 1-15
    • Pack, G.R.1    Wong, L.2    Lamm, G.3
  • 33
    • 0023046573 scopus 로고
    • Counterion distribution around DNA: Variation with conformation and sequence
    • Pack, G. R., L. Wong, and C. V. Prasad. 1986b. Counterion distribution around DNA: variation with conformation and sequence. Nucleic Acids Res. 14:1479-1493, 5547.
    • (1986) Nucleic Acids Res. , vol.14 , pp. 1479-1493
    • Pack, G.R.1    Wong, L.2    Prasad, C.V.3
  • 34
    • 0017380736 scopus 로고
    • Electrical double layer, zeta potential, and electrophoretic charge of double-stranded DNA
    • Schellman, J. A., and D. Stigter. 1977. Electrical double layer, zeta potential, and electrophoretic charge of double-stranded DNA. Biopolymers. 16:1415-1434.
    • (1977) Biopolymers , vol.16 , pp. 1415-1434
    • Schellman, J.A.1    Stigter, D.2
  • 35
    • 33751552991 scopus 로고
    • Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation
    • Sharp, K. A., and B. Honig. 1990. Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation. J. Phys. Chem. 94: 7684-7692.
    • (1990) J. Phys. Chem. , vol.94 , pp. 7684-7692
    • Sharp, K.A.1    Honig, B.2
  • 36
    • 84988053694 scopus 로고
    • An all-atom force field for simulations of proteins and nucleic acids
    • Weiner, S. J., P. A. Kollman, D. T. Nguyen, and D. A. Case. 1986. An all-atom force field for simulations of proteins and nucleic acids. J. Comp. Chem. 7:230-252.
    • (1986) J. Comp. Chem. , vol.7 , pp. 230-252
    • Weiner, S.J.1    Kollman, P.A.2    Nguyen, D.T.3    Case, D.A.4
  • 37
    • 0018819243 scopus 로고
    • Comparison of polyelectrolyte theories of the binding of cations to DNA
    • Wilson, R. W., D. C. Rau, and V. A. Bloomfield. 1980. Comparison of polyelectrolyte theories of the binding of cations to DNA. Biophys. J. 30:317-325.
    • (1980) Biophys. J. , vol.30 , pp. 317-325
    • Wilson, R.W.1    Rau, D.C.2    Bloomfield, V.A.3


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