-
2
-
-
0025308916
-
Ion distributions around DNA and other cylindrical polyions: Theoretical descriptions and physical implications
-
Anderson, C. F., and M. T. Record, Jr. 1990. Ion distributions around DNA and other cylindrical polyions: theoretical descriptions and physical implications. Annu. Rev. Biophys. Biophys. Chem. 19:423-465.
-
(1990)
Annu. Rev. Biophys. Biophys. Chem.
, vol.19
, pp. 423-465
-
-
Anderson, C.F.1
Record M.T., Jr.2
-
4
-
-
0015863627
-
The electrostatic potential of a discretely charged cylinder in solution
-
Bailey, J. M. 1973. The electrostatic potential of a discretely charged cylinder in solution. Biopolymers. 12:559-574.
-
(1973)
Biopolymers
, vol.12
, pp. 559-574
-
-
Bailey, J.M.1
-
6
-
-
0024398799
-
A re-examination of the crystal structure of A-DNA using fiber diffraction data
-
Chandrasekaran, R., M. Wang, R.-G. He, L. C. Puigjaner, M. A. Byler, R. P. Millane, and S. Arnott. 1989. A re-examination of the crystal structure of A-DNA using fiber diffraction data. J. Biomol. Struct. Dyn. 6:1189-1202.
-
(1989)
J. Biomol. Struct. Dyn.
, vol.6
, pp. 1189-1202
-
-
Chandrasekaran, R.1
Wang, M.2
He, R.-G.3
Puigjaner, L.C.4
Byler, M.A.5
Millane, R.P.6
Arnott, S.7
-
7
-
-
4243463817
-
Electrostatics in biomolecular structure and dynamics
-
Davis, M. E., and J. A. McCammon, 1990. Electrostatics in biomolecular structure and dynamics. Chem. Rev. 90:509-521.
-
(1990)
Chem. Rev.
, vol.90
, pp. 509-521
-
-
Davis, M.E.1
McCammon, J.A.2
-
8
-
-
0027381083
-
Composite cylinder models of DNA: Application to the electrostatics of the B-Z transition
-
Demaret, J.-P., and M. Gueron. 1993. Composite cylinder models of DNA: application to the electrostatics of the B-Z transition. Biophys. J. 65: 1700-1713.
-
(1993)
Biophys. J.
, vol.65
, pp. 1700-1713
-
-
Demaret, J.-P.1
Gueron, M.2
-
9
-
-
0029972107
-
Electrostatic effects on the stability of condensed DNA in the presence of divalent cations
-
Duguid, J. G., and V. A. Bloomfield. 1996. Electrostatic effects on the stability of condensed DNA in the presence of divalent cations. Biophys. J. 70:2838-2846.
-
(1996)
Biophys. J.
, vol.70
, pp. 2838-2846
-
-
Duguid, J.G.1
Bloomfield, V.A.2
-
10
-
-
0009033547
-
Structure in the electric potential emanating from DNA
-
Edwards, G., D. Hochberg, and T. W. Kephart. 1994. Structure in the electric potential emanating from DNA. Phys. Rev. E. 50:R698-R701.
-
(1994)
Phys. Rev. E.
, vol.50
-
-
Edwards, G.1
Hochberg, D.2
Kephart, T.W.3
-
11
-
-
0025672928
-
Approach to the limit of counterion condensation
-
Fenley, M. O., G. S. Manning, and W. K. Olson. 1990. Approach to the limit of counterion condensation. Biopolymers. 30:1191-1203.
-
(1990)
Biopolymers
, vol.30
, pp. 1191-1203
-
-
Fenley, M.O.1
Manning, G.S.2
Olson, W.K.3
-
12
-
-
38149010969
-
Refined derivation, exact solutions, and singular limits of the Poisson-Boltzmann equation
-
Garrett, A. J. M., and L. Poladian. 1988. Refined derivation, exact solutions, and singular limits of the Poisson-Boltzmann equation. Ann. Phys. 188:386-435.
-
(1988)
Ann. Phys.
, vol.188
, pp. 386-435
-
-
Garrett, A.J.M.1
Poladian, L.2
-
13
-
-
84988087911
-
Calculating the electrostatic potential of molecules in solution: Method and error assessment
-
Gilson, M. K., K. A. Sharp, and B. H. Honig. 1987. Calculating the electrostatic potential of molecules in solution: method and error assessment. J. Comp. Chem. 9:327-335.
-
(1987)
J. Comp. Chem.
, vol.9
, pp. 327-335
-
-
Gilson, M.K.1
Sharp, K.A.2
Honig, B.H.3
-
14
-
-
21944448053
-
Electrostatic potentials near the surface of DNA: Comparing theory and experiment
-
Hecht, J. L., B. Honig, Y.-K. Shin, and W. L. Hubbard. 1995. Electrostatic potentials near the surface of DNA: comparing theory and experiment. J. Phys. Chem. 99:7782-7786.
-
(1995)
J. Phys. Chem.
, vol.99
, pp. 7782-7786
-
-
Hecht, J.L.1
Honig, B.2
Shin, Y.-K.3
Hubbard, W.L.4
-
15
-
-
0001202132
-
Approximate calculation of the electrostatic free energy of nucleic acids and other cylindrical macromolecules
-
Hill, T. L. 1955. Approximate calculation of the electrostatic free energy of nucleic acids and other cylindrical macromolecules. Arch. Biochem. Biophys. 57:229-239.
-
(1955)
Arch. Biochem. Biophys.
, vol.57
, pp. 229-239
-
-
Hill, T.L.1
-
16
-
-
84990406847
-
Dielectric effects in biopolymers: The theory of ionic saturation revisited
-
Hingerty, B. E., R. H. Ritchie, T. L. Ferrell, and J. E. Turner. 1985. Dielectric effects in biopolymers: the theory of ionic saturation revisited. Biopolymers. 24:427-439.
-
(1985)
Biopolymers
, vol.24
, pp. 427-439
-
-
Hingerty, B.E.1
Ritchie, R.H.2
Ferrell, T.L.3
Turner, J.E.4
-
17
-
-
0001169279
-
Structural information in the local electric field of dissolved B-DNA
-
Hochberg D., T. W. Kephart, and G. Edwards. 1994. Structural information in the local electric field of dissolved B-DNA. Phys. Rev. E. 49:851-867.
-
(1994)
Phys. Rev. E.
, vol.49
, pp. 851-867
-
-
Hochberg, D.1
Kephart, T.W.2
Edwards, G.3
-
18
-
-
0009070103
-
Representing structural information of helical charge distributions in cylindrical coordinates
-
Hochberg, D., T. W. Kephart, and G. Edwards. 1997. Representing structural information of helical charge distributions in cylindrical coordinates. Phys. Rev. E. 55:3765-3768.
-
(1997)
Phys. Rev. E.
, vol.55
, pp. 3765-3768
-
-
Hochberg, D.1
Kephart, T.W.2
Edwards, G.3
-
19
-
-
0029016182
-
Classical electrostatics in biology and chemistry
-
Honig, B., and A. Nicholls, 1995. Classical electrostatics in biology and chemistry. Science. 268:1144-1149.
-
(1995)
Science
, vol.268
, pp. 1144-1149
-
-
Honig, B.1
Nicholls, A.2
-
21
-
-
0343648651
-
Free energy of an arbitrary charge distribution imbedded in coaxial cylindrical dielectric continua: Application to conformational preferences of DNA in aqueous solutions
-
Jayaram, B., and D. L. Beveridge. 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. 94:4666-4671.
-
(1990)
J. Phys. Chem.
, vol.94
, pp. 4666-4671
-
-
Jayaram, B.1
Beveridge, D.L.2
-
22
-
-
0024580271
-
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
-
24
-
-
0020856901
-
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
-
25
-
-
0025778131
-
Computation of ionic distributions around charged bimolecular structures: Results for right-handed and left-handed DNA
-
Klement, R., D. M. Soumpasis, and T. M. Jovin. 1991. Computation of ionic distributions around charged bimolecular structures: results for right-handed and left-handed DNA. Proc. Natl. Acad. Sci. USA. 88: 4631-4635.
-
(1991)
Proc. Natl. Acad. Sci. USA
, vol.88
, pp. 4631-4635
-
-
Klement, R.1
Soumpasis, D.M.2
Jovin, T.M.3
-
26
-
-
0028007197
-
Direct measurement of the forces between complementary strands of DNA
-
Lee, G. U., L. A. Chrisey, and R. J. Colton. 1994. Direct measurement of the forces between complementary strands of DNA. Science. 266: 771-773.
-
(1994)
Science
, vol.266
, pp. 771-773
-
-
Lee, G.U.1
Chrisey, L.A.2
Colton, R.J.3
-
28
-
-
0008992707
-
Helical coordinate system and electrostatic fields of double-helix charge distributions
-
Lin-Chung P J., and A. K. Rajagopal. 1995. Helical coordinate system and electrostatic fields of double-helix charge distributions. Phys. Rev. E. 52:901-906.
-
(1995)
Phys. Rev. E.
, vol.52
, pp. 901-906
-
-
Lin-Chung, P.J.1
Rajagopal, A.K.2
-
29
-
-
0027055691
-
Atomic force microscopy imaging of double stranded DNA and RNA
-
Lyubchenko Y. L., A. A. Gall, L. S. Shlyakhtenko, R. E. Harrington, B. L. Jacobs P I. Oden, and S. M. Lindsay. 1992. Atomic force microscopy imaging of double stranded DNA and RNA. J. Biomol. Struct. Dyn. 10:589-606.
-
(1992)
J. Biomol. Struct. Dyn.
, vol.10
, pp. 589-606
-
-
Lyubchenko, Y.L.1
Gall, A.A.2
Shlyakhtenko, L.S.3
Harrington, R.E.4
Jacobs, B.L.5
Oden, P.I.6
Lindsay, S.M.7
-
30
-
-
0027502354
-
Atomic force microscopy of long DNA: Imaging in air and under water
-
Lyubchenko, Y., L. Shlyakhtenko, R. Harrington, P. Oden, and S. Lindsay. 1993. Atomic force microscopy of long DNA: imaging in air and under water. Proc. Natl. Acad. Sci. USA. 90:2137-2140.
-
(1993)
Proc. Natl. Acad. Sci. USA
, vol.90
, pp. 2137-2140
-
-
Lyubchenko, Y.1
Shlyakhtenko, L.2
Harrington, R.3
Oden, P.4
Lindsay, S.5
-
31
-
-
0017895903
-
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
-
32
-
-
0000001012
-
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. Phys. Chem. 89:3984-3994.
-
(1985)
J. Phys. Chem.
, vol.89
, pp. 3984-3994
-
-
Mills, P.1
Anderson, C.F.2
Record M.T., Jr.3
-
33
-
-
0028239626
-
Salt effects on protein-DNA interactions. The λcI repressor and endonuclease
-
Misra, V. K., J. L. Hecht, K. A. Sharp, R. A. Friedman, and B. Honig. 1994a. Salt effects on protein-DNA interactions. The λcI repressor and endonuclease. J. Mol. Biol. 238:264-280.
-
(1994)
J. Mol. Biol.
, vol.238
, pp. 264-280
-
-
Misra, V.K.1
Hecht, J.L.2
Sharp, K.A.3
Friedman, R.A.4
Honig, B.5
-
34
-
-
0028246710
-
Salt effects on ligand-DNA binding. Minor groove binding antibiotics
-
Misra, V. K., K. A. Sharp, R. A. Friedman, and B. Honig. 1994b. Salt effects on ligand-DNA binding. Minor groove binding antibiotics. J. Mol. Biol. 238:245-263.
-
(1994)
J. Mol. Biol.
, vol.238
, pp. 245-263
-
-
Misra, V.K.1
Sharp, K.A.2
Friedman, R.A.3
Honig, B.4
-
35
-
-
36449001060
-
Ionic distribution around simple DNA models. I. Cylindrically averaged properties
-
Montoro, J., C. Gil, and J. L. F. Abascal. 1995. Ionic distribution around simple DNA models. I. Cylindrically averaged properties. J. Chem. Phys. 103:8273-8284.
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8273-8284
-
-
Montoro, J.1
Gil, C.2
Abascal, J.L.F.3
-
36
-
-
0027379329
-
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
-
37
-
-
0021667810
-
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
-
38
-
-
0343783562
-
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. D. L. Beveridge and R. Lavery, editors. Adenine Press, New York. 237-246.
-
(1990)
Theoretical Biochemistry and Molecular Biophysics
, pp. 237-246
-
-
Pack, G.R.1
Lamm, G.2
Wong, L.3
Clifton, D.4
-
39
-
-
0023046573
-
Counterion distribution around DNA: Variation with conformation and sequence
-
Pack, G. R., L. Wong, and C. V. Prasad. 1986. Counterion distribution around DNA: variation with conformation and sequence. Nucleic Acids Res. 14:1479-1493.
-
(1986)
Nucleic Acids Res.
, vol.14
, pp. 1479-1493
-
-
Pack, G.R.1
Wong, L.2
Prasad, C.V.3
-
40
-
-
0025186647
-
Atomic charges for DNA constituents derived from single-crystal x-ray diffraction data
-
Pearlman, D. A., and S. Kim. 1990. Atomic charges for DNA constituents derived from single-crystal x-ray diffraction data. J. Mol. Biol. 211: 171-187.
-
(1990)
J. Mol. Biol.
, vol.211
, pp. 171-187
-
-
Pearlman, D.A.1
Kim, S.2
-
41
-
-
0003474751
-
-
Cambridge University Press, Cambridge
-
Press, W., S. Teukolsky, W. Vetterling, and B. Flannery. 1995. Numerical Recipes in C: The Art of Scientific Computing, 2nd Ed. Cambridge University Press, Cambridge.
-
(1995)
Numerical Recipes in C: The Art of Scientific Computing, 2nd Ed.
-
-
Press, W.1
Teukolsky, S.2
Vetterling, W.3
Flannery, B.4
-
42
-
-
0019598899
-
Molecular electrostatic potential of the nucleic acids
-
Pullman, A., and B. Pullman. 1981. Molecular electrostatic potential of the nucleic acids. Q. Rev. Biophys. 14:289-380.
-
(1981)
Q. Rev. Biophys.
, vol.14
, pp. 289-380
-
-
Pullman, A.1
Pullman, B.2
-
43
-
-
0026558204
-
Direct measurement of the intermolecular forces between counterion-condensed DNA double helices. Evidence for long range attractive hydration forces
-
Rau, D. C., and V. A. Parsegian. 1992. Direct measurement of the intermolecular forces between counterion-condensed DNA double helices. Evidence for long range attractive hydration forces. Biophys. J. 61: 246-259.
-
(1992)
Biophys. J.
, vol.61
, pp. 246-259
-
-
Rau, D.C.1
Parsegian, V.A.2
-
44
-
-
0014178170
-
Electrostatic effects on polynucleotide transitions. I. Behavior at neutral pH
-
Record, M. 1967. Electrostatic effects on polynucleotide transitions. I. Behavior at neutral pH. Biopolymers. 5:975-992.
-
(1967)
Biopolymers
, vol.5
, pp. 975-992
-
-
Record, M.1
-
45
-
-
0017380736
-
Electrical double layer, zeta potential, and electrophoretic charge of double-stranded DNA
-
Schellman, J. A. 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
-
47
-
-
33751552991
-
Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation
-
Sharp, K. A., and B. Honig. 1990b. 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
-
48
-
-
0026749856
-
Determination of electrostatic potentials at biological interfaces using electron-electron double resonance
-
Shin, Y., and W. Hubbell. 1992. Determination of electrostatic potentials at biological interfaces using electron-electron double resonance. Biophys. J. 61:1443-1453.
-
(1992)
Biophys. J.
, vol.61
, pp. 1443-1453
-
-
Shin, Y.1
Hubbell, W.2
-
49
-
-
0342343482
-
Debye-Huckel theory of model polyelectrolytes
-
Soumpasis, D. 1978. Debye-Huckel theory of model polyelectrolytes. J. Chem. Phys. 69:3190-3196.
-
(1978)
J. Chem. Phys.
, vol.69
, pp. 3190-3196
-
-
Soumpasis, D.1
-
50
-
-
0001419428
-
The charged colloidal cylinder with a Gouy double layer
-
Stigter, D. 1975. The charged colloidal cylinder with a Gouy double layer. J. Colloid Interface Sci. 53:296-306.
-
(1975)
J. Colloid Interface Sci.
, vol.53
, pp. 296-306
-
-
Stigter, D.1
-
51
-
-
0029099524
-
Evaluation of the counterion condensation theory of polyelectrolytes
-
Stigter, D. 1995. Evaluation of the counterion condensation theory of polyelectrolytes. Biophys. J. 69:380-388.
-
(1995)
Biophys. J.
, vol.69
, pp. 380-388
-
-
Stigter, D.1
-
52
-
-
0015104180
-
Equations for calculating the dielectric constant of saline water
-
Stogryn, A. 1971. Equations for calculating the dielectric constant of saline water. IEEE Trans. Microwave Theory Tech. 19:733-736.
-
(1971)
IEEE Trans. Microwave Theory Tech.
, vol.19
, pp. 733-736
-
-
Stogryn, A.1
-
53
-
-
0029159251
-
Modeling of long-range electrostatic interactions in DNA
-
Vologodskii, A., and N. Cozzarelli. 1994. Modeling of long-range electrostatic interactions in DNA. Biopolymers. 35:289-296.
-
(1994)
Biopolymers
, vol.35
, pp. 289-296
-
-
Vologodskii, A.1
Cozzarelli, N.2
-
54
-
-
0019875825
-
Left-handed double helical DNA: Variations in the backbone conformation
-
Wang, A. H., G. J. Quigley, F. J. Kolpak, G. van Der Marel, J. H. van Boom, and A. Rich. 1981. Left-handed double helical DNA: variations in the backbone conformation. Science. 211:171-176.
-
(1981)
Science
, vol.211
, pp. 171-176
-
-
Wang, A.H.1
Quigley, G.J.2
Kolpak, F.J.3
Van Der Marel, G.4
Van Boom, J.H.5
Rich, A.6
-
55
-
-
33845556751
-
Polyelectrolyte theory. 3. the surface potential in mixed-salt solutions
-
Weisbuch, G., and M. Gueron. 1981. Polyelectrolyte theory. 3. The surface potential in mixed-salt solutions. J. Phys. Chem. 85:517-525.
-
(1981)
J. Phys. Chem.
, vol.85
, pp. 517-525
-
-
Weisbuch, G.1
Gueron, M.2
|