Sodium and chlorine ions as part of the DNA solvation shell

Biophysical Journal

Volumn 77, Issue 4, 1999, Pages 1769-1781

  Feig, Michael ^a   Pettitt, B Montgomery ^a  

^a University of Houston   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHLORIDE ION; DNA; DNA FRAGMENT; SODIUM ION;

ARTICLE; BASE PAIRING; DNA CONFORMATION; DNA SEQUENCE; DNA STRUCTURE; MOLECULAR DYNAMICS; MOLECULAR MODEL; SOLVATION;

EID: 0032851951     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(99)77023-2     Document Type: Article

References (72)

1. Allen, M. P., and D. J. Tildesley. 1987. Computer Simulation of Liquids. Oxford University Press, New York, 1st edition.
2. Allison, S. A. 1994. End effects in electrostatic potentials of cylinders: models for DNA fragments. J. Phys. Chem. 98:12091-12096.
3. 6meA-T-C-G: A B-DNA helix with 10.6 base pairs per turn. J. Mol. Biol. 231:768-784.
4. Benevides, J. M., A. H.-J. Wang, A. Rich, Y. Kyogoku, G. A. van der Marel, J. H. van Boom, and G. J. Thomas. 1986. The Raman spectra of single crystals of r(GCG)d(CGC) and d(CCCCGGGG) as model for A-DNA, their structure transitions in aqueous solution and comparison with double helical poly(dG) · poly(dC). Biochemistry. 25:41-50.
5. Berman, H. M., W. K. Olson, D. L. Beveridge, J. Westbrook, A. Gelbin, T. Demeny, S.-H. Hsieh, A. R. Srinivasan, and B. Schneider. 1992. The nucleic acid database: a comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J. 63:751.
6. Bleam, M. L., C. F. Anderson, and M. T. Record. 1980. Relative binding affinities of monovalent cations for double-stranded DNA. Proc. Natl. Acad. Sci. USA. 77:3085-3089.
7. 23Na nuclear magnetic resonance studies of cation-deoxyribonucleic acid interactions. Biochemistry. 22:5418-5425.
8. 23Na-NMR investigations of counterion exchange reactions of helical DNA. Biopolymers. 25:205-214.
9. Bruge, F., E. Parisi, and S. L. Fornili. 1996. Effects of simple model solutes on water dynamics: residence time analysis. Chem. Phys. Lett. 250: 443-449.
10. Brunne, R. M., E. Liepinsh, G. Otting, K. Wüthrich, and W. F. van Gunsteren. 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.
11. Camerman, N., J. K. Fawcett, and A. Camerman. 1976. Molecular structure of deoxyribose-dinucleotide, sodium thymidylyl-(5′-3′)-thymidylate-(5′) hydrate (pTpT), and a possible structural model for polythymidylate. J. Mol. Biol. 107:601-621.
12. 2 in the presence of hexaamminecobalt(III). Structure. 15:1297-1311.
13. Coll, M., X. Solans, M. Font-Altaba, and J. A. Subirana. 1987. Crystal and molecular structure of the sodium salt of the dinucleotide duplex d(CpG). J. Biomol. Struct. Dyn. 4:797-811.
14. Cornell, W. D., P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman. 1995. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117: 5179-5197.
15. de Leeuw, S. W., J. W. Perram, and E. R. Smith. 1980. Simulation of electrostatic systems in periodic boundary conditions. I. Lattice sums and dielectric constants. Proc. R. Soc. Lond. A. 373:27-56.
16. Feig, M., and B. M. Pettitt. 1998. Structural equilibrium of DNA represented with different force fields. Biophys. J. 75:134-149.
17. Feig, M., and B. M. Pettitt. 1999. Modeling high-resolution hydration patterns in correlation with DNA sequence and conformation. J. Mol. Biol. 286:1075-1095.
18. Forester, T. R., and I. R. McDonald. 1991. Molecular dynamics studies of the behaviour of water molecules and small ions in concentrated solutions of polymeric B-DNA. Mol. Phys. 72:643-660.
19. Gil Montoro, J. C., and J. L. F. Abascal. 1998. Ionic distribution around simple B-DNA models. II. deviations from cylindrical symmetry. J. Chem. Phys. 109:6200-6210.
20. 23Na relaxation in Isotropic and anisotropic liquid-crystalline DNA solutions. J. Phys. Chem. 98:2699-2705.
21. Gulbrand, L. E., T. R. Forester, and R. M. Lynden-Bell. 1989. Distribution and dynamics of mobile ions in systems of ordered B-DNA. Mol. Phys. 67:473-493.
22. Harmouchi, M., G. Albiser, and S. Premilat. 1990. Changes of hydration during conformational transitions of DNA. Eur. Biophys. J. 19:87-92.
23. Jayaram, B., and D. L. Beveridge. 1996. Modeling DNA in aqueous solutions: Theoretical and computer simulation studies on the ion atmosphere of DNA. Annu. Rev. Biophys. Biomol. Struct. 25:367-394.
24. Jayaram, B., and K. A. Sharp. 1989. The electrostatic potential of B-DNA. Biopolymers. 28:975-993.
25. Jayaram, B., D. Sprous, M. A. Young, and D. L. Beveridge. 1998. Free energy analysis of the conformational preferences of A and B forms of DNA in solution. J. Am. Chem. Soc. 120:10629-10633.
26. Jayaram, B., S. Swaminathan, D. L. Beveridge, K. Sharp, and B. Honig. 1990. Monte carlo simulation studies on the structure of the counterion atmosphere of B-DNA. Variations on the primitive dielectric model. Macromolecules. 23:3156-3165.
27. Jorgensen, W., J. Chandrasekhar, J. Madura, R. Impey, and M. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
28. Kubinec, M. G., and D. E. Wemmer. 1992. NMR evidence for DNA bound water in solution. J. Am. Chem. Soc. 114:8739-8740.
29. Laughton, C. A., F. J. Luque, and M. Orozco. 1995. Counterion distribution around DNA studied by molecular dynamics and quantum mechanical simulations. J. Phys. Chem. 99:11591-11599.
30. MacKerell Jr., A. D., J. Wiorkiewicz-Juczera, and M. Karplus. 1995. An all-atom empirical energy function for the simulation of nucleic acids. J. Am. Chem. Soc. 117:11946-11975.
31. Makarov, V. A., B. K. Andrews, and B. M. Pettitt. 1998a. Reconstructing the protein-water interface. Biopolymers. 45:469-478.
32. Makarov, V. A., M. Feig, and B. M. Pettitt. 1998b. Diffusion of solvent around biomolecular solutes. A molecular dynamics simulations study. Biophys. J. 75:150-158.
33. Manning, G. S. 1978. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Q. Rev. Biophys. 11:179-246.
34. 2 in the B, A, and wrinkled D conformations. Biopolymers. 32:1491-1501.
35. Misra, V. K., K. A. Sharp, R. A. Friedman, and B. J. Honig. 1994. Salt effects on ligand-DNA binding. J. Mol. Biol. 238:245-263.
36. Mohan, V., P. E. Smith, and B. M. Pettitt. 1993. Molecular dynamics simulation of ions and water around triplex DNA. J. Phys. Chem. 97:12984-12990.
37. + binding sites. J. Mol. Biol. 256:228-234.
38. Nishimura, Y., C. Torigoe, and M. Tsuboi. 1986. Salt induced B-A transition of poly(dG) · poly(dC) and the stabilization of A form by its methylation. Nucleic Acids Res. 14:2737-2748.
39. Olmsted, M. C. 1996. The effect of nucleic acid geometry on counterion association. J. Biomol. Struct. Dyn. 13:885-902.
40. Olmsted, M. C., C. F. Anderson, and M. T. Record, Jr. 1989. Monte Carlo description of oligoelectrolyte properties of DNA oligomers: range of the end effect and the approach of molecular and thermodynamic properties to the polyelectrolyte limits. Proc. Natl. Acad. Sci. USA. 86: 7766-7770.
41. 8+) to the center of DNA oligomers. Biophys. J. 68:634-647.
42. Pack, G., G. 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.
43. Rajasekaran, E., and B. Jayaram. 1994. Counterion condensation in DNA systems: the cylindrical poisson-boltzmann model revisited. Biopolymers. 34:443-445.
44. Rau, D. C., and 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.
45. Record, M. T., C. F. Anderson, and T. M. Lohman. 1978. Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity. Q. Rev. Biophys. 11: 103-178.
46. Rinkel, L. J., M. R. Sanderson, G. A. van der Marel, and C. Altona. 1986. Conformational analysis of the octamer d(GGCCGGCC) in aqueous solution. Eur. J. Biochem. 159:85-93.
47. Rocchi, C., A. R. Bizzarri, and S. Cannistraro. 1997. Water residence times around copper plastocyanin: a molecular dynamics simulation approach. Chem. Phys. 214:261-276.
48. Rosenberg, J. M., N. C. Seeman, R. O. Day, and A. Rich. 1976. RNA double-helical fragments at atomic resolution: II. The crystal structure of sodium guanylyl-3′,5′-cytidine nonahydrate. J. Mol. Biol. 104:145-167.
49. Roux, B., B. Prodhom, and M. Karplus. 1995. Ion transport in the gramicidin channel: Molecular dynamics study of single and double occupancy. Biophys. J. 68:876.
50. Rudnicki, W. R., and B. M. Pettitt. 1996. Modeling the DNA-solvent interface. Biopolymers. 41:107-119.
51. Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J. Comput. Phys. 23: 327-341.
52. Saenger, W. 1984. Principles of Nucleic Acid Structure. Springer Verlag, New York.
53. Saenger, W. 1987. Structure and dynamics of water surrounding biomolecules. Annu. Rev. Biophys. Biophys. Chem. 16:93-114.
54. Savage, H., and A. Wlodawer. 1986. Determination of water structure around biomolecules using X-ray and neutron diffraction methods. Methods Enzymol. 127:162-183.
55. Schneider, B., and H. M. Berman. 1995. Hydration of the DNA bases is local. Biophys. J. 69:2661-2669.
56. Seeman, N. C., J. M. Rosenberg, and A. Rich. 1976. Sequence-specific recognition of double helical nucleic acids by proteins. Proc. Natl. Acad. Sci. USA. 73:804-808.
57. Sharp, K. A., and B. Honig. 1995. Salt effects on nucleic acids. Curr. Opin. Struct. Biol. 5:323-328.
58. Shui, X., L. McFail-Isom, G. G. Hu, and L. D. Williams. 1998. The B-DNA dodecamer at high resolution reveals a spine of water on sodium. Biochemistry. 37:8341-8355.
59. Smith, P. E., M. E. Holder, L. X. Dang, M. Feig, and B. M. Pettitt. 1996. Extended System Program, University of Houston, Houston, TX.
60. Smith, P. E., and B. M. Pettitt. 1994. Modeling solvent in biomolecular systems. J. Phys. Chem. 98:9700-9711.
61. 23Na NMR. Biophys. J. 68:1063-1072.
62. 23Na NMR of concentrated DNA solutions: salt concentration and temperature effects. J. Phys. Chem. 96:7796-7807.
63. Urabe, H., M. Kato, and Y. Tominaga. 1990. Counterion dependence of water of hydration in DNA gel. J. Chem. Phys. 92:768-774.
64. van Dijk, L., M. L. H. Gruwel, W. Jesse, J. de Bleijser, and J. C. Leyte. 1987. Sodium ion and solvent nuclear relaxation results in aqueous solutions of DNA. Biopolymers. 26:261-284.
65. Wahl, M. C., and M. Sundaralingam. 1997. Crystal structures of A-DNA duplexes. Biopolymers (Nucleic Acid Sci.). 44:45-63.
66. Wang, J. H. 1955. The hydration of deoxyribonucleic acid. J. Am. Chem. Soc. 77:258-260.
67. Wang, Y., G. A. Thomas, and W. L. Peticolas. 1989. A duplex of the oligonucleotides d(GGGGGTTTTT) and d(AAAAACCCCC) forms an A to B conformational junction in concentrated salt solutions. J. Biomol. Struct. Dyn. 6:1177-1187.
68. Weerasinghe, S., P. E. Smith, V. Mohan, Y.-K. Cheng, and B. M. Pettitt. 1995. Nanosecond dynamics and structure of a model DNA triple helix in saltwater solution. J. Am. Chem. Soc. 117:2147-2158.
69. Westhof, E. 1988. Water: an integral part of nucleic acid structure. Annu. Rev. Biophys. Biophys. Chem. 17:125-144.
70. 3), a B-family duplex in solution. Biochemistry. 28:2452-2459.
71. Young, M. A., B. Jayaram, and D. L. Beveridge. 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.
72. 8+) binding to single-stranded DNA oligomers. Biophys. J. 76:1008-1017.