Solvent influence on base stacking

Biophysical Journal

Volumn 74, Issue 1, 1998, Pages 394-402

  Norberg, Jan ^a,b   Nilsson, Lennart ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

^b Columbia University ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHLOROFORM; DIMETHYL SULFOXIDE; DINUCLEOSIDE PHOSPHATE; METHANOL; ORGANIC SOLVENT; SOLVENT; WATER;

AQUEOUS SOLUTION; ARTICLE; DIELECTRIC CONSTANT; ENERGY TRANSFER; FORCE; MOLECULAR DYNAMICS; SIMULATION;

EID: 0031972564     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(98)77796-3     Document Type: Article

References (62)

1. Aida, M. 1988. An ab initio molecular orbital study on the sequence-dependency of DNA conformation: an evaluation of intra- and interstrand stacking interaction energy. J. Theor. Biol. 130:327-335.
2. Alden, C. J., and S.-H. Kim. 1979. Solvent-accessible surfaces of nucleic acids. J. Mol. Biol. 132:411-434.
3. Altona, C., and M. Sundaralingam. 1972. Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation. J. Am. Chem. Soc. 94:8205-8212.
4. Arnott, S., P. J. C. Smith, and R. Chandrasekaran. 1976. Atomic coordinates and molecular conformations for DNA-DNA, RNA-RNA, and DNA-RNA helices. In CRC Handbook of Biochemistry and Molecular Biology: Nucleic Acids, Vol. 2, 3rd Ed. G. D. Fasman, editor. CRC Press, Cleveland, OH. 411-422.
5. Beveridge, D. L., and F. M. DiCapua. 1989. Free energy via molecular simulation: applications to chemical and biomolecular systems. Annu. Rev. Biophys. Biophys. Chem. 18:431-492.
6. Boczko, E. M., and C. L. Brooks, III. 1993. Constant-temperature free energy surfaces for physical and chemical processes. J. Phys. Chem. 97:4509-4513.
7. Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM: a program for macromolecular energy, minimizations, and dynamics calculations. J. Comp. Chem. 4:187-217.
8. Brooks, C. L., III, B. M. Pettitt, and M. Karplus. 1985. Structural and energetic effects of truncating long ranged interactions in ionic and polar fluids. J. Chem. Phys. 83:5897-5908.
9. Broyde, S. B., R. M. Wartell, S. D. Stellman, and B. Hingerty. 1978. Minimum energy conformations of DNA dimeric subunits: potential energy calculations for dGpdC, dApdA, dCpdC, dGpdG, and dTpdT. Biopolymers. 17:1485-1506.
10. Cantor, R. C., and P. R. Schimmel. 1980. Biophysical Chemistry. W. H. Freeman, San Francisco.
11. Chachaty, C., B. Perly, A. Forchioni, and G. Langlet. 1980. Syn-anti equilibrium of purine bases in dinucleoside monophophates as studied by proton longitudinal relaxation. Biopolymers. 19:1211-1239.
12. Dang, L. X., and P. A. Kollman. 1990. Molecular dynamics simulations study of the free energy of association of 9-methyladenine and 1-methylthymine bases in water. J. Am. Chem. Soc. 112:503-507.
13. Davis, J., and I. Tinoco, Jr. 1968. Temperature-dependent properties of dinucleoside phosphates. Biopolymers. 6:223-242.
14. Drew, H. R., R. M. Wing, T. Takano, C. Broka, S. Tanaka, K. Itakura, and R. E. Dickerson. 1981. Structure of a B-DNA dodecamer: conformation and dynamics. Proc. Natl. Acad. Sci. USA. 78:2179-2183.
15. Fogolari, F., A. H. Elcock, G. Esposito, P. Viglino, J. M. Briggs, and J. A. McCammon. 1997. Electrostatic effects in homeodomain-DNA interactions. J. Mol. Biol. 267:368-381.
16. Frechet, D., R. Ehrlich, P. Remy, and J. Gabarro-Arpa. 1979. Thermal perturbation differential spectra of ribonucleic acids. II. Nearest neighbour interactions. Nucleic Acids Res. 7:1981-2001.
17. Guàrdia, E., G. Sesé, and J. A. Padró. 1994. On the hydrogen bonding effects in liquid methanol: a molecular dynamics simulation study. J. Mol. Liq. 62:1-16.
18. Hanlon, S. 1966. The importance of London dispersion forces in the maintenance of the deoxyribonucleic acid helix. Biochem. Biophys. Res. Commun. 23:861-867.
19. Herskovits, T. T., S. S. Singer, and E. P. Geiduschek. 1961. Nonaqueous solution of DNA: denaturation by urea and its methyl derivatives. Arch. Biochem. Biophys. 94:99-114.
20. Johnson, N. P., and T. Schleich. 1974. Circular dichroism studies of the conformational stability of dinucleoside phosphates and related compounds in aqueous neutral salt solutions. Biochemistry. 13:981-987.
21. Jorgensen, W. L. 1986. Optimized intermolecular potential functions for liquid alcohols. J. Phys. Chem. 90:1276-1284.
22. Jorgensen, W. L., J. M. Briggs, and M. L. Contreras. 1990. Relative partition coefficients for organic solutes from fluid simulations. J. Phys. Chem. 94:1683-1686.
23. Jorgensen, W. L., J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
24. Kang, H., P.-J. Chou, W. C. Johnson, Jr., D. Weller, S.-B. Huang, and J. E. Summerton. 1992. Stacking interactions of ApA analogues with modified backbones. Biopolymers. 32:1351-1363.
25. Kondo, N. S., and S. S. Danyluk. 1976. Conformational properties of adenylyl-3′ leads to 5′-adenosine in aqueous solution. Biochemistry. 15:756-768.
26. Kovacs, H., A. E. Mark, J. Johansson, and W. F. van Gunsteren. 1995. The effect of environment on the stability of an integral membrane helix: molecular dynamics simulations of surfactant protein C in chloroform, methanol and water. J. Mol. Biol. 247:808-822.
27. Kumar, S., D. Bouzida, R. H. Swendsen, P. A. Kollman, and J. M. Rosenberg. 1992. The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. J. Comp. Chem 13:1011-1021.
28. Lee, B., and F. M. Richards. 1971. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55:379-400.
29. 1H nuclear magnetic resonance spectroscopy. Investigation of the solution conformations of dinucleoside phosphates. Biochemistry. 16:5403-5414.
30. Lee, H., T. Darden, and L. Pedersen. 1995. Accurate crystal molecular dynamics simulations using particle-mesh-Ewald: RNA dinucleotides -ApU and GpC. Chem. Phys. Lett. 243:229-235.
31. Lide, D. R. 1993. Handbook of Chemistry and Physics. CRC Press, Boca Raton, FL.
32. Lowe, M. J., and J. A. Schellman. 1972. Solvent effects on dinucleotide conformation. J. Mol. Biol. 65:91-109.
33. MacKerell, A. D., Jr. 1997. Influence of magnesium ions on duplex DNA structural, dynamic, and solvation properties. J. Phys. Chem. 101: 646-650.
34. MacKerell, A. D., Jr., J. Wiórkiewics-Kuczera, and M. Karplus. 1995. An all-atom empirical energy function for the simulation of nucleic acids. J. Am. Chem. Soc. 117:11946-11975.
35. McCammon, J. A., and S. C. Harvey. 1987. Dynamics of Proteins and Nucleic Acids. Cambridge University Press, Cambridge.
36. Mierke, D. F., and H. Kessler. 1993. Improved molecular dynamics simulations for the determination of peptide structures. Biopolymers. 33: 1003-1017.
37. Newcomb, L. F., and S. H. Gellman. 1994. Aromatic stacking interactions in aqueous solution: evidence that neither classical hydrophobic effects nor dispersion forces are important. J. Am. Chem. Soc. 116:4993-4994.
38. Norberg, J. 1995. A biophysical perspective of dynamics, structure, and thermodynamics of nucleic acids. Molecular dynamics simulations of nucleic acids. Ph.D. thesis. Karolinska Institutet. Stockholm, Sweden.
39. Norberg, J., and L. Nilsson. 1994a. High-pressure molecular dynamics of a nucleic acid fragment. Chem. Phys. Lett. 224:219-224.
40. Norberg, J., and L. Nilsson. 1994b. Stacking-unstacking of the dinucleoside monophosphate guanylyl-3′,5′-uridine studied with molecular dynamics. Biophys. J. 67:812-824.
41. Norberg, J., and L. Nilsson. 1995a. NMR relaxation times, dynamics, and hydration of a nucleic acid fragment from molecular dynamics simulations. J. Phys. Chem. 99:14876-14884.
42. Norberg, J., and L. Nilsson. 1995b. Potential of mean force calculations of the stacking-unstacking process in single-stranded deoxyribodinucleoside monophosphates. Biophys. J. 69:2277-2285.
43. Norberg, J., and L. Nilsson. 1995c. Stacking free energy profiles for all 16 natural ribonucleoside monophosphates in aqueous solution. J. Am. Chem. Soc. 117:10832-10840.
44. Norberg, J., and L. Nilsson. 1995d. Temperature dependence of the stacking propensity of adenylyl-3′,5′-adenosine. J. Phys. Chem. 99: 13056-13058.
45. Norberg, J., and L. Nilsson. 1996a. A conformational free energy landscape of ApApA from molecular dynamics simulations. J. Phys. Chem. 100:2550-2554.
46. 2. J. Chem. Phys. 104:6052-6057.
47. Norberg, J., and L. Nilsson. 1996c. Influence of adjacent bases on the stacking-unstacking process of single-stranded oligonucleotides. Biopolymers. 39:765-768.
48. 2 in aqueous solution from molecular dynamics simulations. J. Biomol. NMR. 7:305-314.
49. Ogasawara, N., and Y. Inoue. 1976. Titration and temperature-dependent properties of homodinucleoside monophosphates. Evaluation of stacking equilibrium quotients for neutral and half-ionized ApA, CpC, GpG, and UpU. J. Am. Chem. Soc. 98:7054-7060.
50. Pohorille, A., S. K. Burt, and R. D. MacElroy. 1984. Monte Carlo simulation of the influence of solvent on nucleic acid base associations. J. Am. Chem. Soc. 106:402-409.
51. Poland, D., J. M. Vournakis, and H. N. Scheraga. 1966. Cooperative interactions in single-strand oligomers of adenylic acid. Biopolymers. 4:223-235.
52. Powell, J. T., E. G. Richards, and W. B. Gratzer. 1972. The nature of stacking equilibria in polynucleotides. Biopolymers. 11:235-250.
53. 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. Comp. Phys. 23: 327-341.
54. Saenger, W. 1988. Principles of Nucleic Acid Structure. Spinger Verlag, New York.
55. Straatsma, T. P., and J. A. McCammon. 1992. Computational alchemy. Annu. Rev. Phys. Chem. 43:407-435.
56. Thiyagarajan, P., and P. K. Ponnuswamy. 1978. Conformational characteristics of dApdA, dApdT, dTpdA, and dTpdT from energy minimization studies. Biopolymers. 17:533-553.
57. Ts'o, P. O. P., I. S. Melvin, and A. C. Olson. 1963. Interaction and association of bases and nucleosides in aqueous solution. J. Am. Chem. Soc. 85:1289-1296.
58. van Gunsteren, W. F., and H. J. C. Berendsen. 1990. Computer simulation of molecular dynamics: methodology, applications, and prespectives in chemistry. Angew. Chem. Int. Ed. Engl. 29:992-1023.
59. van Holde, K. E., J. Brahms, and A. M. Michelson. 1965. Base interactions of nucleotide polymers in aqueous solution. J. Mol. Biol. 12:726-739.
60. Verlet, L. 1967. Computer "experiments" on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules. Phys. Rev. 159: 98-103.
61. Watts, M. T., and I. Tinoco, Jr. 1978. Role of hypermodified bases in transfer RNA. Solution properties of dinucleoside monophosphates. Biochemistry. 17:2455-2463.
62. Zheng, Y.-J., and R. L. Ornstein. 1996. A molecular dynamics and quantum mechanics analysis of the effect of DMSO on enzyme structure and dynamics: subtilisin. J. Am. Chem. Soc. 118:4175-4180.