Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution

Journal of Molecular Biology

Volumn 259, Issue 3, 1996, Pages 434-444

  Cheatham III, T E ^a   Kollman, P A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

A DNA; B DNA; Conformational transitions; Molecular dynamics; Nucleic acids

Indexed keywords

DNA A; DNA B; DOUBLE STRANDED DNA;

AQUEOUS SOLUTION; ARTICLE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DNA STRUCTURE; MOLECULAR DYNAMICS; PRIORITY JOURNAL; X RAY CRYSTALLOGRAPHY;

EID: 0029941154     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0330     Document Type: Article

References (62)

1. Altona, C. & Sundaralingam, M. (1972). Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of psuedorotation. J. Am. Chem. Soc. 94, 8205-8212.
2. Anderson, P. & Bauer, W. (1978). Supercoiling in closed circular DNA: dependence upon ion type and concentration. Biochemistry, 7, 594-601.
3. Arnott, S. & Hukins, D. W. L. (1972). Optimized parameters for A-DNA and B-DNA. Biochem. Biophys. Res. Commun. 47, 1504-1509.
4. Barkley M. D. & Zimm, B. H. (1979). Theory of twisting and bending of chain macromolecules; analysis of the fluorescence depolarization of DNA. J. Chem. Phys. 70, 2991-3007.
5. Beveridge, D. L. & Ravishanker, G. (1994). Molecular dynamics studies of DNA. Curr. Opin. Struct. Biol. 4, 246-255.
6. Beveridge, D. L., Swaminathan, S., Ravishanker, G., Withka, J. M., Srinivasan, J., Prevost, C., Louise-May S., Langley D. R., DiCapua, F. M. & Bolton, P. H. (1993). Molecular dynamics simulations on the hydration, structure and motions of DNA oligomers. In Water and Biological Molecules (Westhof, E., ed.), Macmillan Press, pp. 165-225.
7. Board, J. A., Jr, Causey J. W., Leathrum, J. F., Jr, Windemuth, A. & Schulten, K. (1992). Accelerated molecular dynamics simulation with the parallel fast multipole algorithm. Chem. Phys. Letters, 198, 89-94.
8. Brahms, S., Fritsch, V., Brahms, J. G. & Westhof, E. (1992). Investigations on the dynamic structures of adenine- and thymine-containing DNA. J. Mol. Biol. 223, 455-476.
9. Cheatham, T. E., III, Miller, J. L., Fox, T., Darden, T. A. & Kollman, P. A. (1995). Molecular dynamics simulations on solvated biomolecular systems: the particle mesh Ewald methods leads to stable trajectories of DNA, RNA, and proteins. J. Am. Chem. Soc. 117, 4193-4194.
10. Cognet, J. A. H., Boulard, Y. & Fazakerley G. V. (1995). Helical parameters, fluctuations, alternative hydrogen bonding, and bending in oligonucleotides containing a mismatched base-pair by NOESY distance restrained and distance free molecular dynamics. J. Mol. Biol. 246, 209-226.
11. Cornell, W. D., Cieplak, P., Bayly C. I., Gould, I. R., Merz, K. M., Jr, Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W. & Kollman, P. A. (1995). A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117, 5179-5197.
12. Darden, T. A., York, D. & Pedersen, L. G. (1993). Particle mesh Ewald: an Nlog(N) method for Ewald sums in large systems. J. Chem. Phys. 98, 10089-10092.
13. Dickerson, R. E., Drew, H. R., Conner, B. N., Wing, R. M., Fratini, A. V. & Kopka, M. L. (1982). The anatomy of A-, B-, and Z-DNA. Science, 216, 475-485.
14. Dickerson, R. E., Goodsell, D. S., Kopka, M. L. & Pjura, P. E. (1987). The effect of crystal packing on oligonucleotide crystal structures. J. Biomol. Struct. Dynam. 5(3), 557-579.
15. Dickerson, R. E., Goodsell, D. S. & Neile, S. (1994). ". . .the tyranny of the lattice. . .". Proc. Natl Acad. Sci. USA, 91, 3579-3583.
16. Ding, H.-Q., Karasawa, N. & Goddard, W. A. (1992). Atomic level simulations on a million particles - The Cell Multipole Method of Coulomb and London nonbond interactions. J. Chem. Phys. 97, 4309-4315.
17. Eisenburg, H. (1987). DNA flexing, folding and function. Acc. Chem. Res. 20, 276-282.
18. Essmann, U., Perera, L., Berkowitz, M. L., Darden, T. A., Lee, H. & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. J. Chem. Phys. 103(19), 8577-8593.
19. Ewald, P. (1921). Investigations of crystals by means of Roentgen rays. Ann. Phys. (Leipzig), 64, 253-264.
20. Gorin, A. A., Zhurkin, V. B. & Olson, W. K. (1995). B-DNA twisting correlates with base-pair morphology. J. Mol. Biol. 247, 34-48.
21. Hagerman, P. J. (1981). Investigation of the flexibility of DNA using transient electric birefringence. Biopolymers, 20, 1503-1535.
22. Hagerman, P. J. (1988). Flexibility of DNA. Annu. Rev. Biophys. Biophysical Chem. 17, 265-286.
23. Hagerman, P. J. (1994). Straightening out the bends in curved DNA. Biochim. Biophys. Acta, 1131(2), 125-132.
24. Harrington, R. E. & Winicov, I. (1994). New concepts in protein-DNA recognition: sequence directed DNA bending and flexibility Prog. Nucl. Acid Res. Mol. Biol. 47, 195-270.
25. James, T. L. (1995). Nuclear magnetic resonance and nucleic acids. Methods Enzymol. 261.
26. n DNA duplex GCCGTTAACGGC containing the HpaI recognition site. Biochem. 31, 12103-12116.
27. Lavery R. & Sklenar, H. J. (1989). The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dynam. 6, 63-91.
28. Lee, H., Darden, T. A. & Pedersen, L. (1995a). Molecular dynamics simulation studies of a high resolution Z DNA crystal. J. Chem. Phys. 102, 3830-3834.
29. Lee, H., Darden, T. A. & Pedersen, L. (1995b). Accurate crystal molecular dynamics simulations using particle mesh Ewald: RNA dinucleotides-ApU and GpC. Chem. Phys. Letters, 43, 229-235.
30. Levitt, M. (1978). How many base-pairs per turn does DNA have in solution and in chromatin? Some theoretical calculations. Proc. Natl Acad. Sci. USA, 75, 640-644.
31. Lipanov, A., Kopka, M. L., Kaczor-Grzeskowiak, M., Quintana, J. & Dickerson, R. E. (1993). Structure of the B-DNA decamber CCAACITTGG in two different space groups: conformational flexibility of B-DNA. Biochemistry, 32, 1373-1389.
32. Loncharich, R. J. & Brooks, B. R. (1990). Temperature dependence of dynamics of hydrated myoglobin. Comparison of force field calculations with neutron scattering data. J. Mol. Biol. 215, 439-455.
33. Luty B. A., Davis, M. E., Tironi, I. G. & Van Gunsteren, W. F. (1994). A comparison of particle-particle, particle-mesh and Ewald methods for calculating electrostatic interactions in periodic molecular systems. Mol. Sim. 14, 11-20.
34. McConnell, K. J., Nirmala, R., Young, M. A., Ravishanker, G. & Beveridge, D. L. (1994). A nanosecond molecular dynamics trajectory for a B DNA double helix: evidence for substates. J. Am. Chem. Soc. 116, 4461-4462.
35. Olson, W. K., Marky, N. L., Jernigan, R. L. & Zhurkin, V. B. (1993). Influence of fluctuations on DNA curvature. A comparison of flexible and static wedge models of intrinsically bent DNA. J. Mol. Biol. 232, 530-554.
36. Olson, W. K., Babcock, M. S., Gorin, A., Liu, G., Marky N. L., Martino, J. A., Pedersen, S. C., Srinivasan, A. R., Tobias, I., Westcott, T. P. & Zhang, P. (1995). Flexing and folding double helical DNA. Biophys. Chem. 55, 7-29.
37. Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheatham, T. E., III, Ferguson, D. M., Seibel, G. L., Singh, U. C., Weiner, P. K. & Kollman, P. A. (1995). AMBER 4.1, University of California, San Francisco.
38. Peck, L. J. & Wang, J. C. (1981). Sequence dependence of the helical repeat of DNA in solution. Nature, 292, 375-378.
39. Petersen, H. G. (1995). Accuracy and efficiency of the particle mesh Ewald method. J. Chem. Phys. 103, 3668-3679.
40. Poncin, M., Hartmann, B. & Lavery R. (1992). Conformational sub-states in B-DNA. J. Mol. Biol. 226, 775-794.
41. Prive, G. G., Yanagi, K. & Dickerson, R. E. (1991). Structure of the B-DNA decamer CCAACGTTGG and comparison with isomorphous decamers CCAA-GATTGG and CCAGGCCTGG. J. Mol. Biol. 217, 177-199.
42. Ravishankar, G., Swaminathan, S., Beveridge, D. L., Lavery, R. & Sklenar, H. J. (1989). Conformational and helicoidal analysis of 30 ps of molecular dynamics on the d(CGCGAATTCGCG) double helix: "Curves", dials and windows. J. Biomol. Struct. Dynam. 6, 669-699.
43. Rhodes, D. & Klug, A. (1980). Helical periodicity of DNA determined by enzyme digestion. Nature, 286, 573-578.
44. Saenger, W. (1984). Principles of Nucleic Acid Structure, Springer-Verlag, New York.
45. Schreiber, H. & Steinhauser, O. (1992). Cutoff size does strongly influence molecular dynamics results on solvated polypeptides. Biochemistry, 31, 5856-5860.
46. Schultz, S. C., Shields, G. C. & Steitz, T. A. (1991). Crystal structure of a CAP-DNA complex-the DNA is bent by 90 degrees. Science, 253, 1001-1007.
47. Seeman, N. C., Rosenburg, J. M. & Rich, A. (1976). Sequence-specific recognition of double helical nucleic acids by proteins. Proc. Natl Acad. Sci. USA, 73, 804-808.
48. Selvin, P. R., Cook, D. N., Pon, N. G., Bauer, W. R., Klein, M. P. & Hearst, J. P. (1992). Torsional rigidity of positively and negatively supercoiled DNA. Science, 255, 82-85.
49. Smith, P. E. & Pettitt, B. M. (1991). Peptides in ionic solutions: a comparison of the Ewald and switching function techniques. J. Chem. Phys. 95, 8430-8440.
50. + on the persistence length and excluded volume of T7 bacteriophage DNA. Biopolymers, 31, 1559-1564.
51. Steinbach, P. J. & Brooks, B. R. (1994). New spherical-cut-off methods for long-range forces in macromolecular simulation. J. Comp. Chem. 15, 667-683.
52. Ulyanov, N. B. & James, T. L. (1995). Statistical analysis of DNA duplex structural features. Methods Enzymol. 261, 90-125.
53. Ulyanov, N. B., Schmitz, U., Kumar, A. & James, T. L. (1995). Probability assessment of conformational ensembles: sugar repuckering in a DNA duplex in solution. Biophys. J. 68, 13-24.
54. Van Gunsteren, W. F. & Berendsen, H. J. C. (1986). GROMOS86: Groningen Molecular Simulation System. University of Groningen, Groningen, The Netherlands.
55. Van Gunsteren, W. F., Berendsen, H. J. C., Geurtsen, R. G. & Zwinderman, H. R. J. (1986). A molecular dynamics computer simulation of an eight-base-pair DNA fragment in aqueous solution: comparison with experimental two-dimensional NMR data. Computer Simulation of Chemical and Biomolecular Systems. Ann. N.Y. Acad. Sci. 482, 287-303.
56. Wang, J. C. (1969). Variation of the average rotation angle of the DNA helix and the superhelical turns of covalently closed cyclic (bacteriophage) DNA. J. Mol. Biol. 43, 25-39.
57. Weerasinghe, S., Smith, P. E., Mohan, Y., Cheng, Y.-K. & Pettitt, B. M. (1995). Nanosecond dynamics and structure of a model DNA triple helix in saltwater solution. J. Am. Chem. Soc. 117, 2147-2158.
58. York, D. M., Yang, W., Lee, H., Darden, T. A. & Pedersen, L. (1995). Toward accurate modeling of DNA: the importance of long-range electrostatics. J. Am. Chem. Soc. 117, 5001-5002.
59. Young, M. A., Ravishanker, G., Beveridge, D. L. & Berman, H. M. (1995a). Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes. Biophys. J. 68, 2454-2468.
60. 2. Methods Enzymol. 261, 121-144.
61. Zhurkin, V. B., Lysov, Y. P., Florentiev, V. L. & Ivanov, V.I. (1982). Torsional flexibility of B-DNA as revealed by conformational analysis. Nucl Acids Res. 10, 1811-1830.
62. Zhurkin, V. B., Ulyanov, N. B., Gorin, A. A. & Jernigan, R. L. (1991). Static and statistical bending of DNA evaluated by Monte Carlo simulations. Proc. Natl Acad. Sci. USA, 88, 7046-7050.