Insight into the stabilization of A-DNA by specific ion association: Spontaneous B-DNA to A-DNA transitions observed in molecular dynamics simulations of d[ACCCGCGGGT]2 in the presence of hexaamminecobalt(III)

Structure

Volumn 5, Issue 10, 1997, Pages 1297-1311

  Cheatham III, Thomas E ^a   Kollman, Peter A ^b  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

A DNA; Hexaamminecobalt(III); Hydration; Ion association; Molecular dynamics

Indexed keywords

EID: 0031572854     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(97)00282-7     Document Type: Article

References (50)

1. Saenger, W. (1984). Principles of Nucleic Acid Structure. Springer Advanced Texts in Chemistry (Cantor, C.E., Ed.), Springer-Verlag, New York.
2. Herbert, A. & Rich, A. (1996). The biology of left-handed Z-DNA. J. Biol. Chem. 271, 11595-11598.
3. Konig, P. & Rhodes, D. (1997). Recognition of telomeric DNA. Trends Biochem. Sci. 22, 43-47.
4. Mohr, S.C., Sokolov, N.V.H.A., He, C. & Setlow, P. (1991). Binding of small acid-soluble spore proteins from Bacillus subtilis changes the conformation of DNA from B to A. Proc. Natl. Acad. Sci. USA 88, 77-81.
5. Kim, Y., Geiger, J.H., Hahn, S. & Sigler, P.B. (1993). Crystal structure of a yeast TBP/TATA-box complex. Nature 365, 512-520.
6. Kim, J.L., Nikolov, D.B. & Burley, S.K. (1993). Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature 365, 520-527.
7. Guzikevich-Guerstein, G. & Shakked, Z. (1996). A novel form of the DNA double helix imposed on the TAT-box by the TATA-binding protein. Nat. Struct. Biol. 3, 32-37.
8. Robinson, H. & Wang, A.H.-J. (1996). Neomycin, spermine and hexaamminecobalt(III) share common structural motifs in converting B-to A-DNA. Nuc. Acids Res. 24, 676-682.
9. Xu, Q., Shoemaker, R.K. & Braunlin, W.H. (1993). Induction of B-A transitions of deoxyoligonucleotides by multivalent cations in dilute aqueous solution. Biophys. J. 65, 1039-1049.
10. 2+ to A-DNA. Biophys. J. 69, 559-568.
11. Gessner, R.V., et al., & Rich, A. (1985). Structural basis for stabilization of Z-DNA by cobalt hexaammine and magnesium cations. Biochem. 24, 237-240.
12. 3+ binding to the guanine. J. Biomol. Struct. Dyn. 3, 649-665.
13. Braunlin, W.H. & Xu, Q. (1992). Hexaamminecobalt(lll) binding environments on double-helical DNA. Biopolymers 32, 1703-1711.
14. Xu, Q., Jampani, S.R.B. & Braunlin, W.H. (1993). Rotational dynamics of hexaamminecobalt(III) bound to oligomeric DNA: correlation with cation-induced structural transitions. Biochem. 32, 11754-11760.
15. Nunn, C.M. & Neidle, S. (1996). The high resolution crystal structure of the DNA decamer d(AGGCATGCCT). J. Mol. Biol. 256, 340-351.
16. BrCATGCCT): implications for cobalt hexammine binding to DNA. J. Biomol. Struct. Dyn. 14, 49-55.
17. Beveridge, D.L. & Ravishanker, G. (1994). Molecular dynamics studies of DNA. Curr. Opin. Struct. Biol. 4, 246-255.
18. 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.
19. Cornell, W.D., et al., & 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.
20. Mackerell, A.D., Wiorkiewiczkuczera, J. & Karplus, M. (1995). An allatom empirical energy function for the simulation of nucleic acids. J. Am. Chem. Soc. 117, 11946-11975.
21. Steinbach, P.J. & Brooks, B.R. (1994). New spherical-cutoff methods for long-range forces in macromolecular simulation. J. Comp. Chem. 15, 667-683.
22. Essmann, U., et al., & Pedersen, L.G. (1995). A smooth particle mesh Ewald method. J. Chem. Phys. 103, 8577-8593.
23. 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 method leads to stable trajectories of DNA, RNA and proteins. J. Am. Chem. Soc. 117, 4193-4194.
24. Cheatham, T.E., III. & Kollman, P.A. (1997). Molecular dynamics simulations highlight the structural differences in DNA:DNA, RNA:RNA and DNA:RNA hybrid duplexes. J. Am. Chem. Soc. 119, 4805-4825.
25. Young, M.A., Ravishanker, G. & Beveridge, D.L. (1997). A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions and solvation. Biophys. J., in press.
26. Cheatham, T.E., III. & Kollman, P.A. (1996). Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution. J. Mol. Biol. 259, 434-444.
27. Cieplak, P., Cheatham, T.E., III. & Kollman, P.A. (1997). Molecular dynamics simulations find that 3• phosphoramidate modified DNA duplexes undergo a B to A transition and normal DNA duplexes an A to B transition. J. Am. Chem. Soc. 119, 6722-6730.
28. Yang, L.Q. & Pettitt, B.M. (1996). B to A transition of DNA on the nanosecond time scale. J. Phys. Chem. 100, 2564-2566.
29. 2. J. Chem. Phys. 104, 6052-6057.
30. Cheatham, T.E., III, Crowley, M.F., Fox, T. & Kollman, P.A. (1997). A molecular level picture of the stabilization of A-DNA in mixed ethanol-water solutions. Proc. Natl. Acad. Sci. USA, 94, 9626-9630.
31. Kieft, J.S. & Tinoco, I.J. (1997). Solution structure of a metal-binding site in the major groove of RNA complexed with cobalt(III) hexammine. Structure 5, 713-721.
32. Wahl, M.C. & Sundaralingam, M. (1997). Crystal structures of A-DNA duplexes. Biopolymers 44, 45-63.
33. Saenger, W., Hunter, W.N. & Kennard, O. (1986). DNA conformation is determined by economics in the hydration of phosphate groups. Nature 324, 385-388.
34. Steinkopf, S., Garoufis, A., Nerdal, W. & Sletten, E. (1995). Sequence-selective metal ion binding to DNA oligomers. Acta Chimica Scand. 49, 495-502.
35. Hud, N.V. & Feigon, J. (1997). Localization of divalent metal ions in the minor groove of DNA A-tracts. J. Am. Chem. Soc. 119, 5756-5757.
36. Arnott, S. & Hukins, D.W. (1972). Optimised parameters for A-DNA and B-DNA. Biochem. Biophys. Res. Comm. 47, 1504-1509.
37. Pearlman, D.A., et al., & Kollman, P.A. (1995). AMBER, a package of Computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structure and energetic properties of molecules. Comp. Phys. Comm. 91, 1-41.
38. Andzelm, J. & Wimmer, E. (1991). DGAUSS: a density functional method for molecular and electronic structure calculations in the 1990s. Physica B. 172, 307-317.
39. Godbout, N., Salahub, D.R., Andzelm, J. & Wimmer, E. (1992). Optimization of Gaussian-type basis sets for local spin density functional calculations. 1. Boron through Neon, optimization technique and validation. Can. J. Chem. 70, 560-571.
40. Johnson, B.G., Gill, P.M.W. & Pople, J.A. (1993). The performance of a family of density functional methods. J. Chem. Phys. 98, 5612-5626.
41. Becke, A.D. (1988). Density-functional exchange-energy approximation with correct asymptotic behavior. Phys. Rev. A. 38, 3098-3100.
42. Ryckaert, J.P., Ciccotti, G. & Berendsen, H.J.C. (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.
43. Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F., DiNola, A. & Haak, J.R. (1984). Molecular dynamics with coupling to an external bath. J. Comp. Phys. 81, 3684-3690.
44. Ravishanker, G., Swaminathan, S., Beveridge, D.L., Lavery, R. & Sklenar, H. (1989). Conformational and helicoidal analysis of 30 PS of molecular dynamics on the d(CGCGAATTCGCG) double helix: 'curves', dials and windows. J. Biomol. Struct. Dyn. 6, 669-99.
45. Lavery, R. & Sklenar, H. (1988). The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dyn. 6, 63-91.
46. Dickerson, R.E. (1989). Definitions and nomenclature of nucleic acid structure components. Nuc. Acids Res. 17, 1797-1803.
47. Altona, C. & Sundaralingam, M. (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.
48. Ferrin, T.E., Huang, C.C., Jarvis, L.E. & Langridge, R. (1988). The MIDAS display system. J. Mol. Graphics 6, 13-27.
49. Vincent J.J. & Merz, K.M. (1995). A highly portable parallel implementation of Amber4 using the message passing interface standard. J. Comp. Chem. 16, 1420-1427.
50. Berman, H.M., et al. & Schneider, B. (1992). The nucleic acid database-A comprehensive relational database of 3-dimensional structures of nucleic acids. Biophys. J. 63, 751-759.