Observation of an A-DNA to B-DNA transition in a nonhelical nucleic acid hairpin molecule using molecular dynamics

Biophysical Journal

Volumn 73, Issue 5, 1997, Pages 2702-2710

  Miller, Jennifer L ^a   Kollman, Peter A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYURIDINE; DNA A; DNA B; NUCLEIC ACID; THYMINE;

ARTICLE; CONFORMATIONAL TRANSITION; DNA CONFORMATION; MOLECULAR DYNAMICS; SIMULATION;

EID: 0030829239     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(97)78298-5     Document Type: Article

References (25)

1. Allain, F. H. T., and G. Varani. 1995. Structure of the PI helix from group I self-splicing introns. J. Mol. Biol. 250:333-353.
2. B erendsen, H. J. C., J. P. M. Postma, W. F. van Gunsteren, A. DiNola, and J. R. Haak. 1984. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81:3684-3690.
3. Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swami- nathan, and J. Karplus. 1983. CHARMM: a program for macromolecular energy, minimization, and dynamics calculation. J. Comput. Chem. 4:187-217.
4. Cheatham, T. E., III, and P. A. Kollman. 1996. Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution. J. Mol. Biol. 259:434-444.
5. Cheatham, T. E., III, and P. A. Kollman. 1997. Molecular dynamics simulations can reasonably represent the structural differences in DNA: DNA. RNA:RNA and DNA:RNA hybrid duplexes. J. Am. Chem. Soc. 119:4805-4825.
6. 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.
7. Cornell, W. D., P. Cieplak, C. I. Bayly, and P. A. Kollman. 1993. Application of resp charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation. J. Am. Chem. 115:9620-9631.
8. Dickerson, R. E., D. S. Goodsell, M. L. Kopka, and P. E. Pjura. 1987. The effect of crystal packing on oligonucleotide crystal structures. J. Biomol. Struct. Dyn. 5:557-579.
9. Dickerson, R. E., D. S. Goodsell, and S. Neile. 1994. ". . . the tyranny of the lattice. . . ". Proc. Natl. Acad. Sci. USA. 91:3579-3583.
10. Ferrin, T. E., C. C. Huang, L. E. Jarvis, and R. Langridge. 1988. The MIDAS display system. J. Mol. Graph. 6:13-27.
11. James, J. K., and J. I. Tinoco. 1993. The solution structure of a d[C(TTCG)G] DNA hairpin and comparison to the unusually stable RNA analogue. Nucleic Acids. Res. 21:3287-3293.
12. Lipanov, A., M. L. Kopka, M. Kaczor-Grzeskowiak, J. Quintana, and R. E. Dickerson. 1993. Structure of the B-DNA decamer CCAACITTGG in two different space groups: conformational flexibility of B-DNA. Biochemistry. 32:1373-1389.
13. Miller, J. L., and P. A. Kollman. 1997. Theoretical studies of an exceptionally stable RNA tetraloop: observation of convergence from an incorrect NMR structure in the correct one using unrestrained molecular dynamics. J. Mol. Biol. In press.
14. Olson, W. K. 1982. How flexible is the furanose ring? 2. An updated potential energy estimate. J. Am. Chem. Soc. 104:278-286.
15. Pearlman, D. A., D. A. Case, J. W. Caldwell, W. S. Ross. T. E. Cheatham, III, D. M. Ferguson, G. L. Seibel, U. C. Singh, P. K. Weiner, and P. A. Kollman. 1995. AMBER 4.1. University of California, San Francisco, CA.
16. Ravishanker, G., S. Swaminathan, D. L. Beveridge, R. Lavery, and H. Sklenar. 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. 6:669-699.
17. 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.
18. Saenger, W. 1984. Principles of Nucleic Acid Structure. Springer Advanced Texts in Chemistry. C. R. Cantor, editor. Springer Verlag, New York.
19. Sakata, T., H. Hiroaki, Y. Oda, T. Tanaka, M. Ikehara, and S. Uesugi. 1990. Studies on the structure and stabilizing factor of the CUUCGG hairpin RNA using chemically synthesized oligonucleotides. Nucleic Acids Res. 18:3831-3839.
20. Schmitz, U., and T. L. James, editors. 1995. How to generate accurate solution structures of double-helical nucleic acid fragments using nuclear magnetic resonance and restrained molecular dynamics. Methods Enzymol. 261:3-44.
21. Schultz, S. C., G. C. Shields, and T. A. Steitz. 1991. Crystal structure of a CAP-DNA complex-the DNA is bent by 90 degrees. Science. 253:1001-1007.
22. Simmerling, C., R. Elber, and J. Zhang. 1995. MOIL-View-a program for visualization of structure and dynamics of biomolecules and STO-a program for computing stochastic paths. In Modelling of Biomolecular Structures and Mechanisms. A. Pullman. J. Jortner, and B. Pullman. editors. Kluwer Academic Publishers, the Netherlands. 241-265.
23. Ulyanov, N. B., and T. L. James. 1995. Statistical analysis of DNA duplex structural features. Methods Enzymol. 261:90-125.
24. Varani, G., G. Cheong, and I. J. Tinoco. 1991. Structure of an unusually stable RNA hairpin. Biochemistry. 30:3280-3289.
25. Yang, L., and B. M. Pettitt. 1996. B to A transition of DNA on the nanosecond time scale. J. Phys. Chem. 100:2564-2566.