Understanding the thermodynamic stability of an RNA hairpin and its mutant

Biophysical Journal

Volumn 70, Issue 4, 1996, Pages 1940-1948

  Singh, Suresh B ^a   Kollman, Peter A ^b  

^a PFIZER INC   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; RNA CONFORMATION; RNA SEQUENCE; RNA STRUCTURE; THERMODYNAMICS; THERMOSTABILITY;

EID: 0029880445     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(96)79758-8     Document Type: Article

References (26)

1. Arnott, S., D. W. L. Hukins, S. D. Dover, W. Fuller, and A. R. Hodgson. 1973. Structures of synthetic polynucleotides in the A-RNA and A′-RNA conformations: x-ray diffraction analyses of the molecular conformations of polyadenylic acid · polyuridylic acid and polyinosinic acid · polycytidylic acid. J. Mol. Biol. 81:107-122.
2. Boresch, S., G. Archontis, and M. Karplus. 1994. Free energy simulations: the meaning of the individual contributions from a component analysis. Proteins Struct. Fund. Genet. 20:25-33.
3. Boresch, S., and M. Karplus. 1995. The meaning of component analysis-decomposition of the free energy in terms of specific interactions. J. Mol. Biol. 254:801-807.
4. Brady, G. P., and K. A. Sharp. 1995. Decomposition of interaction free energies in proteins and other complex systems. J. Mol. Biol. 254: 77-85.
5. Cheatham, T. E., III, J. L. Miller, T. Fox, T. A. Darden, and P. A. Kollman. 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.
6. Cheong, C. J., G. Varani, and I. Tinoco. Jr. 1990. Solution structure of an unusually stable RNA hairpin. 5′GGAC(UUCG)GUCC. Nature. 346: 680-682.
7. James, J. K., and I. Tinoco, Jr. 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.
8. 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.
9. Kollman, P. A. 1993. Free energy calculations: applications to chemical and biochemical phenomena. Chem. Rev. 93:2395-2417.
10. Mark, A. E., and W. F. van Gunsteren. 1994. Decomposition of the free energy of a system in terms of specific interactions: implications for theoretical and experimental studies. J. Mol. Biol. 240:167-176.
11. McCammon, J. A., and S. C. Harvey. 1987. Dynamics of Proteins and Nucleic Acids. Cambridge University Press, Cambridge, England.
12. Nilsson, L., A. Åhgren-Stalhandske, A. S. Sjögren, S. Hahne, and B-M. Sjöberg. 1990. 3-Dimensional model and molecular dynamics simulation of the active site of the self-splicing intervening sequence of the bacteriophage t4 NRDB messenger RNA. Biochemistry. 29: 10317-10322.
13. Pearlman, D. A., D. A. Case, J. C. Caldwell, G. L. Seibel, U. C. Singh, P. Weiner, and P. A. Kollman. 1991 AMBER(4.0). University of California, San Francisco.
14. 2. J. Am. Chem. Soc 108: 3048-3053.
15. Singh, S. B., Ajay, D. E. Wemmer, and P. A. Kollman. 1994. Relative binding affinities of distamycin and its analog to d(CGCAAGTTGGC) · d(GCCAACTTGCG): comparison of simulation results with experiment. Proc. Natl. Acad. Sci. USA. 91:7673-7677.
16. 3 in the gas phase. J. Am Chem. Soc. 109:1607-1614.
17. Singh, S. B., D. A. Pearlman, and P. A. Kollman. 1993. Free energy component analysis: application to the "Z-phobicity" of A · T base pairs. J. Biomol. Struct. Dyn. 11:303-311.
18. Smith, P. E., and W. F. van Gunsteren. 1994. When are free energy components meaningful? J. Phys. Chem. 98:13735-13740.
19. Stryer, L. 1988. Biochemistry, 3rd Ed. W. H. Freeman and Company, New York.
20. van Gunsteren, W F., and H. J. C. Berendsen. 1977. Algorithms for macromolecular dynamics and constraint dynamics. Mol. Phys. 34: 1311-1327.
21. Varani, G., C. Cheong, and I. Tinoco, Jr. 1991. Structure of an unusually stable RNA hairpin. Biochemistry. 30:3280-3289.
22. Weiner, S. J., P. A. Kollman, D. A. Case, U. C. Singh, C. Ghio, G Alagona, S. Profeta, and P. Weiner. 1984. A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem Soc. 106:765-784.
23. Wimberly, B., G. Varani, and I. Tinoco, Jr. 1991. Structural determinants of RNA function. Curr. Opin. Struct. Biol. 1:405-409.
24. Yunyu, S., A. E. Mark, C. X. Wang, F. H. Huang, H. J. C. Berendsen, and W. F. van Gunsteren. 1993. Can the stability of protein mutants be predicted by free energy calculations? Protein Eng. 6:289-295.
25. Zaug, A J., and T. R. Cech. 1986. The intervening sequence RNA of Tetrahymena is an enzyme. Science. 231:431-475.
26. Zichi, D. A. 1995. Molecular dynamics of RNA with the OPLS force field, aqueous simulation of a hairpin containing a tetranucleotide loop. J. Am. Chem. Soc. 117:2957-2969.