Predicting RNA folding thermodynamics with a reduced chain representation model

RNA

Volumn 11, Issue 12, 2005, Pages 1884-1897

  Cao, Song ^a   Chen, Shi Jie ^a,b  

^a University of Missouri   (United States)

^b UNIVERSITY OF MISSOURI   (United States)

Author keywords

Cooperativity; Misfolded intermediates; RNA folding; Stability

Indexed keywords

RIBOZYME; RNA;

ARTICLE; ATOM; ENERGY; GENE MUTATION; LETHALITY; MOLECULAR MODEL; PREDICTION; PRIORITY JOURNAL; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN TERTIARY STRUCTURE; RNA CONFORMATION; RNA STRUCTURE; STATISTICAL ANALYSIS; TETRAHYMENA; THEORY; THERMODYNAMICS;

ANIMALS; MODELS, MOLECULAR; MODELS, STATISTICAL; MUTATION; NUCLEIC ACID CONFORMATION; RNA; RNA STABILITY; RNA, CATALYTIC; RNA, PROTOZOAN; TEMPERATURE; TETRAHYMENA; THERMODYNAMICS;

TETRAHYMENA;

EID: 28344438036     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2109105     Document Type: Article

References (46)

1. Antao, V.P. and Tinoco Jr. I., 1992. Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops. Nucleic Acids Res. 20: 819-824.
2. Biswas, R., Mitra, S.N., and Sundaralingam, M. 1998. 1.76Å structure of a pyrimidine start alternating A-RNA hexamer r(CGUAC)dG. Acta Cryst. D 54: 570-576.
3. Chan, H.S., Shimizu, S., and Kaya, H. 2004. Cooperativity principles in protein folding. Methods Enzymol. 380: 350-379.
4. Chen, S.-J. and Dill, K.A. 1995. Statistical thermodynamics of double-stranded polymer molecules. J. Chem. Phys. 103: 5802-5813.
5. _. 1998. Theory for the conformational changes of double-stranded chain molecules. J. Chem. Phys. 109: 4602-4616.
6. _. 2000. RNA folding energy landscapes. Proc. Natl. Acad. Sci. 97: 646-651.
7. Correll, C.C. and Swinger, K. 2003. Common and distinctive features of GNRA tetraloops based on a GUAA tetraloop structure at 1.4Å resolution. RNA 9: 355-363.
8. Deng, J., Xiong, Y., Sudarsanakumar, C., Shi, K., and Sundaralingam, M. 2001. Crystal structures of two forms of a 14-mer RNA/DNA chimer duplex with double UU bulges: A novel intramolecular U*(A·U) base triple. RNA 7: 1425-1431.
9. Draper, D.E., Grilley, D., and Soto, A.M. 2005. Ions and RNA folding. Ann. Rev. Biophys. Biol. Mol. Struct. 34: 221-243.
10. Duarte, C.M. and Pyle, A.M. 1998. Stepping through an RNA structure: A novel approach to conformational analysis. J. Mol. Biol. 284: 1465-1478.
11. Duarte, C.M., Wadley, L.M., and Pyle, A.M. 2003. RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space. Nucleic Acids Res. 31: 4755-4761.
12. Flory, P.J. 1969. Statistical mechanics of chain molecules. Wiley, New York.
13. Gluick, T.C. and Draper, D.E. 1994. Thermodynamics of folding a pseudoknotted mRNA fragment. J. Mol. Biol. 241: 246-262.
14. Heus, H.A. and Pardi, A. 1991. Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops. Science 253: 191-194.
15. Jaeger, J.A., Turner, D.H., and Zuker, M. 1989. Improved predictions of secondary structures for RNA. Proc. Natl. Acad. Sci. 86: 7706-7710.
16. Joyce, G.F., van der Horst, G., and Inoue, T. 1989. Catalytic activity is retained in the Tetrahymena group I intron despite removal of the large extension of element P5. Nucleic Acids Res. 17: 7879-7889.
17. Kierzek, R., Burkard, M.E., and Turner, D.H. 1999. Thermodynamics of single mismatches in RNA duplexes. Biochemistry 38: 14214-14223.
18. Koculi, E., Lee, N.K., Thirumalai, D., and Woodson, S.A. 2004. Folding of the Tetrahymena ribozyme by polyamines: Importance of counterion valence and size. J. Mol. Biol. 341: 27-36.
19. Laing, L.G. and Draper, D.E. 1994. Thermodynamics of RNA folding in a conserved ribosomal RNA domain. J. Mol. Biol. 237: 560-576.
20. 2+ and the 2′ OH of guanosine on steps required for substrate binding and reactivity with the Tetrahymena ribozyme reveal several local folding transitions. Biochemistry 36: 11131-11139.
21. Long, K.S. and Crothers, D.M. 1999. Characterization of the solution conformations of unbound and Tat peptide-bound forms of HIV-1 TAR RNA. Biochemistry 38: 10059-10069.
22. Malathi, R. and Yathindra, N. 1981. Virtual bond probe to study ordered and random oil conformations of nucleic acids. Intl. J. Quant. Chem. 20: 241-257.
23. Mathews, D.H., Sabina, J., Zuker, M., and Turner, D.H. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288: 911-940.
24. Mattice, W.L. and Suter, U.M. 1994. Conformational theory of large molecule: The rotational isomeric state model in macromolecular systems. Wiley, New York.
25. McCaskill, J.S. 1990. The equilibrium partition-function and base pair binding probabilities for RNA secondary structure. Biopolymers 29: 1105-1119.
26. Murray, L.J., Arendall III, W.B., Richardson, D.C., and Richardson, J.S. 2003. RNA backbone is rotameric. Proc. Natl. Acad. Sci. 100: 13904-13909.
27. Olson, W.K. 1975. Configuration statistical of polynucleotide chains. A single virtual bond treatment. Macromolecules 8: 272-275.
28. _. 1980. Configurational statistics of polynucleotide chains: An updated virtual bond model to treat effects of base stacking. Macromolecules 13: 721-728.
29. Olson, W.K. and Flory, P.J. 1972. Spatial configuration of polynucleotide chains: I. Steric interactions in polyribonucleotides: A virtual bond model. Biopolymers 11: 1-23.
30. Pan, J., Thirumalai, D., and Woodson, S.A. 1999. Magnesium-dependent folding of self-splicing RNA: Exploring the link between cooperativity, thermodynamics, and kinetics. Proc. Natl. Acad. Sci. 96: 6149-6154.
31. Puglisi, J.D., Tan, R.Y., Calnan, B.J., Frankel, A.D., and Williamson, J.R. 1992. Conformation of the TAR RNA-arginine complex by NMR-spectroscopy. Science 257: 76-80.
32. Puglisi, J.D., Chen, L., Frankel, A.D., and Williamson, J.R. 1993. Role of RNA structure in arginine recognition of TAR RNA. Proc. Natl. Acad. Sci. 90: 3680-3684.
33. Rapold, R.F. and Mattice, W.L. 1995. New high-coordination lattice model for rotational isomeric state polymer-chains. J. Chem. Soc. Faraday Trans. 91: 2435-2441.
34. Rich, A., Crick, F.H.C., Watson, J.D., and Davies, D.R. 1961. Molecular structure of polyadenylic acid. J. Mol. Biol. 3: 71-86.
35. Serra, M.J. and Turner, D.H. 1995. Predicting thermodynamic properties of RNA. Methods Enzymol. 259: 242-261.
36. Serra, M.J., Barnes, T.W., Betschart, K., Gutierrez, M.J., Sprouse, K.J., Riley, C.K., Stewart, L., and Temel, R.E. 1997. Improved parameters for the prediction of RNA hairpin stability. Biochemistry 36: 4844-4851.
37. Silverman, S.K., Zheng, M., Wu, M., Tinoco Jr., I., and Cech, T.R. 1999. Quantifying the energetic interplay of RNA tertiary and secondary structure interactions. RNA 5: 1665-1674.
38. Speek, M. and Lind, A. 1982. Structural analyses of E. coli 5S RNA fragments, their associates and complexes with proteins L18 and L25. Nucleic Acids Res. 10: 947-963.
39. Tan, Z.J. and Chen, S.J. 2005. Electrostatic correlations and fluctuations for ion binding to a finite length polyelectrolyte. J. Chem. Phys. 122: 044903.
40. Tao, J., Chen, L., and Frankel, A.D. 1997. Dissection of the proposed base triple in human immunodeficiency virus TAR RNA indicates the importance of the Hoogsteen interaction. Biochemistry 36: 3491-3495.
41. Thirumalai, D. 1998. Native secondary structure formation in RNA may be a slave to tertiary folding. Proc. Natl. Acad. Sci. 95: 11506-11508.
42. van der Horst, G., Christian, A., and Inoue, T. 1991. Reconstitution of a group-I intron self-splicing reaction with an activator RNA. Proc. Natl. Acad. Sci. 88: 184-188.
43. Wu, M. and Tinoco Jr., I., 1998. RNA folding causes secondary structure rearrangement. Proc. Natl. Acad. Sci. 95: 11555-11560.
44. Zarrinkar, P.P. and Williamson, J.R. 1994. Kinetic intermediates in RNA folding. Science 265: 918-924.
45. Zhang, W. and Chen, S.-J. 2001. A three-dimensional statistical mechanical model of folding double-stranded chain molecules. J. Chem. Phys. 114: 7669-7681.
46. Zheng, M., Wu, M., and Tinoco Jr., I., 2001. Formation of a GNRA tetraloop in P5abc can disrupt an interdomain interaction in the Tetrahymena group I ribozyme. Proc. Natl. Acad. Sci. 98: 3695-3700.