Emerging themes in RNA folding

Folding and Design

Volumn 2, Issue 5, 1997, Pages

  Doudna, Jennifer A ^a   Doherty, Elizabeth A ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; REVIEW; X RAY CRYSTALLOGRAPHY;

BASE SEQUENCE; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA;

EID: 0030627401     PISSN: 13590278     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1359-0278(97)00035-7     Document Type: Review

References (53)

1. Draper, D.E. (1996). Strategies for RNA folding. Trends Biochem. Sci. 21, 145-149.
2. Westhof, E., Masquida, B. & Jaeger, L. (1996). RNA tectonics: towards RNA design. Fold. Des. 1, R78-R88.
3. Westhof, E. & Patel, D. (1997). Nucleic acids: from self-assembly to induced fit recognition. Curr. Opin. Struct. Biol. 7, 305-309.
4. Kim, S.H., er al., & Rich, A. (1973). Three-dimensional structure of yeast phenylalanine transfer RNA: folding of the polynucleotide chain. Science 179, 285-288.
5. Pley, H.W., Raherty, K.M. & McKay, D.B. (1994). Three-dimensional structure of a hammerhead ribozyme. Nature 372, 68-74.
6. Scott, W.G., Finch, J.T. & Klug, A. (1995). The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell 81, 995-1002.
7. Gate, J.H., et al., & Doudna, J.A. (1996). Crystal structure of a group I ribozyme domain: principles of RNA packing. Science 273, 1678-1685.
8. Dill, K.A. (1990). Dominant forces in protein folding. Biochemistry 29, 7133-7155.
9. Matsumura, M., Becktel, W.J. & Matthews, B.W. (1988). Hydrophobic stabilization in T4 lysozyme determined directly by multiple substitutions of lie 3. Nature 334, 406-410.
10. Lim, W.A. & Sauer, R.T. (1989). Alternative packing arrangements in the hydrophobic core of λ repressor. Nature 339, 31-36.
11. Bowie, J.U., Reidhaar-Olson, J.F., Lim, W.A. & Sauer, R.T. (1990). Deciphering the message in protein sequences: tolerance to amino acid substitutions. Science 247, 1306-1310.
12. Privalov, P.L. (1979). Stability of proteins: small globular proteins. Adv. Protein Chem. 33, 167-241.
13. Privalov, P.L. & Gill, S.J. (1988). Stability of protein structure and hydrophobic interaction. Adv. Protein Chem. 39, 191-234.
14. Dill, K.A., Alonso, D.O. & Hutchinson, K. (1989). Thermal stabilities of globular proteins. Biochemistry 28, 5439-5449.
15. Dill, K.A., et al., & Chan, H.S. (1995). Principles of protein folding - a perspective from simple exact models. Protein Sci. 4, 561-602.
16. Kauzman, W. (1959). Some factors in the interpretation of protein denaturation. Adv. Protein Chem. 14, 1-63.
17. Friedman, R.A. & Honig, B. (1995). A free energy analysis of nucleic acid base stacking in aqueous solution. Biophys. J. 69, 1528-1535.
18. Ramachandran, G.N. & Saisekharan, V. (1968). Conformation of polypeptides and proteins. Adv. Protein Chem. 23, 283-437.
19. Jack, A., Ladner, J.E. & Klug, A. (1976). 'Non-rigid' nucleotides in tRNA: a new correlation in the conformation of a ribose. Nature 261, 250-251.
20. Holbrook, S.R., Sussman, J.L., Warrant, R.W. & Kim, S.H. (1978). Crystal structure of yeast phenylalanine transfer RNA. II. Structural features and functional implications. J. Mol. Biol. 123, 631-660.
21. Saenger, W. (1984). Principles of Nucleic Acid Structure. Springer-Verlag, New York.
22. Freier, S.M., et al., & Turner, D.H. (1986). Improved free energy parameters for predictions of RNA duplex stability. Proc. Natl Acad. Sci. USA 83, 9373-9377.
23. Holbrook, S.R., Cheong, C. & Tinoco, I. Jr. (1991). Crystal structure of an RNA double helix incorporating a track of non-Watson-Crick base pairs. Nature 353, 579-581.
24. Betzel, C., et al., & Erdmann, V.A. (1994). Crystal structure of domain A of Thermus flavis 5s rRNA and the contribution of water molecules to its structure. FEBS Lett. 351, 159-164.
25. Cruse, W.B., Saludjian, P., Biala, E., Strazewski, P., Prange, T. & Kennard, O. (1994). Structure of a mispaired RNA double helix at 1.6-Å resolution and implications for the prediction of RNA secondary structure. Proc. Natl Acad. Sci. USA 91, 4160-4164.
26. Egli, M., Portmann, S. & Usman, N. (1996). RNA hydration: a detailed look. Biochemistry 35, 8489-8994.
27. Robertus, J.D., et al., & Klug, A. (1974). Structure of yeast phenylalanine tRNA at 3 Å resolution. Nature 250, 546-551.
28. Schevitz, R.W., Podjarny, A.D., Krishnamachari, N., Hughes, J.J. & Sigler, P.B. (1979). Crystal structure of a eukaryotic initiator tRNA. Nature 278, 188-190.
29. Asp. Nature 288, 669-674.
30. fMet. Nature 286, 346-351.
31. Rich, A., Quigley, G.J. & Wang, A.H.J. (1979). Conformational flexibility of the polynucleotide chain. In Stereodynamics of Molecular Systems. (Sarma, R.H., ed.), pp. 315-330, Pergammon Press, New York.
32. Costa, M. & Michel, F. (1995). Frequent use of the same tertiary motif by self-folding RNAs. EMBO J. 14, 1276-1285.
33. Woese, C.R., Winker, S. & Gutell, R.R. (1990). Architecture of ribosomal RNA: constraints on the sequence of 'tetra-loops'. Proc. Natl Acad. Sci. USA 87, 8467-8471.
34. Heus, H.A. & Pardi, A. (1991). Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops. Science 253, 191-194.
35. Cate, J.H., et al., & Doudna, J.A. (1996). RNA tertiary structure mediation by adenosine platforms. Science 273, 1696-1699.
36. Cole, P.E., Yang, S.K. & Crothers, D.M. (1972). Conformational changes of transfer ribonucleic acid. Equilibrium phase diagrams. Biochemistry 11, 4358-4368.
37. Crothers, D.M., Cole, P.E., Hilbers, C.W. & Shulman, R.G. (1974). The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA. J. Mol. Biol. 87, 63-88.
38. Celander, D.W. & Cech, T.R. (1991). Visualizing the higher order folding of a catalytic RNA molecule. Science 251, 401-407.
39. Liang, L.G. & Draper, D.E. (1994). Thermodynamics of RNA folding in a conserved ribosomal RNA domain. J. Mol. Biol. 237, 560-576.
40. Zarrinkar, P.P. & Williamson, J.R. (1994). Kinetic intermediates in RNA folding. Science 265, 918-924.
41. Downs, W.D. & Cech, T.R. (1996). Kinetic pathway for folding of the Tetrahymena ribozyme revealed by three UV-inducible crosslinks. RNA 2, 718-732.
42. Banerjee, A.R., Jaeger, J.A. & Turner, D.H. (1993). Thermal unfolding of a group I ribozyme: the low-temperature transition is primarily disruption of tertiary structure. Biochemistry 32, 153-163.
43. Laggerbauer, B., Murphy, F.L. & Cech, T.R. (1994). Two major tertiary folding transitions of the Tetrahymena catalytic RNA. EMBO J. 13, 2669-2676.
44. Doherty, E.A. & Doudna, J.A. (1997). The P4-P6 domain directs higher order folding of the Tetrahymena ribozyme core. Biochemistry 36, 3159-3169.
45. Stein, A. & Crothers, D.M. (1976). Conformational changes of transfer RNA. The role of magnesium(II). Biochemistry 15, 160-168.
46. Bassi, G.S., Mollegaard, N.-E., Murchie, A.I.H., von Kitzing, E. & Lilley, D.M.J. (1995). Ionic interactions and the global conformations of the hammerhead ribozyme. Nat. Struct. Biol. 2, 45-55.
47. Christian, E.L. & Yarus, M. (1992). Analysis of the role of phosphate oxygens in the group I intron from Tetrahymena. J. Mol. Biol. 228, 743-758.
48. Pyle, A.M. (1993). Ribozymes: a distinct class of metalloenzymes. Science 261, 709-714.
49. Latham, J.A. & Cech, T.R. (1989). Defining the inside and outside of a catalytic RNA molecule. Science 245, 276-282.
50. Murphy, F.L. & Cech, T.R. (1993). An independently folding domain of RNA tertiary structure within the Tetrahymena ribozyme. Biochemistry 32, 5291-5300.
51. Wang, J.-F. & Cech, T.R. (1994). Metal ion dependence of active-site structure of the Tetrahymena ribozyme revealed by site-specific photocross-linking. J. Am. Chem. Soc. 116, 4178-4182.
52. Sclavi, B., Woodson, S., Sullivan, M., Chance, M.R. & Brenowitz, M. (1997). Time-resolved synchrotron X-ray "footprinting", a new approach to the study of nucleic acid structure and function: application to protein-DNA interactions and RNA folding. J. Mol. Biol. 266, 144-159.
53. Cate, J.H., Hanna, R.L. & Doudna, J.A. (1997). A magnesium ion core at the heart of a ribozyme domain. Nat. Struct. Biol. 4, 553-558.