Hierarchy and dynamics of RNA folding

Annual Review of Biophysics and Biomolecular Structure

Volumn 26, Issue , 1997, Pages 113-137

  Brion, Philippe ^a   Westhof, Eric ^a  

^a CNRS   (France)

Author keywords

3 D motifs; Catalysis; Chaperones; Kinetics; Thermodynamics

Indexed keywords

CHAPERONE; MAGNESIUM ION; NUCLEOTIDE; RNA; RNA BINDING PROTEIN;

PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN RNA BINDING; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; REVIEW; RNA CONFORMATION; THERMODYNAMICS;

ANIMALS; MAGNESIUM; MUTATION; NUCLEIC ACID CONFORMATION; RNA; TETRAHYMENA;

EID: 0031009237     PISSN: 10568700     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.biophys.26.1.113     Document Type: Review

References (121)

1. Antao VP, Lai SY, Tinoco I Jr. 1991. A thermodynamic study of unusually stable RNA and DNA hairpins. Nucleic Acids Res. 19:5901-5
2. Antao VP, Tinoco I Jr. 1992. Thermodynamic parameters for loop formation in RNA and DNA hairpin loops. Nucleic Acids Res. 20:819-24
3. Bachellerie JP, Michot B, Nicoloso M, Balakin A, Ni J, Fournier MJ. 1995. Antisense snoRNAs: a family of nucleolar RNAs with long complementarities to rRNA. Trends Biochem. Sci. 20:261-64
4. Deleted in proof
5. Banerjee AR, Jaeger JA, Turner DH. 1993. Thermal melting of a group I ribozyme: The low temperature transition is primarily disruption of tertiary structure. Biochemistry 32:153-63
6. Banerjee AR, Turner DH. 1995. The time dependence of chemical modification reveals slow steps in the folding of a group I ribozyme.Biochemistry 34:6504-12
7. Beaudry AA, Joyce GF. 1990. Minimum secondary structure requirements for catalytic activity of self-splicing group I intron. Biochemistry 29:6534-39
8. Beebe JA, Kurz JC, Fierke CA. 1996. Magnesium ions are required by Bacillus subtilis RNase P RNA for both binding and cleaving precursor-tRNA (Asp). Biochemistry. In press
9. 1 end. Biochemistry 22:741-45.
10. 1 end. J. Mol. Biol. 139:601-25
11. Brehm SL, Cech TR. 1983. Fate of an intervening sequence ribonucleic acid: excision and cyclization of the Tetrahymena ribosomal ribonucleic acid intervening sequence in vivo. Biochemistry 22:2390-97
12. Burke JM. 1994. The hairpin ribozyme. In Nucleic Acids and Molecular Biology, ed. F Eckstein, DMJ Lilley, 8:105-18. NewYork: Springer-Verlag
13. Caprara MG, Lehnert V, Lambowitz AM, Westhot E. 1996. A Tyrosol-tRNA synthetase recognizes a conserved tRNA-Like structural motif in the Group I Intron Catalytic Core. Cell 87:1-20
14. Caprara MG, Mohr G, Lambowitz AM. 1996. A tyrosyl-tRNA synthetase protein induces tertiary folding of the group I catalytic core. J. Mol. Biol. 257:512-31
15. Cech TR, Herschlag D. 1996. Group I ribozymes: substrate recognition, catalytic strategies, and comparative mechanistic analysis. In Nucleic Acids and Molecular Biology, ed. F Eckstein, DMJ Lilley, 10:1-17. Berlin: Springer-Verlag
16. Celander DW, Cech TR. 1991. Visualizing the higher order folding of a catalytic RNA molecule. Science 251:401-7
17. Coetzee T, Herschlag D, Belfort M. 1994. Escherichia coli proteins, including ribosomal protein S12, facilitate in vitro splicing of phage T4 introns by acting as RNA chaperones. Genes Dev. 8:1575-88
18. Cole PE, Yang SK, Crothers DM. 1972. Conformational changes of transfer ribonucleic acid. Equilibrium phase diagrams. Biochemistry 11:4358-68
19. Costa M, Michel F. 1995. Frequent use of the same tertiary motif by self-folding RNAs. EMBO J. 14:1276-85
20. Asp (Brewer's yeast). Thermodynamic, kinetic, and enzymatic measurements on oligonucleotide fragments and the intact molecule. Biochemistry 13:3938-48
21. Crothers DM, Cole PE, Hilbers CW, Shulman RG. 1974. The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA. J. Mol. Biol. 87:63-88
22. Doudna JA, Cech TR. 1995. Self-assembly of a group I intron active site from its component tertiary structural domains. RNA 1:36-45
23. Draper DE. 1996. Parallel worlds. Nat. Struct. Biol. 3:397-400
24. Duckett DR, Murchie AIH, Lilley DMJ. 1995. The global folding of four-way helical junctions in RNA, including that in U1 snRNA. Cell 83:1027-36
25. Emerick VL, Woodson SA. 1993. Self-splicing of the Tetrahymena pre-rRNA is decreased by misfolding during transcription. Biochemistry 32:14062-67
26. Emerick VL, Woodson SA. 1994. Fingerprinting the folding of a group I precursor RNA. Proc. Natl. Acad. Sci. USA 91:9675-79
27. Ewbank JJ, Creighton TE, Hayer-Hartel MK, Hartel FU. 1995. What is the molten globule? Nat. Struct. Biol. 2:10
28. Franzen JS, Zhang M, Chay TR, Peebles CL. 1994. Thermal activation of a group II intron ribozyme reveals multiple conformational states. Biochemistry 31:11315-26
29. Fresco JR, Adains A, Ascione R, Henley D, Lindahl T. 1966. Tertiary structure in transfer ribonucleic acids. Cold Spring Harbor Symp. Quant. Biol. 31:527-37
30. Gampel A, Cech TR. 1991. Binding of the CBP2 protein to a yeast mitochondrial group I intron requires the catalytic core of the RNA. Genes Dev. 5:1870-80
31. Gluick TC, Draper DE. 1994. Thermodynamics of folding a pseudoknotted mRNA fragment. J. Mol. Biol. 241:246-62
32. Gopalan V, Talbot SJ, Altman S. 1994. RNA-protein interactions in RNAse P. In RNA-Protein Interactions, ed. K Nagai, IW Mattaj, pp. 103-26. Oxford: IRL Press, Oxford Univ. Press
33. Gregorian RSJ, Crothers DM. 1995. Determinants of RNA hairpin loop-loop complex stability. J. Mol. Biol. 248:968-84
34. Groeneveld H, Thimon K, Van Duin J. 1995. Translational control of maturation-protein synthesis in phage MS2: a role for the kinetics of RNA folding. RNA 1:79-88
35. Guéron M, Leroy J-L. 1982. Significance and mechanism of divalent-ion binding to transfer RNA. Biophys. J. 38:231-36
36. Gultyaev AP, van Batenburg FHD, Pleij CWA. 1995. The computer simulation of RNA folding pathways using a genetic algorithm. J. Mol. Biol. 250:37-51
37. Guo Q, Lambowitz AM. 1992. A tyrosyl-tRNA synthetase binds specifically to the group I intron catalytic core. Genes Dev. 6:1357-72
38. 3. Biopolymers 16:1557-66
39. Herschlag D. 1995. RNA chaperones and the RNA folding problem. J. Biol. Chem. 270:20871-74
40. Herschlag D, Khosla M, Tsuchihashi Z, Karpel RL. 1994. An RNA chaperone activity of non-specific RNA binding proteins in hammerhead ribozyme catalysis. EMBO J. 13:2913-24
41. Higgs PG. 1995. Thermodynamic properties of transfer RNA: a computational study. J. Chem. Soc. Faraday Trans. 91:2531-40
42. Hilbers CW, Robillard GT, Shulman RG, Blake RD, Webb PK, et al. 1976. Thermal unfolding of yeast glycine transfer RNA. Biochemistry 15:1874-82
43. Horovitz A, Fersht AR. 1990. Strategy for analysing the co-operativity of intramolecular interactions in peptides and proteins. J. Mol. Biol. 214:613-17
44. Horovitz A, Fersht AR. 1992. Co-operative interactions during protein folding. J. Mol. Biol. 224:733-40
45. Jaeger JA, Turner DH, Zuker M. 1990. Predicting optimal and suboptimal secondary structure for RNA. Methods Enzymol. 183:281-306
46. Jaeger L, Michel F, Westhof E. 1994. Involvement of a GNRA tetraloop in long-range RNA tertiary interactions. J. Mol. Biol. 236:1271-76
47. Jaeger L, Michel F, Westhof E. 1996. The structure of group I ribozymes. In Nucleic Acids and Molecular Biology, eds. F Eckstein, DMJ Lilley, 10:33-51. Berlin: Springer-Verlag
48. Jaeger L, Westhof E, Michel F. 1991. Function of P11, a tertiary base pairing in self-splicing introns of subgroup 1A. J. Mol. Biol. 221:1153-64
49. Jaeger L, Westhof E, Michel F. 1993. Monitoring of the cooperative unfolding of the sunY group I intron of bacteriophage T4. The active form of the sunY ribozyme is stabilized by multiple interactions with 3′ terminal intron components. J. Mol. Biol. 234:331-46
50. Joyce GF, Van der Horst G, 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. 17:7879-89
51. Kawajima K. 1989. The molten globule state as a clue for understanding the folding and cooperativity of globular-protein structure. Proteins: Struct. Funct. Genet. 6:87-103
52. Kramer FR, Mills DR. 1981. Secondary structure formation during RNA synthesis. Nucleic Acids Res. 9:5109-24
53. Krol A, Westhof E, Bach M, Lührmann R, Ebel J-P, Carbon P. 1990. Solution structure of human U1 snRNA. Derivation of a possible three-dimensional model. Nucleic Acids Res. 18:3803-10
54. Laggerbauer B, Murphy FL, Cech TR. 1994. Two major tertiary folding transitions of the Tetrahymena catalytic RNA. EMBO J. 13:2269-76
55. Laing LG, Draper DE. 1994. Thermodynamics of RNA folding in a conserved ribosomal RNA domain. J. Mol. Biol. 237:560-76
56. Laing LG, Gluick TC, Draper DE. 1994. Stabilization of RNA structure by Mg ions. Specific and non-specific effects. J. Mol. Biol. 237:577-87
57. Lambowitz AM, Perlman PS. 1990. Involvement of aminoacyl-tRNA synthetases and other proteins in group I and group II intron splicing. Trends Biochem. Sci. 15:440-44
58. LeCuyer KA, Crothers DM. 1993. The Leptomanas collosoma spliced leader RNA can switch between two alternate structural forms. Trends Biochem. Sci. 32:5301-11
59. LeCuyer KA, Crothers DM. 1994. Kinetics of an RNA conformational switch. Proc. Natl. Acad. Sci. USA 91:3373-77
60. Levinthal C. 1968. Are there pathways for protein folding? J. Chem. Phys. 65:44-47
61. Louise-May S, Auffinger P, Westhof E. 1996. Calculations of nucleic acid conformations. Curr. Opin. Struct. Biol. 6:289-98
62. Lu M, Draper DE. 1994. Bases defining an ammonium and magnesium ion-dependent tertiary structure within the large subunit ribosomal RNA. J. Mol. Biol. 244:572-85
63. Ma CK, Kolesnikow T, Rayner JC, Simons EL, Yim H, Simons RW. 1994. Control of translation by mRNA secondary structure: the importance of the kinetics of structure formation. Mol. Microbiol. 14:1033-47
64. Marino JP, Gregorian RSJ, Csankovszki G, Crothers DM. 1995. Bent helix formation between RNA hairpins with complementary loops. Science 268:1448-54
65. McGraw P, Tzagoloff A. 1983. Assembly of the mitochondrial membrane system. J. Biol. Chem. 258:9459-68
66. Michel F, Ellington AD, Couture S, Szostak JW. 1989. Phylogenetic and genetic evidence for base-triples in the catalytic domain of group I introns. Nature 347:578-80
67. Michel F, Jaeger L, Westhof E, Kuras R, Tihy F, et al. 1992. Activation of the catalytic core of a group I intron by a remote 3′ splice junction. Genes Dev. 6:1373-85
68. Michel F, Westhof E. 1990. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol. Biol. 216:581-606
69. Mohr G, Caprara MG, Guo Q, Lambowitz AM. 1994. A tyrosyl-tRNA synthetase can function similarly to an RNA structure in the Tetrahymena ribozyme. Nature 370:147-50
70. Mohr G, Zhang A, Gianelos JA, Belfort M, Lambowitz AM. 1992. The Neurospora CYT-18 protein suppresses defects in the phage T4 td intron by stabilizing the catalytically active structure of the intron core. Cell 69:483-94
71. Molinaro M, Tinoco I Jr. 1995. Use of ultra stable UNCG tetraloop hairpins to fold RNA structures: thermodynamic and spectroscopic applications. Nucleic Acids Res. 23:3056-63
72. Murphy FL, Cech TR. 1993. An independently folding domain of RNA tertiary structure within the Tetrahymena ribozyme. Biochemistry 32:5291-300
73. Murphy FL, Cech TR. 1994. GAAA tetraloop and conserved bulge stabilize tertiary structure of group I intron domain. J. Mol. Biol. 236:49-63
74. Murphy FL, Wang Y-W, Griffith JD, Cech TR. 1994. Coaxially stacked RNA helices in the catalytic center of the Tetrahymena ribozyme. Science 265:1709-12
75. Nicoloso M, Qu LH, Michot B, Bachellerie JP. 1996. Intron-encoded, antisense small nucleolar RNAs: The characterization of nine novel species points to their direct role as guides for the 2′-O-ribose methylation of rRNAs. J. Mol. Biol. 260:178-95
76. Pan T. 1995. Higher order folding and domain analysis of the ribozyme from Bacillus subtilis ribonuclease P. Biochemistry 34:902-9
77. Pan T, Long DM, Uhlenbeck OC. 1993. Divalent metal ions in RNA folding and catalysis. In RNA World, ed. RF Gesteland, JF Atkins, pp. 271-302. Cold Spring Harbor, NY: Cold Spring Harbor Lab. Press
78. Pley HW, Flaherty KM, McKay DB. 1994. Three-dimensional structure of a hammerhead ribozyme. Nature 372:68-74
79. Pley HW, Flaherty KM, McKay DB. 1994. Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix. Nature 372:111-13
80. Pörschke D. 1977. Elementary steps of base recognition and helix-coil transitions in nucleic acids. In Chemical Relaxation in Molecular Biology, ed. I Pecht, R. Rigler, pp. 191-218. Berlin: Springer-Verlag
81. Privalov PL, Filiminov VV. 1978. Thermodynamic analysis of transfer RNA unfolding. J. Mol. Biol. 122:447-64
82. Ptitsyn OB. 1995. How the molten globule became. Trends Biochem. Sci. 20:376-79
83. Pyle AM, Green JB. 1994. Building a kinetic framework for group II intron ribozyme activity: quantitation of interdomain binding and reaction rate. Biochemistry 33:2716-25
84. Qiu H, Kaluarachchi K, Du Z, Hoffman DW, Giedroc DP. 1996. Thermodynamics of folding of the RNA pseudoknot of the T4 gene 32 autoregulatory messenger RNA. Biochemistry 35:4176-86
85. Rao ST, Rossmann MG. 1973. Comparison of super-secondary structures in proteins. J. Mol. Biol. 76:241-56
86. Rastogi T, Beattie TL, Olive JE, Collins RA. 1996. A long-range pseudoknot is required for activity of the Neurospora VS ribozyme. EMBO J. 15:2820-25
87. Rhodes D. 1977. Initial stages of the thermal unfolding of yeast phenylalanine transfer RNA as studied by chemical modification: the effect of magnesium. Eur. J. Biochem. 81:91-101
88. SantaLucia J Jr, Kierzek R, Turner DH. 1992. Context dependence of hydrogen bond free energy revealed by substitutions in an RNA hairpin. Science 256:217-19
89. Scott WG, Finch JT, Klug A. 1995. The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell 81:991-1002
90. Serra MJ, Turner DH. 1995. Predicting thermodynamic properties of RNA. Methods Enzymol. 259:242-61
91. Shaw LC, Lewin AS. 1995. Protein-induced of a group I intron in cytochrome b pre-mRNA. J. Biol. Chem. 270:21552-62
92. Sheldon CC, Symons RH. 1989. RNA stem stability in the formation of a self-splicing hammerhead structure. Nucleic Acids Res. 17:5665-77
93. Shen LX, Cai Z, Tinoco I Jr. 1995. RNA structure at high resolution. FASEB J. 9:1023-33
94. fMet. Biochemistry 15:157-60
95. Stein A, Crothers DM. 1976. Conformational changes of transfer RNA. The role of magnesium (II). Biochemistry 15:160-67
96. Ile of the purple bacterium Azoarcus. RNA 2:74-83
97. Tanner NK, Schaff S, Thill G, Petit-Koskas E, Crain-Denoyelle A, Westhof E. 1994. A three-dimensional model of hepatitis delta virus ribozyme based on biochemical and mutational analysis. Curr. Biol. 4:488-98
98. Thirumalai D, Woodson SA. 1996. Kinetics of folding of proteins and RNA. Acc. Chem. Res. 29:433-9
99. Thomson JB, Tuschl T, Eckstein F. 1996. The hammerhead ribozyme. In Nucleic Acids and Molecular Biology, vol. 10, ed. F Eckstein, DMJ Lilley, pp. 173-96. New York, NY: Springer-Verlag
100. Tuerk C, Gauss P, Thermes C, Groebe DR, Gayle M, et al. 1988. CUUCGG hairpins: extraordinarily stable RNA secondary structures associated with various biochemical processes. Proc. Natl. Acad. Sci. USA 85:1364-68
101. Turner DH, Sugimoto N, Freier SM. 1988. RNA structure prediction. Annu. Rev. Biophys. Biophys. Chem. 17:167-92
102. Uhlenbeck OC. 1995. Keeping RNA happy. RNA 1:4-6
103. Van der Horst G, Christian A, Inoue T. 1991. Reconstitution of group I intron self-splicing reaction with an activator RNA. Proc. Natl. Acad. Sci. USA 88:184-88
104. von Ahsen U, Noller HF. 1993. Methylation interference experiments identify bases that are essential for distinct catalytic functions of a group I ribozyme. EMBO J. 12:4747-54
105. Walstrum SA, Uhlenbeck OC. 1990. The self-splicing RNA of the Tetrahymena is trapped in a less active conformation by gel purification. Biochemistry 29:10573-76
106. Weeks KM, Cech TR. 1995. Efficient protein-facilitated splicing of the yeast mitochondrial bI5 intron. Biochemistry 34:7728-38
107. Weeks KM, Cech TR. 1995. Protein facilitation of group I intron splicing by assembly of the catalytic core and the 5′ splice site domain. Cell 82:221-30
108. Weeks KM, Cech TR. 1996. Assembly of a ribonucleoprotein catalyst by tertiary structure capture. Science 271:345-48
109. Westhof E, Jaeger L. 1992. RNA pseudoknots: structural and functional aspects. Curr. Opin. Struct. Biol. 2:327-33
110. Westhof E, Michel F. 1994. Prediction and experimental investigation of RNA secondary and tertiary foldings. In RNA-Protein Interactions, ed. K Nagai, IW Mattaj, pp. 25-51. Oxford: IRL Press, Oxford Univ. Press
111. Westhof E, Dumas P, Moras D. 1985. Crystallographic refinement of yeast aspartic acid transfer RNA. J. Mol. Biol. 184:119-45
112. Woese CR, Winker S, Gutell RR. 1990. Architecture of ribosomal RNA: constraints on the sequence of "tetra loops." Proc. Natl. Acad. Sci. USA 87:8467-71
113. Wolynes PG, Onuchic JN, Thirumalai D. 1995. Navigating the folding routes. Science 267:1619-20
114. Woodson SA, Cech TR. 1991. Alternative secondary structures in the 5′ exon affect both forward and reverse self-splicing of the Tetrahymena intervening sequence RNA. Biochemistry 30:2042-50
115. Woodson SA, Emerick VL. 1993. An alternative helix in the 26S rRNA promotes excision and integration of the Tetrahymena intervening sequence. Mol. Cell. Biol. 13:1137-45
116. Wyatt JR, Puglisi JD, Tinoco I Jr. 1990. RNA pseudoknots. Stability and loop size requirements. J. Mol. Biol. 214:455-70
117. Wyatt JR, Tinoco I Jr. 1993. RNA structural elements. In RNA World, ed. RF Gesteland, JF Atkins, pp. 465-97. Cold Spring Harbor, NY: Cold Spring Harbor Lab. Press
118. Zarrinkar PP, Williamson JR. 1994. Kinetic intermediates in RNA folding. Science 265:918-24
119. Zarrinkar PP, Williamson JR. 1996. The P9.1-P9.2 peripheral extension helps guide folding of the Tetrahymena ribozyme. Nucleic Acids Res. 24:854-58
120. Zarrinkar PP, Williamson JR. 1996. The kinetic folding pathway of the Tetrahymena ribozyme reveals possible similarities between RNA and protein folding. Nat. Struct. Biol. 3:432-38
121. Zhang A, Derbyshire V, Galloway Salvo JL, Belfort M. 1995. Escherichia coli protein StpA stimulates self-splicing by promoting RNA assembly in vitro. RNA 1:783-93