On the wobble GoU and related pairs

RNA

Volumn 6, Issue 1, 2000, Pages 9-15

  Masquida, Benoît ^a   Westhof, Eric ^a  

^a CNRS   (France)

Author keywords

A+oC; Covariations; GoC; Stacking; Twist; Wobble

Indexed keywords

RNA;

BASE PAIRING; CRYSTAL STRUCTURE; ESCHERICHIA COLI; EUBACTERIUM; GEOMETRY; NONHUMAN; PRIORITY JOURNAL; REVIEW; RNA STRUCTURE;

BASE PAIRING; MODELS, MOLECULAR; RNA;

ESCHERICHIA COLI;

EID: 0033985575     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838200992082     Document Type: Review

References (59)

1. Allain FH, Varani G. 1995a. Divalent metal ion binding to a conserved wobble pair defining the upstream site of cleavage of group I self-splicing introns. Nucleic Acids Res 23:341-350.
2. Allain FH, Varani G. 1995b. Structure of the P1 helix from group I self-splicing introns. J Mol Biol 250:333-353.
3. Auffinger P, Westhof E. 1998. Hydration of RNA base pairs. J Biomol Struct Dyn 16:693-707.
4. Auffinger P, Westhof E. 1999. Singly and bifurcated hydrogen-bonded base pairs in tRNA anticodon hairpins and ribozymes. J Mol Biol 292:467-483.
5. Baeyens KJ, De Bondt HL, Holbrook SR. 1995. Structure of an RNA double helix including uracil-uracil base pairs in an internal loop. Nature Struct Biol 2:56-62.
6. Been MD, Wickham GS. 1997. Self-cleaving ribozymes of hepatitis delta virus RNA. Eur J Biochem 247:741-753.
7. Benard L, Mathy N, Grunberg-Manago M, Ehresmann B, Ehresmann C, Portier C. 1998. Identification in a pseudoknot of a U.G motif essential for the regulation of the expression of ribosomal protein S15. Proc Natl Acad Sci USA 95:2564-2567.
8. Bevilacqua PC, Li Y, Turner DH. 1994. Fluorescence-detected stopped flow with a pyrene labeled substrate reveals that guanosine facilitates docking of the 5′ cleavage site into a high free energy binding mode in the Tetrahymena ribozyme. Biochemistry 33:11340-11348.
9. Biswas R, Sundaralingam M. 1997. Crystal structure of r(GUGU GUA)dC with tandem GU/UG wobble pairs with strand slippage. J Mol Biol 270:511-519.
10. Biswas R, Wahl MC, Ban C, Sundaralingam M. 1997. Crystal structure of an alternating octamer r(GUAUGUA)dC with adjacent G.U wobble pair. J Mol Biol 267:1149-1156.
11. Burgstaller P, Hermann T, Huber C, Westhof E, Famulok M. 1997. Isoalloxazine derivatives promote photocleavage of natural RNAs at G center dot U base pairs embedded within helices. Nucleic Acids Res 25:4018-4027.
12. Cate JH, Doudna JA. 1996. Metal binding sites in the major groove of a large ribozyme domain. Structure 4:1221-1229.
13. Cavarelli J, Eriani G, Rees B, Ruff M, Boeglin M, Mitschler A, Martin F, Gangloff J, Thierry JC, Moras D. 1994. The active site of yeast aspartyl-tRNA synthetase: Structural and functional aspects of the aminoacylation reaction. EMBO J 13:327-337.
14. Cech TR, Zaug AJ, Grabowski PJ. 1981. In vitro splicing of the ribosomal RNA precursor of Tetrahymena: Involvement of a guanosine nucleotide in the excision of the intervening sequence. Cell 27:487-496.
15. Chang K-Y, Varani G, Bhattacharya S, Choi H, McClain W. 1999. Correlation of deformability at a tRNA recognition site and amino-acylation specificity. Proc Natl Acad Sci USA 96:11764-11769.
16. Chow CS, Barton JK. 1992. Recognition of G-U mismatches by tris(4,7-diphenyl-1,10-phenanthroline)rhodium(III). Biochemistry 31:5423-5429.
17. Correll CC, Freeborn B, Moore PB, Steitz TA. 1997. Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain. Cell 28:705-712.
18. Crick FHC. 1966. Codon-anticodon pairing: The wobble hypothesis. J Mol Biol 19:548-555.
19. Dickerson RE. 1998. DNA bending: The prevalence of kinkiness and the virtues of normality. Nucleic Acids Res 26:1906-1926.
20. Doudna JA, Cormack BP, Szostak JW. 1989. RNA structure, not sequence, determines the 5′ splice-site specificity of a group I intron. Proc Natl Acad Sci USA 86:7402-7406.
21. Frugier M, Schimmel P. 1997. Subtle atomic group discrimination in the RNA minor groove. Proc Natl Acad Sci USA 94:11291-11294.
22. Gautheret D, Konings D, Gutell RR. 1995. G•U base pairing motifs in ribosomal RNA. RNA 1:807-814.
23. Giese MR, Betschart K, Dale T, Riley CK, Rowan C, Sprouse KJ, Serra MJ. 1998. Stability of RNA hairpins closed by wobble base pairs. Biochemistry 37:1094-1100.
24. He L, Kierzek R, SantaLucia J Jr, Walter AE, Turner DH. 1991. Nearest-neighbor parameters for G•U mismatches: 5′G•U3′/3′U•G5′ is destabilizing in the contexts CGUG/GUGC and UGUA/AUGU but stabilizing in GGUC/CCUGG. Biochemistry 30:11124-11132.
25. Hermann T, Westhof E. 1998. Exploration of metal ion binding sites in RNA folds with Brownian dynamics simulations. Structure 6:1303-1315.
26. Holbrook SR, Cheong C, Tinoco I, Kim SH. 1991. Crystal structure of an RNA double-helix incorporating a track of non-Watson-Crick base pairs. Nature 353:579-581.
27. Hou YM, Schimmel P. 1988. A simple structural feature is a major determinant of the identity of a transfer RNA. Nature 333:140-145.
28. Jang SB, Hung LW, Chi YI, Holbrook EL, Carter RJ, Holbrook SR. 1998. Structure of an RNA internal loop consisting of tandem C-A+ base pairs. Biochemistry 37:11726-11731.
29. Jeffrey GA. 1997. An Introduction to Hydrogen Bonding. New York: Oxford University Press.
30. Lavery R, Sklenar H. 1988. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J Biomol Struct Dyn 6:63-91.
31. Leontis NB, Westhof E. 1998. The 5S rRNA loop E: Chemical probing and phylogenetic data versus crystal structure. RNA 4:1134-1153.
32. Leontis NB, Westhof E. 1998a. Conserved geometrical base-pairing patterns in RNA. Q Rev Biophys 37:399-455.
33. Leontis NB, Westhof E. 1999. Recurrent RNA motifs: Analysis at the base-pair level. In: Barciszewski J, Clark BFC, eds. RNA biochemistry and biotechnology, Vol. 3/70. Boston: Kluwer Academic Publishers. pp 45-61.
34. Lietzke SE, Barnes CL, Berglund JA, Kundrot CE. 1996. The structure of an RNA dodecamer shows how tandem U-U base pairs increase the range of stable RNA structures and the diversity of recognition sites. Structure 4:917-930.
35. Masquida B, Sauter C, Westhof E. 1999. A sulfate pocket formed by three GoU pairs in the 0.97 Å resolution X-ray of a nonameric RNA. RNA 5:99-112.
36. McClain WH, Chen Y-M, Foss K, Schneider J. 1988. Association of transfer RNA acceptor identity with a helical irregularity. Science 242:1681-1684.
37. Michel F, Westhof E. 1990. Modelling of the three-dimensional architecture of group-I catalytic introns based on comparative sequence analysis. J Mol Biol 216:585-610.
38. Mizuno H, Sundaralingam M. 1978. Stacking of Crick wobble pair and Watson-Crick pair: Stability rules of G-U pairs at ends of helical stems in tRNAs and the relation to codon-anticodon wobble interaction. Nucleic Acids Res 5:4451-4461.
39. Asp. In: van Knippenberg PH, Hilbers CW, eds. Structure and dynamics of RNA. New York: Plenum Press.
40. Mueller U, Schübel H, Sprinzl M, Heinemann U. 1999. Crystal structure of acceptor stem of tRNAAIa from Escherichia coli shows unique GoU wobble base pair at 1.16 Å resolution. RNA 5:670-677.
41. + mismatches. J Mol Biol 283:977-984.
42. Park SJ, Hou YM, Schimmel P. 1989. A single base pair affects binding and catalytic parameters in the molecular recognition of a transfer RNA. Biochemistry 20:2740-2746.
43. Rould MA, Perona JJ, Soll D, Steitz TA. 1989. Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP at 2.8 Å resolution [see comments]. Science 246:1135-1142.
44. Rousset F, Pelandakis M, Solignac M. 1991. Evolution of compensatory substitutions through G•U intermediate state in Drosophila rRNA. Proc Natl Acad Sci USA 60:10032-10036.
45. Seeman NC, Rosenberg JM, Suddath FL, Kim JJP, Rich A. 1976. RNA double-helical fragment at atomic resolution: The crystal and molecular structure of sodium adenylyl-3′,5′-uridine hexahydrate. J Mol Biol 104:109-144.
46. Shi K, Wahl M, Sundaralingam M. 1999. Crystal structure of an RNA duplex r(GUGCGCUCC)2 with non-adjacent G•U base pairs. Nucleic Acids Res 27:2196-2201.
47. Strobel SA, Cech TR. 1995. Minor groove recognition of the conserved G•U pair at the Tetrahymena ribozyme reaction site. Science 267:675-679.
48. Szymanski M, Specht T, Barciszewska MZ, Barciszewski J, Erdmann VA. 1998. 5S rRNA Data Bank. Nucleic Acids Res 26:156-159.
49. 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 4:488-498.
50. Tinoco I Jr, Uhlenbeck OC, Levine MD. 1971. Estimation of secondary structure in ribonucleic acids. Nature 230:362-367.
51. Trikha J, Filman DJ, Hogle JM. 1999. Crystal structure of a 14 bp RNA duplex with non-symmetrical tandem G•U wobble base pairs. Nucleic Acids Res 27:1728-1739.
52. Van Knippenberg PH, Formenoy LJ, Heus HA. 1990. Is there a special function for U•G base pair in ribosomal RNA? Biochim Biophys Acta 1050:14-17.
53. Varani G, Cheong C, Tinoco I Jr. 1991. Structure of an unusually stable RNA hairpin. Biochemistry 30:3280-3289.
54. Westhof E. 1988. Water: An integral part of nucleic acid structure. Annu Rev Biophys Biophys Chem 17:125-144.
55. Westhof E, Dumas P, Moras D. 1985. Crystallographic refinement of yeast aspartic acid transfer RNA. J Mol Biol 184:119-145.
56. Westhof E, Dumas P, Moras D. 1988. Hydration of transfer RNA molecules: A Crystallographic study. Biochimie 70:145-165.
57. Westhof E, Sundaralingam M. 1986. Restrained refinement of the monoclinic form of yeast phenylalanine transfer RNA. Temperature factors and dynamics, coordinated waters, and base-pair propeller twist angles. Biochemistry 25:4868-4878.
58. White SA, Nilges M, Huang A, Brunger AT, Moore PB. 1992. NMR analysis of helix I from the 5S RNA of Escherichia coli. Biochemistry 37:1610-1621.
59. Wu M, McDowell JA, Turner DH. 1995. A periodic table of symmetric tandem mismatches in RNA. Biochemistry 34:3204-3211.