Solution structure of a GAAA tetraloop receptor RNA

EMBO Journal

Volumn 16, Issue 24, 1997, Pages 7490-7499

  Butcher, Samuel E ^a   Dieckmann, Thorsten ^a   Feigon, Juli ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RECEPTOR; RNA;

ARTICLE; BASE PAIRING; BINDING SITE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PHYLOGENY; PRIORITY JOURNAL; RNA CONFORMATION; RNA SEQUENCE;

BASE SEQUENCE; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; RNA; RNA, CATALYTIC; SOLUTIONS;

EID: 0031463994     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/16.24.7490     Document Type: Article

References (59)

1. Aboul-ela, F., Karn, J. and Varani, G. (1995) The structure of the human immunodeficiency virus type-1 TAR RNA reveals principles of RNA recognition by TAT protein. J. Mol. Biol., 253, 313-332.
2. Allain, F.H.-T. and 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.
3. Allain, F.H.-T. and Varani, G. (1995b) Structure of the P1 helix from group I self-splicing introns. J. Mol. Biol., 250, 333-353.
4. Allain, F.H.-T., Gubser, C.C., Howe, P.W.A., Nagai, K., Neuhaus, D. and Varani, G. (1996) Specificity of ribonucleoprotein interaction determined by RNA folding during complex formulation. Nature, 380, 646-650.
5. Batey, R.T., Inada, M., Kujawinski, E., Puglisi, J.D. and Williamson, J.R. (1992) Preparation of isotopically labeled ribonucleotides for multidimensional NMR spectroscopy of RNA. Nucleic Acids Res., 20, 4515-4523.
6. Battiste, J.L., Mao, H., Rao, N.S., Tan, R., Muhandiram, D.R., Kay, L.E., Frankel, A.D. and Williamson, J.R. (1996) α helix-RNA major groove recognition in an HIV-1 Rev peptide-RRE RNA complex. Science, 273, 1547-1551.
7. Bax, A. and Davis, D.G. (1985) MLEV-17-based two-dimensional homonuclear magnetization transfer spectroscopy. J. Magn. Resonance, 65, 355-360.
8. Bax, A., Clore, G.M., Driscoll, P.C. Gronenborn, A.M., Ikura, M. and Kay, L.E. (1990) Practical aspects of proton-carbon-carbon-proton three-dimensional correlation spectroscopy of 13C-labeled proteins. J. Magn. Resonance, 87, 620-627.
9. Brünger, A.T. (1992) X-PLOR (Version 3.1) Manual. Yale University Press, New Haven CT.
10. Burke, J.M., Belfort, M., Cech, T.R., Davies, R.W., Schweyen, R.J., Shub, D.A., Szostak, J.W. and Tabak, H.F. (1987) Structural conventions for group I introns. Nucleic Acids Res., 15, 7217-7221.
11. Cate, J.H., Gooding, A.R., Podell, E., Zhou, K., Golden, B.L., Kundrot, C.E., Cech, T.R. and Doudna, J.A. (1996a) Crystal structure of a group I ribozyme domain: principles of RNA packing. Science, 273, 1678-1685.
12. Cate, J.H., Gooding, A.R., Podell, E., Zhou, K., Golden, B.L., Szewczak, A.A., Kundrot, C.E., Cech, T.R. and Doudna, J.A. (1996b) RNA tertiary structure mediation by adenosine platforms. Science, 273, 1696-1699.
13. Cheong, C. Varani, G. and Tinoco, I., Jr (1990) Solution structure of an unusually stable RNA hairpin. 5′GGAC(UUCG)GUCC. Nature, 346, 680-682.
14. Chou, S.-H., Zhu, L. and Reid, B.R. (1997) Sheared purine purine pairing in biology. J. Mol. Biol., 267, 1055-1067.
15. 13C resonances of interleukin-1β using double-and triple-resonance heteronuclear three-dimensional NMR spectroscopy. Biochemistry, 29, 8172-8184.
16. Costa, M. and Michel, F. (1995) Frequent use of the same tertiary motif by self-folding RNAs. EMBO J., 14, 1276-1285.
17. Costa, M. and Michel, F. (1997) Rules for RNA recognition of GNRA tetraloops deduced by in vitro selection: comparison with in vivo evolution. EMBO J., 16, 3289-3302.
18. Dieckmann, T. and Feigon, J. (1994) Heteronuclear techniques in NMR studies of RNA and DNA. Curr. Opin. Struct. Biol., 4, 745-749.
19. Dieckmann, T. and Feigon, J. (1997) Assignment methodology for larger oligonucleotides: application to an ATP-binding RNA aptamer. J. Biomol. NMR, 9, 259-272.
20. Dieckmann, T., Suzuki, E., Nakamura, G.K. and Feigon, J. (1996) Solution structure of an ATP-binding RNA aptamer reveals a novel fold. RNA, 2, 628-640.
21. Jaeger, L., Michel, F. and Westhof, E. (1994) Involvement of a GNRA tetraloop in long-range RNA tertiary interactions. J. Mol. Biol., 236, 1271-1276.
22. Jiang, F., Kumar, R.A., Jones, R.A. and Patel, D.J. (1996) Structural basis of RNA folding and recognition in an AMP-RNA aptamer complex. Nature, 382, 183-186.
23. Kadkhodaei, M. Hwang, T.L., Tang, J. and Shaka, A.J. (1993) A simple windowless mixing sequence to suppress cross relaxation in TOCSY experiments. J. Magn. Resonance Ser. A, 105, 104-107.
24. Koradi, R., Billeter, M. and Wüthrich, K. (1996) MOLMOL - A program for display and analysis of macromolecular structures. J. Mol. Graphics, 14, 51+.
25. Legault, P. and Pardi, A. (1994) In situ probing of adenine protonation in RNA by C-13 NMR. J. Am. Chem. Soc., 116, 8390-8391.
26. 13C-labeled ribozyme. J. Am. Chem. Soc., 116, 2203-2204.
27. Macura, S., Huang, Y., Suter, D. and Ernst, R.R. (1980) Two-dimensional chemical exchange and cross-relaxation spectroscopy of coupled nuclear spins. J. Magn. Resonance, 43, 259-281.
28. 1H assignment. J. Am. Chem. Soc., 116, 2205-2206.
29. Marion, D., Ikura, M., Tschudin, R. and Bax, A. (1989) Rapid recording of 2d NMR spectra without phase cycling - application to the study of hydrogen exchange in proteins. J. Magn. Reson., 85, 393-399.
30. 2. Biochemistry, 32, 3583-3595.
31. Michel, F. and 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.
32. Milligan, J.R. Groebe, D.R., Witherell, G.W. and Uhlenbeck, O.C. (1987) Oligoribonucleotide synthesis using T7-RN A polymerase and synthetic DNA templates. Nucleic Acids Res., 15, 8783-8798.
33. Murphy, F.L. and Cech, T.R. (1994) GAAA tetraloop and conserved bulge stabilize tertiary structure of a group I intron domain. J. Mol. Biol., 236, 49-63.
34. 15N labeled nucleic acids. J. Mol. Biol., 232, 1141-1156.
35. Nikonowicz, E.P., Sirr, A., Legault, P., Jucker, F.M., Baer, L.M. and Pardi, A. (1992) Preparation of C-13 and N-15 labelled RNAs for heteronuclear multi-dimensional NMR studies. Nucleic Acids Res., 20, 4507-4513.
36. Pardi, A. (1995) Multidimensional heteronuclear NMR experiments for structure determination of isotopically labeled RNA. Methods Enzymol., 261, 350-380.
37. Peterson, R.D. and Feigon, J. (1996) Structural change in Rev Responsive Element RNA of HIV-1 on binding Rev peptide. J. Mol. Biol., 264, 863-877.
38. Peterson, R.D., Bartel, D.P., Szostak, J.W., Horvath, S.J. and Feigon, J. (1994) 1H NMR studies of the high-affinity Rev binding site of the Rev Responsive Element of HIV-1 mRNA: base pairing in the core binding element. Biochemistry, 33, 5357-5366.
39. Pley, H.W., Flaherty, K.M. and McKay, D.B. (1994a) Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix. Nature, 372, 111-113.
40. Pley, H.W., Flaherty, K.M. and McKay, D.B. (1994b) Three-dimensional structure of a hammerhead ribozyme. Nature, 372, 68-74.
41. Puglisi, J.D. and Wyatt, J.R. (1995) Biochemical and NMR studies of RNA conformation with an emphasis on RNA pseudoknots. Methods Enzymol., 261, 323-350.
42. 1H NMR spectra of proteins via double quantum altering. Biochem. Biophys. Res. Commun., 117, 479-485.
43. Robertus, J.D., Ladner, J.E., Finch, J.T., Rhodes, D., Brown, R.S., Clark, B.F.C. and Klug, A. (1974) Structure of yeast phenylalanine tRNA at 3 Å resolution. Nature, 250, 546-551.
44. Asp. Science, 252, 1682-1689.
45. Saenger, W. (1984) Principles of Nucleic Acid Structure. Springer-Verlag, New York.
46. Santoro, J. and King, G. (1992) A constant-time 2d overbodengausen experiment for inverse correlation of isotopically enriched species. J. Magn. Resonance, 97, 202-207.
47. Scott, W.G., Finch, J.T. and Klug, A. (1995) The crystal structure of an all-RNA hammerhead ribozyme - a proposed mechanism for RNA catalytic cleavage. Cell, 81, 991-1002.
48. Serra, M.J. and Turner, D.H. (1995) Predicting thermodynamic properties of RNA. Method Enzymol., 259, 242-261.
49. Shaka, A.J., Barker, P. and Freeman, R. (1985) Computer-optimized decoupling scheme for wideband applications and low-level operation. J. Magn. Resonance, 64, 547-552.
50. 31P resonances in oligonucleotides by two-dimensional NMR spectroscopy. FEBS Lett., 208, 94-98.
51. Sklenář, V., Tschudin, R. and Bax, A. (1987) Water suppression using a combination of hard and soft pulses. J. Magn. Resonance, 75, 352-357.
52. 15N-labeled RNA oligonucleotides. J. Am. Chem. Soc., 115, 12181-12182.
53. 15N HSQC experiments. J. Biomol. NMR, 4, 117-122.
54. Szewczak, A.A., Moore, P.B., Chan, Y.-L. and Wool, I.G. (1993) The conformation of the sarcin/ricin loop from 28S ribosomal RNA. Proc. Natl Acad. Sci. USA, 90, 9581-9585.
55. Tanner, M. (1997) Bacterial group I ribozymes and their tertiary interactions. PhD Thesis, University of Colorado.
56. Tanner, M.A. and Cech, T.R. (1995) An important RNA tertiary interaction of group I and group II introns is implicated in gram-positive RNase P RNAs RNA, 1, 349-350.
57. Varani, G., Aboul-ela, F. and Allain, F.H.-T. (1996) NMR investigation of RNA structure. Prog. NMR Spectrosc., 29, 51-127.
58. Wimberly, B., Varani, G. and Tinoco, I., Jr (1993) The conformation of loop E of eukaryotic 5S ribosomal RNA. Biochemistry, 32, 1078-1087.
59. Zimmermann, G.R., Jenison, R.D., Wick, C.L., Simorre, J.-P. and Pardi, A. (1997) Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA. Nature Struct. Biol., 4, 644-649.