Hammering away at RNA global structure

Current Opinion in Structural Biology

Volumn 6, Issue 3, 1996, Pages 317-321

  Hagerman, Paul J ^a   Amiri, Khaled M A ^a  

^a UNIVERSITY OF COLORADO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL RNA; PHENYLALANINE TRANSFER RNA;

NONHUMAN; PRIORITY JOURNAL; RNA CLEAVAGE; RNA SEQUENCE; RNA STRUCTURE; SHORT SURVEY; YEAST;

EID: 0029889498     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(96)80049-2     Document Type: Article

References (21)

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2. Holbrook SR, Sussman JL, Warrant RW, Kim SH: Crystal structure of yeast phenylalanine transfer RNA. II. Structural features and functional implications. J Mol Biol 1978, 123:631-660.
3. Hingerty B, Brown RS, Jack A: Further refinement of the structure of yeast tRNA(Phe). J Mol Biol 1978, 124:523-534.
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5. Basavappa R, Sigler PB: The 3 Å crystal structure of yeast initiator tRNA: functional implications in initiator/elongator discrimination. EMBO J 1991, 10:3105-3111.
6. Ruff M, Krishnaswamy S, Boeglin M, Poterszman A, Mitschler A, Podjarny A, Rees B, Thierry JC, Moras D: Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp). Science 1991, 252:1682-1689.
7. Normanly J, Abelson J: tRNA identity. Annu Rev Biochem 1989, 58:1029-1049.
8. Friederich MW, Gast F-U, Vacano E, Hagerman PJ: Determination of the angle between the anticodon and aminoacyl acceptor stems of yeast phenylalanyl tRNA in solution. Proc Natl Acad Sci USA 1995, 92:4803-4807. The first direct determination of the angle between the acceptor and anticodon stems of a tRNA in solution provides striking confirmation of the similarity of this global feature in solution and in the crystal. The method of transient electric birefringence (TEB) is well-suited for the determination of such long-range structural features.
9. Nakamura T, Wang Y-H, Zaug AJ, Griffith JD, Cech TR: Relative orientation of RNA helices in a group I ribozyme determined by helix extension electron microscopy. EMBO J 1995, 14:4849-4859. This electron microscopic investigation of the global conformation of a group I ribozyme provides a tantalizing glimpse of both the spatial organization and the angular variation of the helices within this complex RNA molecule. During the course of this investigation, the tRNA construct described in [8••] was examined, and the mean interstem angle was found to be essentially indistinguishable from the solution and crystal values. The EM method holds the potential for defining the angle dispersion between two helices.
10. Sampson JR, Uhlenbeck OC: Biochemical and physical characterization of an unmodified yeast phenylalanine transfer RNA transcribed in vitro. Proc Natl Acad Sci USA 1988, 85:1033-1037.
11. Hutchins CJ, Rathjen PD, Forster AC, Symons RH: Self cleavage of plus and minus transcripts of avocado sunblotch viroid. Nucleic Acids Res 1986, 14:3627-3640.
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14. Ruffner DE, Dahm SC, Uhlenbeck OC: Studies on the hammerhead RNA self-cleaving domain. Gene 1989, 82:31-41.
15. Pley HW, Flaherty KM, McKay DB: Three-dimensional structure of a hammerhead ribozyme. Nature 1994, 372:68-74. The work described in this paper constitutes a crystallographic milestone in the study of RNA structure, with the determination of the structure of an RNA-DNA hybrid analog of the hammerhead ribozyme. The investigation provides new views of structural elements such as the GAAA tetraloop and the 'U-turn'. However, the structure remains an intriguing cipher with regard to the cleavage site itself.
16. Scott WG, Finch JT, Klug A: The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell 1995, 81:991-1002. This paper describes a second, equally important, crystal structure of the hammerhead element, made all the more significant by the fact that it was obtained for an all-RNA ribozyme modified only at the 2′ position at the active site to prevent cleavage. The structure displays remarkable similarity to molecule 2 of the Pley et al. structure [15••]. The all-RNA structure has led to the identification of additional stabilizing interactions not present in the RNA-DNA hybrid.
17. Tuschl T, Gohlke C, Jovin TM, Westhof E, Eckstein F: A three-dimensional model for the hammerhead ribozyme based on fluorescence measurements. Science 1994, 266:785-789. A detailed analysis of the solution structure of a hammerhead ribozyme by fluorescence energy transfer (FRET). The residues in the molecules used were all RNA except for a single deoxy residue at the cleavage site. The FRET-derived model, although stated as provisional, bears a close resemblance to the crystal structures with respect to the spatial positioning of the three helices flanking the core.
18. Amiri KMA, Hagerman PJ: Global conformation of a self-cleaving hammerhead RNA. Biochemistry 1994, 33:13172-13177. This paper constitutes the first examination of the spatial positioning of the three helices of the hammerhead domain using all-RNA molecules that are fully active in self-cleavage. Using the TEB method, we demonstrate that the average spatial positions of the helices are close to those observed for the FRET and crystal species, but with some repositioning of stem I. Notably, the position of stem I changed very little following self-cleavage, which may account for the significant back-reaction (ligation).
19. Sigurdsson ST, Tuschl T, Eckstein F: Probing RNA tertiary structure: interhelical crosslinking of the hammerhead ribozyme. RNA 1995, 1:575-583. This important follow-up to the FRET study of these authors was aimed at an examination of the different torsional alignments of stems I and II obtained by FRET and crystal studies. Using an elegant crosslinking approach, the authors determined that the alignment represented by the crystal structure is most consistent with catalytic activity.
20. Shen Z, Hagerman PJ: Conformation of the central, three-helix junction of the 5S ribosomal RNA of Sulfolobus acidocaldarius. J Mol Biol 1994, 241:415-430. This study of the geometry of the central A loop in a 5S ribosomal RNA using TEB provides a direct demonstration of the existence of significant flexibility within a three-helix branch.
21. Eis PS, Millar DP: Conformational distributions of a four-way DNA junction revealed by time-resolved fluorescence resonance energy transfer. Biochemistry 1993, 32:13852-13860.