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0026771509
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Numbering system for the hammerhead
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Pley, H.W.1
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5
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0029073091
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The crystal structure of an all-RNA hammerhead ribozyme: A proposed mechanism for RNA catalytic cleavage
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In this paper, the hammerhead ribozyme is complexed with an RNA inhibitor modified at the cleavage site. Solved in low salt conditions, the structure reveals several divalent metal ion binding sites. The authors propose a mechanism based on one of the metal ion sites in the U-turn. of outstanding interest
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Scott WG, Finch JT, Klug A. The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell. 81:1995;995-1002 In this paper, the hammerhead ribozyme is complexed with an RNA inhibitor modified at the cleavage site. Solved in low salt conditions, the structure reveals several divalent metal ion binding sites. The authors propose a mechanism based on one of the metal ion sites in the U-turn. of outstanding interest.
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Scott, W.G.1
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0015929511
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8
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0343011133
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Three-dimensional structure of the hammerhead ribozyme
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F. Eckstein, Lilley D.M.J. New York: Springer-Verlag
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McKay DB. Three-dimensional structure of the hammerhead ribozyme. Eckstein F, Lilley DMJ. Catalytic RNA. 1996;161-172 Springer-Verlag, New York.
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McKay, D.B.1
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9
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0027973506
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A three-dimensional model for the hammerhead ribozyme based on fluorescence measurements
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Tuschl T, Gohlke C, Jovin TM, Westhof E, Eckstein F. A three-dimensional model for the hammerhead ribozyme based on fluorescence measurements. Science. 266:1994;785-788.
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Tuschl, T.1
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Eckstein, F.5
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10
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0029348087
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Probing RNA tertiary structure: Interhelical cross-linking of the hammerhead ribozyme
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The authors use FRET measurements to build a model of the global ribozyme conformation. These four studies [9,10,11,17] directly address the relevance of the X-ray structures to the active ribozyme conformation. of special interest
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Sigurdsson ST, Tuschl T, Eckstein F. Probing RNA tertiary structure: interhelical cross-linking of the hammerhead ribozyme. RNA. 1:1995;575-583 The authors use FRET measurements to build a model of the global ribozyme conformation. These four studies [9,10,11,17] directly address the relevance of the X-ray structures to the active ribozyme conformation. of special interest.
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RNA
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Sigurdsson, S.T.1
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0028004021
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Amiri KMA, Hagerman PJ. Global conformation of a self-cleaving hammerhead RNA. Biochemistry. 33:1994;13172-13177.
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Amiri, K.M.A.1
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12
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0030476765
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Capturing the structure of a catalytic RNA intermediate: The hammerhead ribozyme
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The authors solve three structures of a hammerhead ribozyme complexed with a cleavable substrate. In the crystal lattice, the ribozyme is active, which allows the authors to 'trap' an intermediate conformation. On the basis of the trapped conformation, the authors propose a new transition-state model in which only a local rearrangement of the active site needs to occur. of outstanding interest
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Scott WG, Murray JB, Arnold JRP, Stoddard BL, Klug A. Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme. Science. 274:1996;2065-2069 The authors solve three structures of a hammerhead ribozyme complexed with a cleavable substrate. In the crystal lattice, the ribozyme is active, which allows the authors to 'trap' an intermediate conformation. On the basis of the trapped conformation, the authors propose a new transition-state model in which only a local rearrangement of the active site needs to occur. of outstanding interest.
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Science
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Scott, W.G.1
Murray, J.B.2
Arnold, J.R.P.3
Stoddard, B.L.4
Klug, A.5
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0025335881
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Two autolytic processing reactions of a satellite RNA proceed with inversion of configuration
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Van Tol, H.1
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0026102040
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Configurationally defined phosphorothioate-containing oligoribonucleotides in the study of the mechanism of cleavage of hammerhead ribozymes
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Slim G, Gait MJ. Configurationally defined phosphorothioate-containing oligoribonucleotides in the study of the mechanism of cleavage of hammerhead ribozymes. Nucleic Acids Res. 19:1991;1183-1188.
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Slim, G.1
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2+ binding
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[Published erratum appears in Biochemistry, 1992; 31:4156]
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2+ binding. Biochemistry. 30:1991;5145-5150. [Published erratum appears in Biochemistry, 1992; 31:4156].
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Koizumi, M.1
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McKay DB. Structure and function of the hammerhead ribozyme: an unfinished story. RNA. 2:1996;395-403.
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RNA
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McKay, D.B.1
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17
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0028962525
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Ionic interactions and the global conformations of the hammerhead ribozyme
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See annotation [10]. of special interest
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Bassi GS, Mollegaard NE, Murchie AI, von Kitzing E, Lilley DM. Ionic interactions and the global conformations of the hammerhead ribozyme. Nat Struct Biol. 2:1995;45-55 See annotation [10]. of special interest.
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Nat Struct Biol
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Bassi, G.S.1
Mollegaard, N.E.2
Murchie, A.I.3
Von Kitzing, E.4
Lilley, D.M.5
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18
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0001417431
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The hammerhead ribozyme
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F. Eckstein, Lilley D.M.J. New York: Springer-Verlag
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Thomson JB, Tuschl T, Eckstein F. The hammerhead ribozyme. Eckstein F, Lilley DMJ. Catalytic RNA. 1996;173-196 Springer-Verlag, New York.
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Catalytic RNA
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Thomson, J.B.1
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Eckstein, F.3
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19
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0027426257
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Importance of exocyclic base functional groups of central core guanosines for hammerhead ribozyme activity
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[Published erratum appears in Biochemistry 1994, 33:848]
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Tuschl T, Ng MM, Pieken W, Benseler F, Eckstein F. Importance of exocyclic base functional groups of central core guanosines for hammerhead ribozyme activity. Biochemistry. 32:1993;11658-11668. [Published erratum appears in Biochemistry 1994, 33:848].
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Biochemistry
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Tuschl, T.1
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0027146665
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2 in solution from NMR and restrained molecular dynamics
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2 in solution from NMR and restrained molecular dynamics. Biochemistry. 32:1993;12612-12623.
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Biochemistry
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Santalucia J., Jr.1
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Walter AE, Wu M, Turner DH. The stability and structure of tandem G·A mismatches in RNA depend on closing base pairs. Biochemistry. 33:1994;11349-11354.
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Walter, A.E.1
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22
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0029744135
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2 by two-dimensional NMR and the iterative relaxation matrix approach
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These three papers [20,21,22] show the dramatic effects of the context of tandem G·A mismatch base pairs. The sheared G·A pairs can switch from a sheared conformation to a symmetric heteropurine pair by merely changing the flanking Watson - Crick base pairs. of special interest
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2 by two-dimensional NMR and the iterative relaxation matrix approach. Biochemistry. 35:1996;9677-9689 These three papers [20,21,22] show the dramatic effects of the context of tandem G·A mismatch base pairs. The sheared G·A pairs can switch from a sheared conformation to a symmetric heteropurine pair by merely changing the flanking Watson - Crick base pairs. of special interest.
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Biochemistry
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Wu, M.1
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0029258928
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Keeping RNA happy
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This paper describes the pitfalls one may encounter in trying to 'renature' RNAs synthesized in vitro. of special interest
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Uhlenbeck OC. Keeping RNA happy. RNA. 1:1995;4-6 This paper describes the pitfalls one may encounter in trying to 'renature' RNAs synthesized in vitro. of special interest.
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Cech TR. Self-splicing of group I introns. Annu Rev Biochem. 59:1990;543-568.
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Michel F, Westhof E. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J Mol Biol. 216:1990;585-610.
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Michel, F.1
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0027173193
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An independently folding domain of RNA tertiary structure within the Tetrahymena ribozyme
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Murphy FL, Cech TR. An independently folding domain of RNA tertiary structure within the Tetrahymena ribozyme. Biochemistry. 32:1993;5291-5300.
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Murphy, F.L.1
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Celander DW, Cech TR. Visualizing the higher order folding of a catalytic RNA molecule. Science. 251:1991;401-407.
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0026017131
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0029820625
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Crystal structure of a group I ribozyme domain: Principles of RNA packing
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The largest RNA structure solved to date, the P4-P6 domain shows a number of new folding motifs likely to be common in large structured RNAs. of outstanding interest
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Cate JH, Gooding AR, Podell E, Zhou K, Golden BL, Kundrot CE, Cech TR, Doudna JA. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science. 273:1996;1678-1686 The largest RNA structure solved to date, the P4-P6 domain shows a number of new folding motifs likely to be common in large structured RNAs. of outstanding interest.
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Science
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Cate, J.H.1
Gooding, A.R.2
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Cech, T.R.7
Doudna, J.A.8
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30
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0028921811
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Frequent use of the same tertiary motif by self-folding RNAs
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The authors identify a commonly occurring motif (the tetraloop receptor, [29]), which phylogenetically covaries with GAAA tetraloops. They then show the importance of this tertiary interaction in both a group I and a group II intron. of outstanding interest of special interest
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Costa M, Michel F. Frequent use of the same tertiary motif by self-folding RNAs. EMBO J. 14:1995;1276-1285 The authors identify a commonly occurring motif (the tetraloop receptor, [29]), which phylogenetically covaries with GAAA tetraloops. They then show the importance of this tertiary interaction in both a group I and a group II intron. of outstanding interest of special interest.
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(1995)
EMBO J
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Costa, M.1
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GAAA tetraloop and conserved bulge stabilize tertiary structure of a group I intron domain
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Murphy FL, Cech TR. GAAA tetraloop and conserved bulge stabilize tertiary structure of a group I intron domain. J Mol Biol. 236:1994;49-63.
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Murphy, F.L.1
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Heus HA, Pardi A. Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops. Science. 253:1991;191-194.
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Heus, H.A.1
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Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix
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Pley H, Flaherty K, McKay D. Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix. Nature. 372:1994;111-113.
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Nature
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Pley, H.1
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McKay, D.3
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34
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0029670279
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Catalytic role of 2'-hydroxyl groups within a group II intron active site
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-1 to binding. The nucleotides involved match precisely those observed in the P4-P6 structure [29] and in the hammerhead crystal contact ([33]; see also [30]). of outstanding interest of special interest
-
-1 to binding. The nucleotides involved match precisely those observed in the P4-P6 structure [29] and in the hammerhead crystal contact ([33]; see also [30]). of outstanding interest of special interest.
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(1996)
Science
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Abramovitz, D.L.1
Friedman, R.A.2
Pyle, A.M.3
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35
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0029796982
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RNA tertiary structure mediation by adenosine platforms
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At three locations in the P4-P6 structure, adenosine platforms are involved in tertiary interactions. On the basis of previous biochemical data [26], all three platforms are likely to be involved in tertiary interactions in the intact intron. of outstanding interest
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Cate JH, Gooding AR, Podell E, Golden BL, Zhou K, Szewczak A, Kundrot CE, Cech TR, Doudna JA. RNA tertiary structure mediation by adenosine platforms. Science. 273:1996;1692-1694 At three locations in the P4-P6 structure, adenosine platforms are involved in tertiary interactions. On the basis of previous biochemical data [26], all three platforms are likely to be involved in tertiary interactions in the intact intron. of outstanding interest.
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Science
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Cate, J.H.1
Gooding, A.R.2
Podell, E.3
Golden, B.L.4
Zhou, K.5
Szewczak, A.6
Kundrot, C.E.7
Cech, T.R.8
Doudna, J.A.9
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36
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0029825658
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Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic
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The A-site in prokaryotic ribosomes has a distinctive dimethyl sulfate chemical modification pattern, similar to that observed for AA platforms [35]. In [35], the authors propose that the A-site may contain an AA platform, but this NMR structure [36] contains a different conformation of the adjacent adenosines. of outstanding interest of special interest
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Fourmy D, Recht MI, Blanchard SC, Puglisi JD. Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic. Science. 274:1996;1367-1371 The A-site in prokaryotic ribosomes has a distinctive dimethyl sulfate chemical modification pattern, similar to that observed for AA platforms [35]. In [35], the authors propose that the A-site may contain an AA platform, but this NMR structure [36] contains a different conformation of the adjacent adenosines. of outstanding interest of special interest.
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Science
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Fourmy, D.1
Recht, M.I.2
Blanchard, S.C.3
Puglisi, J.D.4
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37
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0030587890
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Metal binding sites in the major groove of a large ribozyme domain
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2+ in the native structure in two out of three cases. All three sites involve only guanosine and uridine residues. Two of the sites may be useful for engineering metal ion binding sites in RNA, in other words, for crystallographic purposes. of outstanding interest
-
2+ in the native structure in two out of three cases. All three sites involve only guanosine and uridine residues. Two of the sites may be useful for engineering metal ion binding sites in RNA, in other words, for crystallographic purposes. of outstanding interest.
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(1996)
Structure
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Cate, J.H.1
Doudna, J.A.2
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38
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0029382234
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G-U base pairing motifs in ribosomal RNA
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Gautheret D, Konings D, Gutell RR. G-U base pairing motifs in ribosomal RNA. RNA. 1:1996;807-814.
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RNA
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Gautheret, D.1
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0027183545
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Ribozymes: A distinct class of metalloenzymes
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Pyle AM. Ribozymes: a distinct class of metalloenzymes. Science. 261:1993;709-714.
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Science
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Pyle, A.M.1
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40
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0029822046
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A curved RNA helix incorporating an internal loop with G·A and A·A non-Watson - Crick base pairing
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This duplex structure contains a divalent metal binding site similar to that in the hammerhead domain II [4,5,12]. of outstanding interest
-
Baeyens KJ, De Bondt HL, Pardi A, Holbrook SR. A curved RNA helix incorporating an internal loop with G·A and A·A non-Watson - Crick base pairing. Proc Natl Acad Sci USA. 93:1996;12851-12855 This duplex structure contains a divalent metal binding site similar to that in the hammerhead domain II [4,5,12]. of outstanding interest.
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(1996)
Proc Natl Acad Sci USA
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Baeyens, K.J.1
De Bondt, H.L.2
Pardi, A.3
Holbrook, S.R.4
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0029147392
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Structurally complex and highly active RNA ligases derived from random RNA sequences
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Ekland EH, Szostak JW, Bartel DP. Structurally complex and highly active RNA ligases derived from random RNA sequences. Science. 269:1995;364-370.
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Science
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Ekland, E.H.1
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42
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0026669321
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Pan T, Uhlenbeck OC. A small metalloribozyme with a two-step mechanism. Nature. 358:1992;560-563.
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Nature
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Pan, T.1
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0027956537
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A major family of motifs involving G·A mismatches in ribosomal RNA
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Gautheret D, Konings D, Gutell RR. A major family of motifs involving G·A mismatches in ribosomal RNA. J Mol Biol. 242:1994;1-8.
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Gautheret, D.1
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44
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0028261409
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Gutell RR, Larsen N, Woese CR. Lessons from an evolving RNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol Rev. 58:1994;10-26.
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Microbiol Rev
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Gutell, R.R.1
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45
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0028917227
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A periodic table of symmetric tandem mismatches in RNA
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The stability of tandem mismatches depends quite strongly on the flanking base pairs. G·A and U·U tandems are among the most stable, depending on the sequences flanking them. of special interest
-
Wu M, McDowell JA, Turner DH. A periodic table of symmetric tandem mismatches in RNA. Biochemistry. 34:1995;3204-3211 The stability of tandem mismatches depends quite strongly on the flanking base pairs. G·A and U·U tandems are among the most stable, depending on the sequences flanking them. of special interest.
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(1995)
Biochemistry
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, pp. 3204-3211
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Wu, M.1
McDowell, J.A.2
Turner, D.H.3
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46
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0029855518
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Thermodynamics of coaxially stacked helixes with G·A and C·C mismatches
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Kim J, Walter AE, Turner DH. Thermodynamics of coaxially stacked helixes with G·A and C·C mismatches. Biochemistry. 35:1996;13753-13761.
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Biochemistry
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Kim, J.1
Walter, A.E.2
Turner, D.H.3
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47
-
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0028902990
-
Structure of an RNA double helix including uracil - uracil base pairs in an internal loop
-
See annotation [49]. of outstanding interest
-
Baeyens KJ, De Bondt HL, Holbrook SR. Structure of an RNA double helix including uracil - uracil base pairs in an internal loop. Nat Struct Biol. 2:1995;56-62 See annotation [49]. of outstanding interest.
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(1995)
Nat Struct Biol
, vol.2
, pp. 56-62
-
-
Baeyens, K.J.1
De Bondt, H.L.2
Holbrook, S.R.3
-
48
-
-
0030044773
-
The structure of r(UUCGCG) has a 5'-UU-overhang exhibiting Hoogsteen-like trans U·U base pairs
-
See also [49]. This structure, at 1.4 Å resolution, also shows hydration of the duplex, CH-O hydrogen bonds, and provides a model for U·ψ base pairs. of outstanding interest
-
Wahl M, Rao ST, Sundaralingam M. The structure of r(UUCGCG) has a 5'-UU-overhang exhibiting Hoogsteen-like trans U·U base pairs. Nat Struct Biol. 3:1996;24-31 See also [49]. This structure, at 1.4 Å resolution, also shows hydration of the duplex, CH-O hydrogen bonds, and provides a model for U·ψ base pairs. of outstanding interest.
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(1996)
Nat Struct Biol
, vol.3
, pp. 24-31
-
-
Wahl, M.1
Rao, S.T.2
Sundaralingam, M.3
-
49
-
-
0030586821
-
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
-
These three structures [47-49] show different conformations of the commonly occurring U·U tandem mismatch base pairs [44]. of outstanding interest
-
Lietzke SE, Barnes CL, Berglund JA, Kundrot CE. 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. 4:1996;917-930 These three structures [47-49] show different conformations of the commonly occurring U·U tandem mismatch base pairs [44]. of outstanding interest.
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(1996)
Structure
, vol.4
, pp. 917-930
-
-
Lietzke, S.E.1
Barnes, C.L.2
Berglund, J.A.3
Kundrot, C.E.4
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50
-
-
0028904988
-
A positive entropy change for guanosine binding and for the chemical step in the Tetrahymena ribozyme reaction
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McConnell TS, Cech TR. A positive entropy change for guanosine binding and for the chemical step in the Tetrahymena ribozyme reaction. Biochemistry. 34:1995;4056-4067.
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(1995)
Biochemistry
, vol.34
, pp. 4056-4067
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McConnell, T.S.1
Cech, T.R.2
-
51
-
-
0028824549
-
Thermodynamic and activation parameters for binding of a pyrene-labeled substrate by the Tetrahymena ribozyme: Docking is not diffusion-controlled and is driven by a favorable entropy change
-
Li Y, Bevilacqua PC, Mathews D, Turner DH. Thermodynamic and activation parameters for binding of a pyrene-labeled substrate by the Tetrahymena ribozyme: docking is not diffusion-controlled and is driven by a favorable entropy change. Biochemistry. 34:1995;14394-14399.
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Biochemistry
, vol.34
, pp. 14394-14399
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Li, Y.1
Bevilacqua, P.C.2
Mathews, D.3
Turner, D.H.4
-
52
-
-
0030090986
-
Crystal structure of an A-form duplex with single-adenosine bulges and a conformational basis for site-specific RNA self-cleavage
-
Two crystal structures of an RNA - DNA chimera are solved in different packing arrangements. A single deoxyadenosine is looped out in each duplex strand. of special interest
-
Portmann S, Grimm S, Workman C, Usman N, Egli M. Crystal structure of an A-form duplex with single-adenosine bulges and a conformational basis for site-specific RNA self-cleavage. Chem Biol. 3:1996;173-184 Two crystal structures of an RNA - DNA chimera are solved in different packing arrangements. A single deoxyadenosine is looped out in each duplex strand. of special interest.
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(1996)
Chem Biol
, vol.3
, pp. 173-184
-
-
Portmann, S.1
Grimm, S.2
Workman, C.3
Usman, N.4
Egli, M.5
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53
-
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0029051383
-
The crystal structure of r(CCCCGGGG) in two distinct lattices
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Portmann S, Usman N, Egli M. The crystal structure of r(CCCCGGGG) in two distinct lattices. Biochemistry. 34:1995;7569-7575.
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(1995)
Biochemistry
, vol.34
, pp. 7569-7575
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Portmann, S.1
Usman, N.2
Egli, M.3
-
54
-
-
0029956116
-
RNA hydration: A detailed look
-
p phosphate oxygens are heavily hydrated. of outstanding interest
-
p phosphate oxygens are heavily hydrated. of outstanding interest.
-
(1996)
Biochemistry
, vol.35
, pp. 8489-8494
-
-
Egli, M.1
Portmann, S.2
Usman, N.3
-
55
-
-
0030497977
-
Structure of the purine - pyrimidine alternating RNA double helix, r(GUAUAUA)d(C), with a 3'-terminal deoxy residue
-
This structure is at slightly lower resolution (2.2 Å) than those in [48,54] but provides a view of the hydration of an A·U-rich duplex. The authors do not use R-free for refinement. of special interest
-
Wahl MC, Ban C, Sekharudu C, Ramakrishnan B, Sundaralingam M. Structure of the purine - pyrimidine alternating RNA double helix, r(GUAUAUA)d(C), with a 3'-terminal deoxy residue. Acta Crystallogr D. 52:1996;655-667 This structure is at slightly lower resolution (2.2 Å) than those in [48,54] but provides a view of the hydration of an A·U-rich duplex. The authors do not use R-free for refinement. of special interest.
-
(1996)
Acta Crystallogr D
, vol.52
, pp. 655-667
-
-
Wahl, M.C.1
Ban, C.2
Sekharudu, C.3
Ramakrishnan, B.4
Sundaralingam, M.5
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56
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0024469851
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2
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2. J Mol Biol. 209:1989;459-474.
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Dock-Bregeon, A.C.1
Chevrier, B.2
Podjarny, A.3
Johnson, J.4
De Baer, J.S.5
Gough, G.R.6
Gilham, P.T.7
Moras, D.8
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57
-
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0026347806
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Comparison of binding of mixed ribose-deoxyribose analogues of CUCU to a ribozyme and to GGAGAA by equilibrium dialysis: Evidence for ribozyme specific interactions with 2'OH groups
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Bevilacqua PC, Turner DH. Comparison of binding of mixed ribose-deoxyribose analogues of CUCU to a ribozyme and to GGAGAA by equilibrium dialysis: evidence for ribozyme specific interactions with 2'OH groups. Biochemistry. 30:1991;10632-10640.
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Biochemistry
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Bevilacqua, P.C.1
Turner, D.H.2
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58
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0026427239
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Ribozyme recognition of RNA by tertiary interactions with specific ribose 2'-OH groups
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Pyle AM, Cech TR. Ribozyme recognition of RNA by tertiary interactions with specific ribose 2'-OH groups. Nature. 350:1991;628-631.
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Nature
, vol.350
, pp. 628-631
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Pyle, A.M.1
Cech, T.R.2
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59
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0027767532
-
Tertiary interactions with the internal guide sequence mediate docking of the P1 helix into the catalytic core of the Tetrahymena ribozyme
-
Strobel SA, Cech TR. Tertiary interactions with the internal guide sequence mediate docking of the P1 helix into the catalytic core of the Tetrahymena ribozyme. Biochemistry. 32:1993;13593-13604.
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Biochemistry
, vol.32
, pp. 13593-13604
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Strobel, S.A.1
Cech, T.R.2
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60
-
-
0029044469
-
Crystal structure of an RNA dodecamer containing the Escherichia coli Shine - Dalgarno sequence
-
The ribose 2'-OH is found to be a major component of the crystal packing. of special interest
-
Schindelin H, Zhang M, Bald R, Furste JP, Erdmann VA, Heinemann U. Crystal structure of an RNA dodecamer containing the Escherichia coli Shine - Dalgarno sequence. J Mol Biol. 249:1995;595-603 The ribose 2'-OH is found to be a major component of the crystal packing. of special interest.
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J Mol Biol
, vol.249
, pp. 595-603
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Schindelin, H.1
Zhang, M.2
Bald, R.3
Furste, J.P.4
Erdmann, V.A.5
Heinemann, U.6
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62
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0028441183
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Representation of the secondary and tertiary structure of group I introns
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Cech T, Damberger S, Gutell R. Representation of the secondary and tertiary structure of group I introns. Nat Struct Biol. 1:1994;273-280.
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Nat Struct Biol
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Cech, T.1
Damberger, S.2
Gutell, R.3
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