-
1
-
-
0003604405
-
-
Cold Spring Harbor Laboratory Press, New York
-
The RNA World, 2nd edn (eds Gesteland, R. F., Cech, T. R. & Atkins, J. F.) (Cold Spring Harbor Laboratory Press, New York, 1999).
-
(1999)
The RNA World, 2nd Edn
-
-
Gesteland, R.F.1
Cech, T.R.2
Atkins, J.F.3
-
2
-
-
0035805213
-
Crystal structure of the ribosome at 5.5 Å resolution
-
Yusupov, M. M. et al. Crystal structure of the ribosome at 5.5 Å resolution. Science 292, 883-896 (2001).
-
(2001)
Science
, vol.292
, pp. 883-896
-
-
Yusupov, M.M.1
-
3
-
-
0034637161
-
The structural basis of ribosome activity in peptide bond synthesis
-
Nissen, P., Hansen, J., Ban, N., Moore, P. & Steitz, T. The structural basis of ribosome activity in peptide bond synthesis. Science 289, 920-930 (2000). The crystal structures of the large ribosomal subunit and of complexes with two substrate analogues demonstrate that the ribosome is a catalytic RNA and identify the nucleotide functional groups in the RNA active site.
-
(2000)
Science
, vol.289
, pp. 920-930
-
-
Nissen, P.1
Hansen, J.2
Ban, N.3
Moore, P.4
Steitz, T.5
-
4
-
-
1642586299
-
Control of gene expression by a natural metabolite-responsive ribozyme
-
Winkler, W. C., Nahvi, A., Roth, A., Collins, J. A. & Breaker, R. R. Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428, 281-286 (2004).
-
(2004)
Nature
, vol.428
, pp. 281-286
-
-
Winkler, W.C.1
Nahvi, A.2
Roth, A.3
Collins, J.A.4
Breaker, R.R.5
-
5
-
-
9644270488
-
Autocatalytic RNA cleavage in the human β-globin pre-mRNA promotes transcription termination
-
Teixeira, A. et al. Autocatalytic RNA cleavage in the human β-globin pre-mRNA promotes transcription termination. Nature 432, 526-530 (2004).
-
(2004)
Nature
, vol.432
, pp. 526-530
-
-
Teixeira, A.1
-
6
-
-
0028063567
-
Three-dimensional structure of a hammerhead ribozyme
-
Pley, H. W., Flaherty, K. M. & McKay, D. B. Three-dimensional structure of a hammerhead ribozyme. Nature 372, 68-74 (1994).
-
(1994)
Nature
, vol.372
, pp. 68-74
-
-
Pley, H.W.1
Flaherty, K.M.2
McKay, D.B.3
-
7
-
-
0029073091
-
The crystal structure of an all-RNA hammerhead ribozyme: A proposed mechanism for RNA catalytic cleavage
-
Scott, W. G., Finch, J. T & Klug, A. The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell 81, 991-1002 (1995).
-
(1995)
Cell
, vol.81
, pp. 991-1002
-
-
Scott, W.G.1
Finch, J.T.2
Klug, A.3
-
8
-
-
0030476765
-
Capturing the structure of a catalytic RNA intermediate: The hammerhead ribozyme
-
Scott, W. G., Murray, J. B., Arnold, J. R., Stoddard, B. L. & Klug, A. Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme. Science 274, 2065-2069 (1996).
-
(1996)
Science
, vol.274
, pp. 2065-2069
-
-
Scott, W.G.1
Murray, J.B.2
Arnold, J.R.3
Stoddard, B.L.4
Klug, A.5
-
9
-
-
0033860560
-
Capture and visualization of a catalytic RNA enzyme-product complex using crystal lattice trapping and X-ray holographic reconstruction
-
Murray, J. B., Szoke, H., Szoke, A. & Scott, W. G. Capture and visualization of a catalytic RNA enzyme-product complex using crystal lattice trapping and X-ray holographic reconstruction. Mol. Cells 5, 279-287 (2000).
-
(2000)
Mol. Cells
, vol.5
, pp. 279-287
-
-
Murray, J.B.1
Szoke, H.2
Szoke, A.3
Scott, W.G.4
-
10
-
-
0036436791
-
Visualizing the structure and mechanism of a small nucleolytic ribozyme
-
Scott, W. G. Visualizing the structure and mechanism of a small nucleolytic ribozyme. Methods 28, 302-306 (2002).
-
(2002)
Methods
, vol.28
, pp. 302-306
-
-
Scott, W.G.1
-
11
-
-
0032489357
-
The structural basis of hammerhead ribozyme self-cleavage
-
Murray, J. B. et al. The structural basis of hammerhead ribozyme self-cleavage. Cell 92, 665-673 (1998).
-
(1998)
Cell
, vol.92
, pp. 665-673
-
-
Murray, J.B.1
-
12
-
-
0033325108
-
Biophysical and biochemical investigations of RNA catalysis in the hammerhead ribozyme
-
Scott, W. G. Biophysical and biochemical investigations of RNA catalysis in the hammerhead ribozyme. Q. Rev. Biophys. 32, 241-284 (1999).
-
(1999)
Q. Rev. Biophys.
, vol.32
, pp. 241-284
-
-
Scott, W.G.1
-
13
-
-
0032497521
-
Crystal structure of a hepatitis delta virus ribozyme
-
Ferré-D'Amaré, A. R., Zhou, K. & Doudna, J. A. Crystal structure of a hepatitis delta virus ribozyme. Nature 395, 567-574 (1998). The crystal structure of the 3′ product of the HDV ribozyme self-cleavage places C75in a solvent-Inaccessible cleft near the 5′-oxygen leaving group, where it might mediate general acid catalysis. There is no evidence of an active-site metal ion.
-
(1998)
Nature
, vol.395
, pp. 567-574
-
-
Ferré-D'Amaré, A.R.1
Zhou, K.2
Doudna, J.A.3
-
14
-
-
2442641641
-
A conformational switch controls hepatitis delta virus ribozyme catalysis
-
Ke, A., Zhou, K., Ding, F., Cate, J. H. & Doudna, J. A. A conformational switch controls hepatitis delta virus ribozyme catalysis. Nature 429, 201-205 (2004). The crystal structure of an uncleaved HDV ribozyme inactivated by a C75U mutation shows U75 near the 2′-oxygen nucleophile, where the wild-type C7S nucleotide base might mediate general base catalysis, and a divalent metal in position for a water-mediated interaction with the 5′-oxygen leaving group.
-
(2004)
Nature
, vol.429
, pp. 201-205
-
-
Ke, A.1
Zhou, K.2
Ding, F.3
Cate, J.H.4
Doudna, J.A.5
-
15
-
-
0035848837
-
Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis
-
N2-type attack mechanism and places the Watson-Crick face of G8 near the reactive phosphate.
-
(2001)
Nature
, vol.410
, pp. 780-786
-
-
Rupert, P.B.1
Ferré-D'Amaré, A.R.2
-
16
-
-
0037111875
-
Transition state stabilization by a catalytic RNA
-
Rupert, P. B., Massey A. P., Sigurdsson, S. T. & Ferré- D'Amaré, A. R. Transition state stabilization by a catalytic RNA. Science 298, 1421-1424 (2002). The crystal structure of a hairpin ribozyme complex with vanadate, a transition state mimic, shows interactions with functional groups on the Watson-Crick faces of G8 and A38.
-
(2002)
Science
, vol.298
, pp. 1421-1424
-
-
Rupert, P.B.1
Massey, A.P.2
Sigurdsson, S.T.3
Ferré-D'Amaré, A.R.4
-
17
-
-
3042848954
-
Crystal structure of a self-splicing group I intron with both exons
-
Adams, P. L., Stahley, M. R., Kosek, A. B., Wang, J. & Strobel, S. A. Crystal structure of a self-splicing group I intron with both exons. Nature 430, 45-50 (2004). The crystal structure of a pre-tRNA intron with both exons that is inactivated by deoxynucleotide substitutions shows the 3′ oxygen of the 5′ exon in position for a nucleophilic attack on the reactive phosphate. The active site contains two of the three active-site metals that have been implicated in the catalysis of self-splicing by biochemical experiments.
-
(2004)
Nature
, vol.430
, pp. 45-50
-
-
Adams, P.L.1
Stahley, M.R.2
Kosek, A.B.3
Wang, J.4
Strobel, S.A.5
-
18
-
-
8644229237
-
Structure of the Tetrahymena ribozyme: Base triple sandwich and metal ion at the active site
-
Guo, F., Gooding, A. R. & Cech, T. R. Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site. Mol. Cell 16, 351-362 (2004).
-
(2004)
Mol. Cell
, vol.16
, pp. 351-362
-
-
Guo, F.1
Gooding, A.R.2
Cech, T.R.3
-
19
-
-
9344232753
-
Crystal structure of a group I intron splicing intermediate
-
Adams, P. L. et al. Crystal structure of a group I intron splicing intermediate. RNA 10, 1867-1887 (2004).
-
(2004)
RNA
, vol.10
, pp. 1867-1887
-
-
Adams, P.L.1
-
20
-
-
11444263264
-
Crystal structure of a phage Twort group I ribozyme-product complex
-
Golden, B. L., Kim, H. & Chase, E. Crystal structure of a phage Twort group I ribozyme-product complex. Nature Struct. Mol. Biol. 12, 82-89 (2005).
-
(2005)
Nature Struct. Mol. Biol.
, vol.12
, pp. 82-89
-
-
Golden, B.L.1
Kim, H.2
Chase, E.3
-
21
-
-
0037321497
-
After the ribosome structures: How does peptidyl transferase work?
-
Moore, P. B. & Steitz, T. A. After the ribosome structures: how does peptidyl transferase work? RNA 9, 155-159 (2003).
-
(2003)
RNA
, vol.9
, pp. 155-159
-
-
Moore, P.B.1
Steitz, T.A.2
-
22
-
-
0037145032
-
The path to perdition is paved with protons
-
Green, R. & Lorsch, J. R. The path to perdition is paved with protons. Cell 110, 665-668 (2002).
-
(2002)
Cell
, vol.110
, pp. 665-668
-
-
Green, R.1
Lorsch, J.R.2
-
23
-
-
77956945325
-
-
ed. Boyer, P. D. Academic Press, New York
-
Benkovic, S. & Schray, K. in The Enzymes Vol. 8 (ed. Boyer, P. D.) 201-238 (Academic Press, New York, 1973).
-
(1973)
The Enzymes
, vol.8
, pp. 201-238
-
-
Benkovic, S.1
Schray, K.2
-
24
-
-
0018881742
-
Enzyme-catalyzed phosphoryl transfer reactions
-
Knowles, J. R. Enzyme-catalyzed phosphoryl transfer reactions. Annu. Rev. Biochem. 49, 877-919 (1980).
-
(1980)
Annu. Rev. Biochem.
, vol.49
, pp. 877-919
-
-
Knowles, J.R.1
-
25
-
-
0027184481
-
A general two-metal mechanism for catalytic RNA
-
Steitz, T. A. & Steitz, J. A. A general two-metal mechanism for catalytic RNA. Proc. Natl Acad. Sci. USA 90, 6498-6502 (1993).
-
(1993)
Proc. Natl. Acad. Sci. USA
, vol.90
, pp. 6498-6502
-
-
Steitz, T.A.1
Steitz, J.A.2
-
26
-
-
0035997396
-
Catalytic strategies of the hepatitis delta virus ribozymes
-
Shih, I. & Been, M. D. Catalytic strategies of the hepatitis delta virus ribozymes. Annu. Rev. Biochem. 71, 887-917 (2002).
-
(2002)
Annu. Rev. Biochem.
, vol.71
, pp. 887-917
-
-
Shih, I.1
Been, M.D.2
-
27
-
-
0034695419
-
Crystallization and structure determination of a hepatitis delta virus ribozyme: Use of the RNA-binding protein U1A as a crystallization module
-
Ferré-D'Amaré, A. R. & Doudna, J. A. Crystallization and structure determination of a hepatitis delta virus ribozyme: use of the RNA-binding protein U1A as a crystallization module. J. Mol. Biol. 295, 541-556 (2000).
-
(2000)
J. Mol. Biol.
, vol.295
, pp. 541-556
-
-
Ferré-D'Amaré, A.R.1
Doudna, J.A.2
-
28
-
-
0031194873
-
A unique mechanism for RNA catalysis: The role of metal cofactors in hairpin ribozyme cleavage
-
Hampel, A. & Cowan, J. A. A unique mechanism for RNA catalysis: the role of metal cofactors in hairpin ribozyme cleavage. Chem. Biol. 4, 513-517 (1997).
-
(1997)
Chem. Biol.
, vol.4
, pp. 513-517
-
-
Hampel, A.1
Cowan, J.A.2
-
29
-
-
0031215134
-
An unusual pH-independent and metal-ion-independent mechanism for hairpin ribozyme catalysis
-
Nesbitt, S., Hegg, L. A. & Fedor, M. J. An unusual pH-independent and metal-ion-independent mechanism for hairpin ribozyme catalysis. Chem. Biol. 4, 619-630 (1997).
-
(1997)
Chem. Biol.
, vol.4
, pp. 619-630
-
-
Nesbitt, S.1
Hegg, L.A.2
Fedor, M.J.3
-
30
-
-
0030967825
-
Metal ions play a passive role in the hairpin ribozyme catalysed reaction
-
Young, K. J., Gill, F. & Grasby, J. A. Metal ions play a passive role in the hairpin ribozyme catalysed reaction Nucleic Acids Res. 25, 3760-3766 (1997).
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3760-3766
-
-
Young, K.J.1
Gill, F.2
Grasby, J.A.3
-
31
-
-
0032192761
-
The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone
-
Murray, J. B., Seyhan, A. ., Walter, N. G., Burke, J. M. & Scott, W. G. The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone. Chem. Biol. 5, 587-595 (1998).
-
(1998)
Chem. Biol.
, vol.5
, pp. 587-595
-
-
Murray, J.B.1
Seyhan, A.2
Walter, N.G.3
Burke, J.M.4
Scott, W.G.5
-
32
-
-
0033215448
-
Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme
-
Perrotta, A. T., Shih, I. & Been, M. D. Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme. Science 286, 123-126 (1999).
-
(1999)
Science
, vol.286
, pp. 123-126
-
-
Perrotta, A.T.1
Shih, I.2
Been, M.D.3
-
34
-
-
0037133526
-
a perturbation in genomic hepatitis delta virus ribozyme catalysis evidenced by nucleotide analogue interference mapping
-
a perturbation in genomic hepatitis delta virus ribozyme catalysis evidenced by nucleotide analogue interference mapping. Biochemistry 41, 3667-3675 (2002).
-
(2002)
Biochemistry
, vol.41
, pp. 3667-3675
-
-
Oyelere, A.K.1
Kardon, J.R.2
Strobel, S.A.3
-
35
-
-
0034712097
-
General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme
-
Nakano, S., Chadalavada, D. M. & Bevilacqua, P. C. General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme. Science 287, 1493-1497 (2000).
-
(2000)
Science
, vol.287
, pp. 1493-1497
-
-
Nakano, S.1
Chadalavada, D.M.2
Bevilacqua, P.C.3
-
36
-
-
0035852640
-
Involvement of a cytosine side chain in proton transfer in the rate-determining step of ribozyme self-cleavage
-
Shih, I. & Been, M. D. Involvement of a cytosine side chain in proton transfer in the rate-determining step of ribozyme self-cleavage. Proc. Natl Acad. Sci. USA 98, 1489-1494 (2001). Changes in the pH-rate profiles that result from cytosine mutations and the rescue of cytosine mutations with exogenous imidazole analogues implicate an active-site cytosine in general acid-base catalysis of HDV ribozyme self-cleavage.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 1489-1494
-
-
Shih, I.1
Been, M.D.2
-
37
-
-
0024478059
-
Direct Brønsted analysis of the restoration of activity to a mutant enzyme by exogenous amines
-
Toney, M. & Kirsch, J. Direct Brønsted analysis of the restoration of activity to a mutant enzyme by exogenous amines. Science 243, 1485-1488 (1989).
-
(1989)
Science
, vol.243
, pp. 1485-1488
-
-
Toney, M.1
Kirsch, J.2
-
39
-
-
0035833978
-
Mechanistic characterization of the HDV genomic ribozyme: Assessing the catalytic and structural contributions of divalent metal ions within a multichannel reaction mechanism
-
Nakano, S., Proctor, D. J. & Bevilacqua, P. C. Mechanistic characterization of the HDV genomic ribozyme: assessing the catalytic and structural contributions of divalent metal ions within a multichannel reaction mechanism. Biochemistry 40, 12022-12038 (2001).
-
(2001)
Biochemistry
, vol.40
, pp. 12022-12038
-
-
Nakano, S.1
Proctor, D.J.2
Bevilacqua, P.C.3
-
40
-
-
0034708334
-
Structure and function of the hairpin ribozyme
-
Fedor, M. J. Structure and function of the hairpin ribozyme. J. Mol. Biol. 297, 269-291 (2000).
-
(2000)
J. Mol. Biol.
, vol.297
, pp. 269-291
-
-
Fedor, M.J.1
-
41
-
-
0032522574
-
Tertiary structure formation in the hairpin ribozyme monitored by fluorescence resonance energy transfer
-
Walter, N. G., Hampel, K. J., Brown, K. M. & Burke, J. M. Tertiary structure formation in the hairpin ribozyme monitored by fluorescence resonance energy transfer. EMBO J. 17, 2378-2391 (1998).
-
(1998)
EMBO J.
, vol.17
, pp. 2378-2391
-
-
Walter, N.G.1
Hampel, K.J.2
Brown, K.M.3
Burke, J.M.4
-
42
-
-
0032979707
-
Stability of hairpin ribozyme tertiary structure is governed by the interdomain junction
-
Walter, N. G., Burke, J. M. & Millar, D. P. Stability of hairpin ribozyme tertiary structure is governed by the interdomain junction. Nature Struct. Biol. 6, 544-549 (1999).
-
(1999)
Nature Struct. Biol.
, vol.6
, pp. 544-549
-
-
Walter, N.G.1
Burke, J.M.2
Millar, D.P.3
-
43
-
-
0034545071
-
The folding of the hairpin ribozyme: Dependence on the loops and the junction
-
Zhao, Z., Wilson, T., Maxwell, K. & Lilley, D. The folding of the hairpin ribozyme: dependence on the loops and the junction. RNA 6, 1833-1846 (2000).
-
(2000)
RNA
, vol.6
, pp. 1833-1846
-
-
Zhao, Z.1
Wilson, T.2
Maxwell, K.3
Lilley, D.4
-
44
-
-
0024340908
-
RNA catalytic properties of the minimum (-)sTRSV sequence
-
Hampel, A. & Tritz, R. RNA catalytic properties of the minimum (-)sTRSV sequence. Biochemistry 28, 4929-4933 (1989).
-
(1989)
Biochemistry
, vol.28
, pp. 4929-4933
-
-
Hampel, A.1
Tritz, R.2
-
45
-
-
0033600553
-
Tertiary structure stabilization promotes hairpin ribozyme ligation
-
Fedor, M. J. Tertiary structure stabilization promotes hairpin ribozyme ligation. Biochemistry 38, 11040-11050 (1999).
-
(1999)
Biochemistry
, vol.38
, pp. 11040-11050
-
-
Fedor, M.J.1
-
46
-
-
0035875909
-
Hairpin ribozymes with four-way helical junctions mediate intracellular RNA ligation
-
Yadava, R., Choi, A., Lebruska, L. & Fedor, M. Hairpin ribozymes with four-way helical junctions mediate intracellular RNA ligation. J. Mol. Biol. 309, 893-902 (2001).
-
(2001)
J. Mol. Biol.
, vol.309
, pp. 893-902
-
-
Yadava, R.1
Choi, A.2
Lebruska, L.3
Fedor, M.4
-
47
-
-
0035909052
-
Tertiary structure stability of the hairpin ribozyme in its natural and minimal forms: Different energetic contributions from a ribose zipper motif
-
Klostermeier, D. & Millar, D. P. Tertiary structure stability of the hairpin ribozyme in its natural and minimal forms: different energetic contributions from a ribose zipper motif. Biochemistry 40, 11211-11218 (2001).
-
(2001)
Biochemistry
, vol.40
, pp. 11211-11218
-
-
Klostermeier, D.1
Millar, D.P.2
-
48
-
-
0036863323
-
The hairpin ribozyme: From crystal structure to function
-
Ferré-D'Amaré, A. R. & Rupert, P. B. The hairpin ribozyme: from crystal structure to function. Biochem. Soc. Trans. 30, 1105-1109 (2001).
-
(2001)
Biochem. Soc. Trans.
, vol.30
, pp. 1105-1109
-
-
Ferré-D'Amaré, A.R.1
Rupert, P.B.2
-
49
-
-
0037085738
-
Comparative analysis of hairpin ribozyme structures and interference data
-
Ryder, S. P. & Strobel, S. A. Comparative analysis of hairpin ribozyme structures and interference data. Nucleic Acids Res. 30, 1287-1291 (2002).
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 1287-1291
-
-
Ryder, S.P.1
Strobel, S.A.2
-
50
-
-
0347133497
-
The hairpin ribozyme
-
Ferré-D'Amaré, A. R. The hairpin ribozyme. Biopolymers 73, 71-78 (2004).
-
(2004)
Biopolymers
, vol.73
, pp. 71-78
-
-
Ferré-D'Amaré, A.R.1
-
51
-
-
0025335881
-
Two autolytic processing reactions of a satellite RNA proceed with inversion of configuration
-
van Tol, H., Buzayan, J. M., Feldstein, P. A., Eckstein, F. & Bruening, G. Two autolytic processing reactions of a satellite RNA proceed with inversion of configuration. Nucleic Acids Res. 18, 1971-1975 (1990).
-
(1990)
Nucleic Acids Res.
, vol.18
, pp. 1971-1975
-
-
Van Tol, H.1
Buzayan, J.M.2
Feldstein, P.A.3
Eckstein, F.4
Bruening, G.5
-
52
-
-
0037418547
-
Mechanistic considerations for general acid-base catalysis by RNA: Revisiting the mechanism of the hairpin ribozyme
-
Bevilacqua, P. C. Mechanistic considerations for general acid-base catalysis by RNA: revisiting the mechanism of the hairpin ribozyme. Biochemistry 42, 2259-2265 (2003).
-
(2003)
Biochemistry
, vol.42
, pp. 2259-2265
-
-
Bevilacqua, P.C.1
-
53
-
-
0035890245
-
Functional involvement of G8 in the hairpin ribozyme cleavage mechanism
-
Pinard, R. et al. Functional involvement of G8 in the hairpin ribozyme cleavage mechanism. EMBO J. 20, 6434-6442 (2001).
-
(2001)
EMBO J.
, vol.20
, pp. 6434-6442
-
-
Pinard, R.1
-
54
-
-
2942577491
-
Role of an active site guanine in hairpin ribozyme catalysis probed by exogenous nucleobase rescue
-
Kuzmin, Y. I., Da Costa, C. C. & Fedor, M. J. Role of an active site guanine in hairpin ribozyme catalysis probed by exogenous nucleobase rescue. J. Mol. Biol. 340, 233-251 (2004).
-
(2004)
J. Mol. Biol.
, vol.340
, pp. 233-251
-
-
Kuzmin, Y.I.1
Da Costa, C.C.2
Fedor, M.J.3
-
55
-
-
0036237379
-
Rescue of an abasic hairpin ribozyme by cationic nucleobases. Evidence for a novel mechanism of RNA catalysis
-
Lebruska, L. L., Kuzmine, I. I. & Fedor, M. J. Rescue of an abasic hairpin ribozyme by cationic nucleobases. Evidence for a novel mechanism of RNA catalysis. Chem. Biol. 9, 465-473 (2002).
-
(2002)
Chem. Biol.
, vol.9
, pp. 465-473
-
-
Lebruska, L.L.1
Kuzmine, I.I.2
Fedor, M.J.3
-
56
-
-
18344379398
-
Contribution of an active site adenosine to hairpin ribozyme catalysis
-
in the press
-
Kuzmin, Y. I., DaCosta, C. P., Cottrell, J. & Fedor, M. J. Contribution of an active site adenosine to hairpin ribozyme catalysis. J. Mol. Biol. (in the press).
-
J. Mol. Biol.
-
-
Kuzmin, Y.I.1
DaCosta, C.P.2
Cottrell, J.3
Fedor, M.J.4
-
57
-
-
0023047510
-
Self-cleavage of plus and minus transcripts of avocado sunblotch viroid
-
Hutchins, C. J., Rathjen, P. D., Forster, A. C. & Symons, R. H. Self-cleavage of plus and minus transcripts of avocado sunblotch viroid. Nucleic Acids Res. 14, 3627-3640 (1986).
-
(1986)
Nucleic Acids Res.
, vol.14
, pp. 3627-3640
-
-
Hutchins, C.J.1
Rathjen, P.D.2
Forster, A.C.3
Symons, R.H.4
-
58
-
-
0022504693
-
Nonenzymatic cleavage and ligation of RNAs complementary to a plant virus satellite RNA
-
Buzayan, J. M., Gerlach, W. L. & Bruening, G. Nonenzymatic cleavage and ligation of RNAs complementary to a plant virus satellite RNA. Nature 323, 349-353 (1986).
-
(1986)
Nature
, vol.323
, pp. 349-353
-
-
Buzayan, J.M.1
Gerlach, W.L.2
Bruening, G.3
-
59
-
-
0036863387
-
Hairpin and hammerhead ribozymes: How different are they?
-
Burke, J. M. Hairpin and hammerhead ribozymes: how different are they? Biochem. Soc. Trans. 30, 1115-1118 (2002).
-
(2002)
Biochem. Soc. Trans.
, vol.30
, pp. 1115-1118
-
-
Burke, J.M.1
-
61
-
-
0036903567
-
Folding and activity of the hammerhead ribozyme
-
Hammann, C. & Lilley, D. M. Folding and activity of the hammerhead ribozyme. Chembiochem 3, 690-700 (2002).
-
(2002)
Chembiochem
, vol.3
, pp. 690-700
-
-
Hammann, C.1
Lilley, D.M.2
-
63
-
-
0029949701
-
Structure and function of the hammerhead ribozyme: An unfinished story
-
McKay, D. B. Structure and function of the hammerhead ribozyme: an unfinished story. RNA 2, 395-403 (1996).
-
(1996)
RNA
, vol.2
, pp. 395-403
-
-
McKay, D.B.1
-
64
-
-
0030876444
-
Involvement of a specific metal ion in the transition of the hammerhead ribozyme to its catalytic conformation
-
Peracchi, A., Beigelman, L., Scott, E. C., Uhlenbeck, O. C. & Herschlag, D. Involvement of a specific metal ion in the transition of the hammerhead ribozyme to its catalytic conformation. J. Biol. Chem. 272, 26822-26826 (1997).
-
(1997)
J. Biol. Chem.
, vol.272
, pp. 26822-26826
-
-
Peracchi, A.1
Beigelman, L.2
Scott, E.C.3
Uhlenbeck, O.C.4
Herschlag, D.5
-
65
-
-
0033607198
-
Identification of the hammerhead ribozyme metal ion binding site responsible for rescue of the deleterious effect of a cleavage site phosphorothioate
-
Wang, S., Karbstein, K., Peracchi, A., Beigelman, L. & Herschlag, D. Identification of the hammerhead ribozyme metal ion binding site responsible for rescue of the deleterious effect of a cleavage site phosphorothioate. Biochemistry 38, 14363-14378 (1999).
-
(1999)
Biochemistry
, vol.38
, pp. 14363-14378
-
-
Wang, S.1
Karbstein, K.2
Peracchi, A.3
Beigelman, L.4
Herschlag, D.5
-
66
-
-
0043009734
-
Sequence elements outside the hammerhead ribozyme catalytic core enable intracellar activity
-
Khvorova, A., Lescoute, A., Westhof, E. & Jayasena, S. D. Sequence elements outside the hammerhead ribozyme catalytic core enable intracellar activity. Nature Struct. Biol. 10, 708-712 (2003).
-
(2003)
Nature Struct. Biol.
, vol.10
, pp. 708-712
-
-
Khvorova, A.1
Lescoute, A.2
Westhof, E.3
Jayasena, S.D.4
-
67
-
-
0142105383
-
Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity
-
De la Pena, M., Gago, S. & Flores, R. Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity. EMBO J. 22, 5561-5570 (2003).
-
(2003)
EMBO J.
, vol.22
, pp. 5561-5570
-
-
De La Pena, M.1
Gago, S.2
Flores, R.3
-
68
-
-
1942533453
-
Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements
-
Penedo, J. C., Wilson, T. J., Jayasena, S. D., Khvorova, A. & Lilley, D. M. Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements. RNA 10, 880-888 (2004).
-
(2004)
RNA
, vol.10
, pp. 880-888
-
-
Penedo, J.C.1
Wilson, T.J.2
Jayasena, S.D.3
Khvorova, A.4
Lilley, D.M.5
-
69
-
-
4444297561
-
Fast cleavage kinetics of a natural hammerhead ribozyme
-
Canny, M. D. et al. Fast cleavage kinetics of a natural hammerhead ribozyme. J. Am. Chem. Soc. 126, 10848-10849 (2004).
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 10848-10849
-
-
Canny, M.D.1
-
70
-
-
9344265166
-
Artificial tertiary motifs stabilize trans-cleaving hammerhead ribozymes under conditions of submillimolar divalent ions and high temperatures
-
Saksmerprome, V., Roychowdhury-Saha, M., Jayasena, S., Khvorova, A. & Burke, D. H. Artificial tertiary motifs stabilize trans-cleaving hammerhead ribozymes under conditions of submillimolar divalent ions and high temperatures. RNA 10, 1916-1924 (2004).
-
(2004)
RNA
, vol.10
, pp. 1916-1924
-
-
Saksmerprome, V.1
Roychowdhury-Saha, M.2
Jayasena, S.3
Khvorova, A.4
Burke, D.H.5
-
71
-
-
0002160687
-
-
eds Gesteland, R. F., Cech, T. R. & Atkins, J. F. Cold Spring Harbor Laboratory Press, New York
-
Cech, T. R. & Golden, B. L. in The RNA World, 2nd edn (eds Gesteland, R. F., Cech, T. R. & Atkins, J. F.) 321-349 (Cold Spring Harbor Laboratory Press, New York, 1999).
-
(1999)
The RNA World, 2nd Edn
, pp. 321-349
-
-
Cech, T.R.1
Golden, B.L.2
-
73
-
-
0036601149
-
The role of metal ions in RNA catalysis
-
Fedor, M. J. The role of metal ions in RNA catalysis. Curr. Opin. Struct. Biol. 12, 289-295 (2002).
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 289-295
-
-
Fedor, M.J.1
-
74
-
-
0030800470
-
A second catalytic metal ion in group I ribozyme
-
Weinstein, L. B., Jones, B. C., Cosstick, R. & Cech, T. R. A second catalytic metal ion in group I ribozyme. Nature 388, 805-808 (1997).
-
(1997)
Nature
, vol.388
, pp. 805-808
-
-
Weinstein, L.B.1
Jones, B.C.2
Cosstick, R.3
Cech, T.R.4
-
75
-
-
0033600571
-
Probing the role of metal ions in RNA catalysis: Kinetic and thermodynamic characterization of a metal ion interaction with the 2′-moiety of the guanosine nucleophile in the Tetrahymena group I ribozyme
-
Shan, S. & Herschlag, D. Probing the role of metal ions in RNA catalysis: kinetic and thermodynamic characterization of a metal ion interaction with the 2′-moiety of the guanosine nucleophile in the Tetrahymena group I ribozyme. Biochemistry 38, 10958-10975 (1999).
-
(1999)
Biochemistry
, vol.38
, pp. 10958-10975
-
-
Shan, S.1
Herschlag, D.2
-
76
-
-
0033607225
-
Three metal ions at the active site of the Tetrahymena group I ribozyme
-
Shan, S., Yoshida, A., Sun, S., Piccirilli, J. A. & Herschlag, D. Three metal ions at the active site of the Tetrahymena group I ribozyme. Proc. Natl Acad. Sci. USA 96, 12299-12304 (1999). Metal-cation specificity-switch experiments support a three-metal mechanism of group-I intron splicing, in which three distinct metal cations interact with the 3′ oxygen of the oligonucleotide substrate and the 3′ and 2′ oxygens of the guanosine nucleophile.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 12299-12304
-
-
Shan, S.1
Yoshida, A.2
Sun, S.3
Piccirilli, J.A.4
Herschlag, D.5
-
77
-
-
0032893740
-
A new metal ion interaction in the Tetrahymena ribozyme reaction revealed by double sulfur substitution
-
Yoshida, A., Sun, S. & Piccirilli, J. A. A new metal ion interaction in the Tetrahymena ribozyme reaction revealed by double sulfur substitution. Nature Struct. Biol. 6, 318-321 (1999).
-
(1999)
Nature Struct. Biol.
, vol.6
, pp. 318-321
-
-
Yoshida, A.1
Sun, S.2
Piccirilli, J.A.3
-
78
-
-
0035340961
-
Defining the catalytic metal ion interactions in the Tetrahymena ribozyme reaction
-
Shan, S., Kravchuk, A. V., Piccirilli, J. A. & Herschlag, D. Defining the catalytic metal ion interactions in the Tetrahymena ribozyme reaction. Biochemistry 40, 5161-5171 (2001).
-
(2001)
Biochemistry
, vol.40
, pp. 5161-5171
-
-
Shan, S.1
Kravchuk, A.V.2
Piccirilli, J.A.3
Herschlag, D.4
-
79
-
-
0242271642
-
Metal ion interaction with cosubstrate in self-splicing of group I introns
-
Sjögren, A. S., Pettersson, E., Sjöberg, B. M. & Strömberg, R. Metal ion interaction with cosubstrate in self-splicing of group I introns. Nucleic Acids Res. 25, 648-653 (1997).
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 648-653
-
-
Sjögren, A.S.1
Pettersson, E.2
Sjöberg, B.M.3
Strömberg, R.4
-
80
-
-
0026639881
-
Unusual resistance of peptidyl transferase to protein extraction methods
-
Noller, H. F., Hoffarth, V. & Zimniak, L. Unusual resistance of peptidyl transferase to protein extraction methods. Science 256, 1416-1419 (1992).
-
(1992)
Science
, vol.256
, pp. 1416-1419
-
-
Noller, H.F.1
Hoffarth, V.2
Zimniak, L.3
-
82
-
-
0035942753
-
Ribosomal peptidyl transferase can withstand mutations at the putative catalytic nucleotide
-
Polacek, N., Gaynor, M., Yassin, A. & Mankin, A. S. Ribosomal peptidyl transferase can withstand mutations at the putative catalytic nucleotide. Nature 411, 498-501 (2001).
-
(2001)
Nature
, vol.411
, pp. 498-501
-
-
Polacek, N.1
Gaynor, M.2
Yassin, A.3
Mankin, A.S.4
-
83
-
-
0034757629
-
pH-dependent conformational flexibility within the ribosomal peptidyl transferase center
-
Muth, G. W., Chen, L., Kosek, A. B. & Strobel, S. A. pH-dependent conformational flexibility within the ribosomal peptidyl transferase center. RNA 7, 1403-1415 (2001).
-
(2001)
RNA
, vol.7
, pp. 1403-1415
-
-
Muth, G.W.1
Chen, L.2
Kosek, A.B.3
Strobel, S.A.4
-
84
-
-
0036671344
-
Important contribution to catalysis of peptide bond formation by a single ionizing group within the ribosome
-
Katunin, V. I., Muth, G. W., Strobel, S. A., Wintermeyer, W. & Rodnina, M. V. Important contribution to catalysis of peptide bond formation by a single ionizing group within the ribosome. Mol. Cell 10, 339-346 (2002).
-
(2002)
Mol. Cell
, vol.10
, pp. 339-346
-
-
Katunin, V.I.1
Muth, G.W.2
Strobel, S.A.3
Wintermeyer, W.4
Rodnina, M.V.5
-
85
-
-
0038508659
-
Peptide bond formation on the ribosome: Structure and mechanism
-
Rodnina, M. V. & Wintermeyer, W. Peptide bond formation on the ribosome: structure and mechanism. Curr. Opin. Struct. Biol. 13, 334-340 (2003).
-
(2003)
Curr. Opin. Struct. Biol.
, vol.13
, pp. 334-340
-
-
Rodnina, M.V.1
Wintermeyer, W.2
-
86
-
-
2542564300
-
The ribosome as an entropy trap
-
Sievers, A., Beringer, M., Rodnina, M. V. & Wolfenden, R. The ribosome as an entropy trap. Proc. Natl Acad. Sci. USA 101, 7897-7901 (2004).
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 7897-7901
-
-
Sievers, A.1
Beringer, M.2
Rodnina, M.V.3
Wolfenden, R.4
-
87
-
-
7544220590
-
Substrate-assisted catalysis of peptide bond formation by the ribosome
-
Weinger, J. S., Parnell, K. M., Dorner, S., Green, R. & Strobel, S. A. Substrate-assisted catalysis of peptide bond formation by the ribosome. Nature Struct. Mol. Biol. 11, 1101-1106 (2004).
-
(2004)
Nature Struct. Mol. Biol.
, vol.11
, pp. 1101-1106
-
-
Weinger, J.S.1
Parnell, K.M.2
Dorner, S.3
Green, R.4
Strobel, S.A.5
-
88
-
-
2542470615
-
The active site of the ribosome is composed of two layers of conserved nucleotides with distinct roles in peptide bond formation and peptide release
-
Youngman, E. M., Brunelle, J. L., Kochaniak, A. B. & Green, R. The active site of the ribosome is composed of two layers of conserved nucleotides with distinct roles in peptide bond formation and peptide release. Cell 117, 589-599 (2004).
-
(2004)
Cell
, vol.117
, pp. 589-599
-
-
Youngman, E.M.1
Brunelle, J.L.2
Kochaniak, A.B.3
Green, R.4
-
89
-
-
0030902181
-
Unifying the current data on the mechanism of cleavage- transesterification of RNA
-
Perrault, D. M. & Anslyn, E. V. Unifying the current data on the mechanism of cleavage-transesterification of RNA. Angew. Chem. Int. Ed. Engl. 36, 432-450 (1997).
-
(1997)
Angew. Chem. Int. Ed. Engl.
, vol.36
, pp. 432-450
-
-
Perrault, D.M.1
Anslyn, E.V.2
-
90
-
-
0001005285
-
Ribonuclease A
-
Raines, R. T. Ribonuclease A. Chem. Rev. 98, 1045-1066 (1998).
-
(1998)
Chem. Rev.
, vol.98
, pp. 1045-1066
-
-
Raines, R.T.1
-
91
-
-
0001055719
-
Kinetics and mechanisms for the cleavage and isomerization of the phosphodiester bonds of RNA by Brønsted acids and bases
-
Oivanen, M., Kuusela, S.& Lönnberg, H. Kinetics and mechanisms for the cleavage and isomerization of the phosphodiester bonds of RNA by Brønsted acids and bases. Chem. Rev. 98, 961-990 (1998).
-
(1998)
Chem. Rev.
, vol.98
, pp. 961-990
-
-
Oivanen, M.1
Kuusela, S.2
Lönnberg, H.3
-
92
-
-
0008934076
-
-
ed. Brown, D. J. John Wiley & Sons, New York
-
Lister, J. H. in Fused pyrimidines Vol. 24 (ed. Brown, D. J.) 478-496 (John Wiley & Sons, New York, 1971).
-
(1971)
Fused Pyrimidines
, vol.24
, pp. 478-496
-
-
Lister, J.H.1
-
93
-
-
0001036515
-
-
ed. Taylor, E. G. John Wiley & Sons, New York
-
Brown, D. J. in The Pyrimidines Vol. 52 (ed. Taylor, E. G.) 823-853 (John Wiley & Sons, New York, 1994).
-
(1994)
The Pyrimidines
, vol.52
, pp. 823-853
-
-
Brown, D.J.1
-
94
-
-
0003768234
-
-
eds Kochetkov, N. K. & Budovskii, E. I. Plenum, New York
-
Kochetkov, N. K. & Budovskii, E. I. in Organic Chemistry of Nucleic Acids (eds Kochetkov, N. K. & Budovskii, E. I.) 148-165 (Plenum, New York, 1971).
-
(1971)
Organic Chemistry of Nucleic Acids
, pp. 148-165
-
-
Kochetkov, N.K.1
Budovskii, E.I.2
-
95
-
-
0030968710
-
Mechanistic aspects of enzymatic catalysis: Lessons from comparison of RNA and protein enzymes
-
Narlikar, G. J. & Herschlag, D. Mechanistic aspects of enzymatic catalysis: lessons from comparison of RNA and protein enzymes. Annu. Rev. Biochem. 66, 19-59 (1997).
-
(1997)
Annu. Rev. Biochem.
, vol.66
, pp. 19-59
-
-
Narlikar, G.J.1
Herschlag, D.2
-
96
-
-
0347763707
-
Catalytic roles for proton transfer and protonation in ribozymes
-
Bevilacqua, P. C., Brown, T. S., Nakano, S. & Yajima, R. Catalytic roles for proton transfer and protonation in ribozymes. Biopolymers 73, 90-109 (2004).
-
(2004)
Biopolymers
, vol.73
, pp. 90-109
-
-
Bevilacqua, P.C.1
Brown, T.S.2
Nakano, S.3
Yajima, R.4
-
97
-
-
1242274330
-
A guide to ions and RNA structure
-
Draper, D. E. A guide to ions and RNA structure. RNA 10, 335-343 (2004).
-
(2004)
RNA
, vol.10
, pp. 335-343
-
-
Draper, D.E.1
-
100
-
-
0022418143
-
Bond order and charge localization in nucleoside phosphorothioates
-
Frey, P. A. & Sammons, R. D. Bond order and charge localization in nucleoside phosphorothioates. Science 228, 541-545 (1985).
-
(1985)
Science
, vol.228
, pp. 541-545
-
-
Frey, P.A.1
Sammons, R.D.2
-
101
-
-
0032707136
-
Thiophilic metal ion rescue of phosphorothioate interference within the Tetrahymena ribozyme P4-P6 domain
-
Basu, S. & Strabel, S. A. Thiophilic metal ion rescue of phosphorothioate interference within the Tetrahymena ribozyme P4-P6 domain. RNA 5, 1399-1407 (1999).
-
(1999)
RNA
, vol.5
, pp. 1399-1407
-
-
Basu, S.1
Strabel, S.A.2
-
102
-
-
0033787391
-
Ribozyme structures and mechanisms
-
Doherty, E. A. & Doudna, J. A. Ribozyme structures and mechanisms. Annu. Rev. Biochem. 69, 597-615 (2000).
-
(2000)
Annu. Rev. Biochem.
, vol.69
, pp. 597-615
-
-
Doherty, E.A.1
Doudna, J.A.2
-
103
-
-
0032500731
-
A preorganized active site in the crystal structure of the Tetrahymena ribozyme
-
Golden, B. L., Gooding, A. R., Podell, E. R. & Cech, T. R. A preorganized active site in the crystal structure of the Tetrahymena ribozyme. Science 282, 259-264 (1998).
-
(1998)
Science
, vol.282
, pp. 259-264
-
-
Golden, B.L.1
Gooding, A.R.2
Podell, E.R.3
Cech, T.R.4
-
104
-
-
0042658199
-
RNA, the first macromolecular catalyst: The ribosome is a ribozyme
-
Steitz, T. A. & Moore, P. B. RNA, the first macromolecular catalyst: the ribosome is a ribozyme. Trends Biochem. Sci. 28, 411-418 (2003).
-
(2003)
Trends Biochem. Sci.
, vol.28
, pp. 411-418
-
-
Steitz, T.A.1
Moore, P.B.2
-
105
-
-
0037015037
-
Structural insights into peptide bond formation
-
Hansen, J. L., Schmeing, T. M., Moore, P. B. & Steitz, T. A. Structural insights into peptide bond formation. Proc. Natl Acad. Sci. USA 99, 11670-11675 (2002).
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 11670-11675
-
-
Hansen, J.L.1
Schmeing, T.M.2
Moore, P.B.3
Steitz, T.A.4
|