-
1
-
-
0034637161
-
The structural basis of ribosome activity in peptide bond synthesis
-
Nissen, P., Hansen, J., Ban, N., Moore, P.B. & Steitz, T.A. The structural basis of ribosome activity in peptide bond synthesis. Science 289, 920-930 (2000).
-
(2000)
Science
, vol.289
, pp. 920-930
-
-
Nissen, P.1
Hansen, J.2
Ban, N.3
Moore, P.B.4
Steitz, T.A.5
-
2
-
-
84887624226
-
RNA catalyses nuclear pre-mRNA splicing
-
Fica, S.M. et al. RNA catalyses nuclear pre-mRNA splicing. Nature 503, 229-234 (2013).
-
(2013)
Nature
, vol.503
, pp. 229-234
-
-
Fica, S.M.1
-
3
-
-
41749101497
-
-
(eds. Lilley, D.M.J. & Eckstein, F.) Royal Society of Chemistry, Cambridge
-
Lilley, D.M.J. & Eckstein, F. in Ribozymes and RNA Catalysis (eds. Lilley, D.M.J. & Eckstein, F.) 1-318 (Royal Society of Chemistry, Cambridge, 2008).
-
(2008)
Ribozymes and RNA Catalysis
, pp. 1-318
-
-
Lilley, D.M.J.1
Eckstein, F.2
-
4
-
-
84867392525
-
-
(eds. Lilley, D.M. & Sutherland, J.) (Royal Society Publishing, London
-
Lilley, D.M.J. & Sutherland, J. in The Chemical Origins of Life and its Early Evolution (eds. Lilley, D.M. & Sutherland, J.) 2851-2986 (Royal Society Publishing, London, 2011).
-
(2011)
The Chemical Origins of Life and Its Early Evolution
, pp. 2851-2986
-
-
Lilley, D.M.J.1
Sutherland, J.2
-
5
-
-
0022504693
-
Non-enzymatic cleavage and ligation of RNAs complementary to a plant virus satellite RNA
-
Buzayan, J.M., Gerlach, W.L. & Bruening, G. Non-enzymatic 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
-
6
-
-
0023663396
-
Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites
-
Forster, A.C. & Symons, R.H. Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites. Cell 49, 211-220 (1987).
-
(1987)
Cell
, vol.49
, pp. 211-220
-
-
Forster, A.C.1
Symons, R.H.2
-
7
-
-
0024291288
-
Simple RNA enzymes with new and highly specific endoribonuclease activities
-
Haseloff, J. & Gerlach, W.L. Simple RNA enzymes with new and highly specific endoribonuclease activities. Nature 334, 585-591 (1988).
-
(1988)
Nature
, vol.334
, pp. 585-591
-
-
Haseloff, J.1
Gerlach, W.L.2
-
8
-
-
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
-
9
-
-
72449145407
-
Widespread occurrence of self-cleaving ribozymes
-
Webb, C.H., Riccitelli, N.J., Ruminski, D.J. & Luptak, A. Widespread occurrence of self-cleaving ribozymes. Science 326, 953 (2009).
-
(2009)
Science
, vol.326
, pp. 953
-
-
Webb, C.H.1
Riccitelli, N.J.2
Ruminski, D.J.3
Luptak, A.4
-
10
-
-
77956226227
-
Intronic hammerhead ribozymes are ultraconserved in the human genome
-
de la Peña, M. & Garcia-Robles, I. Intronic hammerhead ribozymes are ultraconserved in the human genome. EMBO Rep. 11, 711-716 (2010).
-
(2010)
EMBO Rep.
, vol.11
, pp. 711-716
-
-
De La Peña, M.1
Garcia-Robles, I.2
-
11
-
-
78650501783
-
From alpaca to zebrafish: Hammerhead ribozymes wherever you look
-
Seehafer, C., Kalweit, A., Steger, G., Graf, S. & Hammann, C. From alpaca to zebrafish: hammerhead ribozymes wherever you look. RNA 17, 21-26 (2011).
-
(2011)
RNA
, vol.17
, pp. 21-26
-
-
Seehafer, C.1
Kalweit, A.2
Steger, G.3
Graf, S.4
Hammann, C.5
-
12
-
-
84891008536
-
A widespread self-cleaving ribozyme class is revealed by bioinformatics
-
Roth, A. et al. A widespread self-cleaving ribozyme class is revealed by bioinformatics. Nat. Chem. Biol. 10, 56-60 (2014).
-
(2014)
Nat. Chem. Biol.
, vol.10
, pp. 56-60
-
-
Roth, A.1
-
13
-
-
62449245467
-
The evolution of ribozyme chemistry
-
Wilson, T.J. & Lilley, D.M.J. The evolution of ribozyme chemistry. Science 323, 1436-1438 (2009).
-
(2009)
Science
, vol.323
, pp. 1436-1438
-
-
Wilson, T.J.1
Lilley, D.M.J.2
-
14
-
-
19644391548
-
Model for general acid-base catalysis by the hammerhead ribozyme: PH-activity relationships of G8 and G12 variants at the putative active site
-
Han, J. & Burke, J.M. Model for general acid-base catalysis by the hammerhead ribozyme: pH-activity relationships of G8 and G12 variants at the putative active site. Biochemistry 44, 7864-7870 (2005).
-
(2005)
Biochemistry
, vol.44
, pp. 7864-7870
-
-
Han, J.1
Burke, J.M.2
-
15
-
-
33746228126
-
Tertiary contacts distant from the active site prime a ribozyme for catalysis
-
Martick, M. & Scott, W.G. Tertiary contacts distant from the active site prime a ribozyme for catalysis. Cell 126, 309-320 (2006).
-
(2006)
Cell
, vol.126
, pp. 309-320
-
-
Martick, M.1
Scott, W.G.2
-
16
-
-
36849061230
-
Essential role of an active-site guanine in glmS ribozyme catalysis
-
Klein, D.J., Been, M.D. & Ferré-D'Amaré, A.R. Essential role of an active-site guanine in glmS ribozyme catalysis. J. Am. Chem. Soc. 129, 14858-14859 (2007).
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 14858-14859
-
-
Klein, D.J.1
Been, M.D.2
Ferré-D'Amaré, A.R.3
-
17
-
-
34249098371
-
A guanine nucleobase important for catalysis by the VS ribozyme
-
Wilson, T.J., McLeod, A.C. & Lilley, D.M.J. A guanine nucleobase important for catalysis by the VS ribozyme. EMBO J. 26, 2489-2500 (2007).
-
(2007)
EMBO J.
, vol.26
, pp. 2489-2500
-
-
Wilson, T.J.1
McLeod, A.C.2
Lilley, D.M.J.3
-
18
-
-
65249184394
-
Structural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozyme
-
Cochrane, J.C., Lipchock, S.V., Smith, K.D. & Strobel, S.A. Structural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozyme. Biochemistry 48, 3239-3246 (2009).
-
(2009)
Biochemistry
, vol.48
, pp. 3239-3246
-
-
Cochrane, J.C.1
Lipchock, S.V.2
Smith, K.D.3
Strobel, S.A.4
-
19
-
-
84867356016
-
General acid-base catalysis mediated by nucleobases in the hairpin ribozyme
-
Kath-Schorr, S. et al. General acid-base catalysis mediated by nucleobases in the hairpin ribozyme. J. Am. Chem. Soc. 134, 16717-16724 (2012).
-
(2012)
J. Am. Chem. Soc.
, vol.134
, pp. 16717-16724
-
-
Kath-Schorr, S.1
-
20
-
-
0035965132
-
The A730 loop is an important component of the active site of the VS ribozyme
-
Lafontaine, D.A., Wilson, T.J., Norman, D.G. & Lilley, D.M.J. The A730 loop is an important component of the active site of the VS ribozyme. J. Mol. Biol. 312, 663-674 (2001).
-
(2001)
J. Mol. Biol.
, vol.312
, pp. 663-674
-
-
Lafontaine, D.A.1
Wilson, T.J.2
Norman, D.G.3
Lilley, D.M.J.4
-
21
-
-
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).
-
(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
-
22
-
-
77955394614
-
Nucleobase-mediated general acid-base catalysis in the Varkud satellite ribozyme
-
Wilson, T.J. et al. Nucleobase-mediated general acid-base catalysis in the Varkud satellite ribozyme. Proc. Natl. Acad. Sci. USA 107, 11751-11756 (2010).
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 11751-11756
-
-
Wilson, T.J.1
-
23
-
-
78751487465
-
Do the hairpin and VS ribozymes share a common catalytic mechanism based on general acid-base catalysis? A critical assessment of available experimental data
-
Wilson, T.J. & Lilley, D.M.J. Do the hairpin and VS ribozymes share a common catalytic mechanism based on general acid-base catalysis? A critical assessment of available experimental data. RNA 17, 213-221 (2011).
-
(2011)
RNA
, vol.17
, pp. 213-221
-
-
Wilson, T.J.1
Lilley, D.M.J.2
-
24
-
-
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
-
25
-
-
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).
-
(2004)
Nature
, vol.429
, pp. 201-205
-
-
Ke, A.1
Zhou, K.2
Ding, F.3
Cate, J.H.4
Doudna, J.A.5
-
26
-
-
24644454458
-
General acid catalysis by the hepatitis delta virus ribozyme
-
Das, S.R. & Piccirilli, J.A. General acid catalysis by the hepatitis delta virus ribozyme. Nat. Chem. Biol. 1, 45-52 (2005).
-
(2005)
Nat. Chem. Biol.
, vol.1
, pp. 45-52
-
-
Das, S.R.1
Piccirilli, J.A.2
-
27
-
-
77955258795
-
A 1.9-A crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage
-
Chen, J.H. et al. A 1.9-A crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage. Biochemistry 49, 6508-6518 (2010).
-
(2010)
Biochemistry
, vol.49
, pp. 6508-6518
-
-
Chen, J.H.1
-
28
-
-
41449099097
-
2+ in hammerhead ribozyme catalysis from molecular simulation
-
2+ in hammerhead ribozyme catalysis from molecular simulation. J. Am. Chem. Soc. 130, 3053-3064 (2008).
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 3053-3064
-
-
Lee, T.S.1
-
29
-
-
61749098364
-
Probing general acid catalysis in the hammerhead ribozyme
-
Thomas, J.M. & Perrin, D.M. Probing general acid catalysis in the hammerhead ribozyme. J. Am. Chem. Soc. 131, 1135-1143 (2009).
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 1135-1143
-
-
Thomas, J.M.1
Perrin, D.M.2
-
30
-
-
0035848837
-
Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis
-
Rupert, P.B. & Ferré-D'Amaré, A.R. Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis. Nature 410, 780-786 (2001).
-
(2001)
Nature
, vol.410
, pp. 780-786
-
-
Rupert, P.B.1
Ferré-D'Amaré, A.R.2
-
31
-
-
33846279049
-
Structural investigation of the GlmS ribozyme bound to its catalytic cofactor
-
Cochrane, J.C., Lipchock, S.V. & Strobel, S.A. Structural investigation of the GlmS ribozyme bound to its catalytic cofactor. Chem. Biol. 14, 97-105 (2007).
-
(2007)
Chem. Biol.
, vol.14
, pp. 97-105
-
-
Cochrane, J.C.1
Lipchock, S.V.2
Strobel, S.A.3
-
32
-
-
33748325570
-
Structural basis of glmS ribozyme activation by glucosamine-6-phosphate
-
Klein, D.J. & Ferré-D'Amaré, A.R. Structural basis of glmS ribozyme activation by glucosamine-6-phosphate. Science 313, 1752-1756 (2006).
-
(2006)
Science
, vol.313
, pp. 1752-1756
-
-
Klein, D.J.1
Ferré-D'Amaré, A.R.2
-
33
-
-
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
-
34
-
-
77955121660
-
Structure of the three-way helical junction of the hepatitis C virus IRES element
-
Ouellet, J., Melcher, S.E., Iqbal, A., Ding, Y. & Lilley, D.M.J. Structure of the three-way helical junction of the hepatitis C virus IRES element. RNA 16, 1597-1609 (2010).
-
(2010)
RNA
, vol.16
, pp. 1597-1609
-
-
Ouellet, J.1
Melcher, S.E.2
Iqbal, A.3
Ding, Y.4
Lilley, D.M.J.5
-
35
-
-
0043009768
-
A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate
-
Tan, E. et al. A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate. Proc. Natl. Acad. Sci. USA 100, 9308-9313 (2003).
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 9308-9313
-
-
Tan, E.1
-
36
-
-
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
-
37
-
-
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
-
38
-
-
50649108803
-
The complete VS ribozyme in solution studied by small-angle X-ray scattering
-
Lipfert, J., Ouellet, J., Norman, D.G., Doniach, S. & Lilley, D.M.J. The complete VS ribozyme in solution studied by small-angle X-ray scattering. Structure 16, 1357-1367 (2008).
-
(2008)
Structure
, vol.16
, pp. 1357-1367
-
-
Lipfert, J.1
Ouellet, J.2
Norman, D.G.3
Doniach, S.4
Lilley, D.M.J.5
-
39
-
-
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).
-
(1998)
Nature
, vol.395
, pp. 567-574
-
-
Ferré-D'Amaré, A.R.1
Zhou, K.2
Doudna, J.A.3
-
40
-
-
0041702195
-
Ribozyme speed limits
-
Emilsson, G.M., Nakamura, S., Roth, A. & Breaker, R.R. Ribozyme speed limits. RNA 9, 907-918 (2003).
-
(2003)
RNA
, vol.9
, pp. 907-918
-
-
Emilsson, G.M.1
Nakamura, S.2
Roth, A.3
Breaker, R.R.4
-
41
-
-
20344405966
-
Role of an active site adenine in hairpin ribozyme catalysis
-
Kuzmin, Y.I., Da Costa, C.P., Cottrell, J.W. & Fedor, M.J. Role of an active site adenine in hairpin ribozyme catalysis. J. Mol. Biol. 349, 989-1010 (2005).
-
(2005)
J. Mol. Biol.
, vol.349
, pp. 989-1010
-
-
Kuzmin, Y.I.1
Da Costa, C.P.2
Cottrell, J.W.3
Fedor, M.J.4
-
42
-
-
49149135789
-
Deoxynucleoside phosphoramidites - A new class of key intermediates for deoxypolynucleotide synthesis
-
Beaucage, S.L. & Caruthers, M.H. Deoxynucleoside phosphoramidites-a new class of key intermediates for deoxypolynucleotide synthesis. Tetrahedr. Lett. 22, 1859-1862 (1981).
-
(1981)
Tetrahedr. Lett.
, vol.22
, pp. 1859-1862
-
-
Beaucage, S.L.1
Caruthers, M.H.2
-
43
-
-
0035916297
-
Importance of specific nucleotides in the folding of the natural form of the hairpin ribozyme
-
Wilson, T.J., Zhao, Z.-Y., Maxwell, K., Kontogiannis, L. & Lilley, D.M.J. Importance of specific nucleotides in the folding of the natural form of the hairpin ribozyme. Biochemistry 40, 2291-2302 (2001).
-
(2001)
Biochemistry
, vol.40
, pp. 2291-2302
-
-
Wilson, T.J.1
Zhao, Z.-Y.2
Maxwell, K.3
Kontogiannis, L.4
Lilley, D.M.J.5
-
44
-
-
0000861288
-
High yield selective 3′-silylation of ribonucleosides
-
Hakimelahi, G.H., Proba, Z.A. & Ogilvie, K.K. High yield selective 3′-silylation of ribonucleosides. Tetrahedr. Lett. 22, 5243-5246 (1981).
-
(1981)
Tetrahedr. Lett.
, vol.22
, pp. 5243-5246
-
-
Hakimelahi, G.H.1
Proba, Z.A.2
Ogilvie, K.K.3
-
45
-
-
0025264597
-
Mixed deoxyribo- and ribooligonucleotides with catalytic activity
-
Perreault, J.-P., Wu, T., Cousineau, B., Ogilvie, K.K. & Cedergren, R. Mixed deoxyribo- and ribooligonucleotides with catalytic activity. Nature 344, 565-567 (1990).
-
(1990)
Nature
, vol.344
, pp. 565-567
-
-
Perreault, J.-P.1
Wu, T.2
Cousineau, B.3
Ogilvie, K.K.4
Cedergren, R.5
-
46
-
-
0023651444
-
Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates
-
Milligan, J.F., Groebe, D.R., Witherall, G.W. & Uhlenbeck, O.C. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 15, 8783-8798 (1987).
-
(1987)
Nucleic Acids Res.
, vol.15
, pp. 8783-8798
-
-
Milligan, J.F.1
Groebe, D.R.2
Witherall, G.W.3
Uhlenbeck, O.C.4
-
48
-
-
79953737180
-
Overview of the CCP4 suite and current developments
-
Winn, M.D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. D Biol. Crystallogr. 67, 235-242 (2011).
-
(2011)
Acta Crystallogr. D Biol. Crystallogr.
, vol.67
, pp. 235-242
-
-
Winn, M.D.1
-
49
-
-
76449098262
-
PHENIX: A comprehensive Python-based system for macromolecular structure solution
-
Adams, P.D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213-221 (2010).
-
(2010)
Acta Crystallogr. D Biol. Crystallogr.
, vol.66
, pp. 213-221
-
-
Adams, P.D.1
-
50
-
-
34447508216
-
Phaser crystallographic software
-
McCoy, A.J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658-674 (2007).
-
(2007)
J. Appl. Crystallogr.
, vol.40
, pp. 658-674
-
-
McCoy, A.J.1
-
51
-
-
77949535720
-
Features and development of Coot
-
Emsley, P., Lohkamp, B., Scott, W.G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486-501 (2010).
-
(2010)
Acta Crystallogr. D Biol. Crystallogr.
, vol.66
, pp. 486-501
-
-
Emsley, P.1
Lohkamp, B.2
Scott, W.G.3
Cowtan, K.4
-
52
-
-
79953763877
-
REFMAC5 for the refinement of macromolecular crystal structures
-
Murshudov, G.N. et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D Biol. Crystallogr. 67, 355-367 (2011).
-
(2011)
Acta Crystallogr. D Biol. Crystallogr.
, vol.67
, pp. 355-367
-
-
Murshudov, G.N.1
|