-
1
-
-
0021012648
-
Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids
-
Woese, C. R., Gutell, R., Gupta, R. and Noller, H. F. (1983) Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids. Microbiol. Rev., 47, 621-669.
-
(1983)
Microbiol. Rev.
, vol.47
, pp. 621-669
-
-
Woese, C.R.1
Gutell, R.2
Gupta, R.3
Noller, H.F.4
-
2
-
-
0001791833
-
-
Zimmermann, R. A. and Dahlberg, A. E. (eds) CRC Press, Boca Raton, Florida
-
Gutell, R. R. (1995) In: Zimmermann, R. A. and Dahlberg, A. E. (eds), Ribosomal RNA: Structure, Evolution, Processing, and Function in Protein Biosynthesis. CRC Press, Boca Raton, Florida, pp. 109-126.
-
(1995)
Ribosomal RNA: Structure, Evolution, Processing, and Function in Protein Biosynthesis
, pp. 109-126
-
-
Gutell, R.R.1
-
3
-
-
0034637111
-
The complete structure of the large ribosomal subunit at 2. 4 A° resolution
-
Ban, N., Nissen, P., Hansen, J., Moore, P. B. and Steitz, T. A. (2000) The complete structure of the large ribosomal subunit at 2. 4 A° resolution. Science, 289, 905-920.
-
(2000)
Science
, vol.289
, pp. 905-920
-
-
Ban, N.1
Nissen, P.2
Hansen, J.3
Moore, P.B.4
Steitz, T.A.5
-
4
-
-
0025678737
-
Modelling of the three-dimensional architecture of group i catalytic introns based on comparative sequence analysis
-
Michel, F. and Westhof, E. (1990) Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol. Biol., 216, 585-610.
-
(1990)
J. Mol. Biol.
, vol.216
, pp. 585-610
-
-
Michel, F.1
Westhof, E.2
-
5
-
-
3042848954
-
Crystal structure of a self-splicing group i intron with both exons
-
Adams, P. L., Stahley, M. R., Kosek, A. B., Wang, J. and Strobel, S. A. (2004) Crystal structure of a self-splicing group I intron with both exons. Nature, 430, 45-50.
-
(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
-
6
-
-
11444263264
-
Crystal structure of a phage Twort group i ribozyme-product complex
-
Golden, B. L., Kim, H. and Chase, E. (2004) Crystal structure of a phage Twort group I ribozyme-product complex. Nat. Struct. Mol. Biol., 12, 82-88.
-
(2004)
Nat. Struct. Mol. Biol.
, vol.12
, pp. 82-88
-
-
Golden, B.L.1
Kim, H.2
Chase, E.3
-
7
-
-
0031581851
-
Structural rules and conformational compensations in the tRNA L-form
-
Steinberg, S., Leclerc, F. and Cedergren, R. (1997) Structural rules and conformational compensations in the tRNA L-form. J. Mol. Biol., 266, 269-282.
-
(1997)
J. Mol. Biol.
, vol.266
, pp. 269-282
-
-
Steinberg, S.1
Leclerc, F.2
Cedergren, R.3
-
8
-
-
0036865381
-
The Neurospora Varkud satellite ribozyme
-
Collins, R. A. (2002) The Neurospora Varkud satellite ribozyme. Bioch. Soc. Trans. Rev., 30, 1122-1126.
-
(2002)
Bioch. Soc. Trans. Rev.
, vol.30
, pp. 1122-1126
-
-
Collins, R.A.1
-
9
-
-
1642580826
-
The Varkud satellite ribozyme
-
Lilley, D. M. (2004) The Varkud satellite ribozyme. RNA, 10, 151-158.
-
(2004)
RNA
, vol.10
, pp. 151-158
-
-
Lilley, D.M.1
-
10
-
-
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. and Lilley, D. M. (2011) 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)
RNA
, vol.17
, pp. 213-221
-
-
Wilson, T.J.1
Lilley, D.M.2
-
11
-
-
0029948820
-
A long-range pseudoknot is required for activity of the Neurospora VS ribozyme
-
Rastogi, T., Beattie, T. L., Olive, J. E. and Collins, R. A. (1996) A long-range pseudoknot is required for activity of the Neurospora VS ribozyme. EMBO J., 15, 2820-2825.
-
(1996)
EMBO J.
, vol.15
, pp. 2820-2825
-
-
Rastogi, T.1
Beattie, T.L.2
Olive, J.E.3
Collins, R.A.4
-
12
-
-
0033680079
-
Rearrangement of a stable RNA secondary structure during VS ribozyme catalysis
-
Andersen, A. and Collins, R. A. (2000) Rearrangement of a stable RNA secondary structure during VS ribozyme catalysis. Mol. Cell, 5, 469-478.
-
(2000)
Mol. Cell
, vol.5
, pp. 469-478
-
-
Andersen, A.1
Collins, R.A.2
-
13
-
-
0034940798
-
Intramolecular secondary structure rearrangement by the kissing interaction of the Neurospora VS ribozyme
-
Andersen, A. A. and Collins, R. A. (2001) Intramolecular secondary structure rearrangement by the kissing interaction of the Neurospora VS ribozyme. Proc. Natl Acad. Sci. USA, 98, 7730-7735.
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 7730-7735
-
-
Andersen, A.A.1
Collins, R.A.2
-
14
-
-
0035476689
-
Rapid formation of a solvent-inaccessible core in the Neurospora Varkud satellite ribozyme
-
Hiley, S. L. and Collins, R. A. (2001) Rapid formation of a solvent-inaccessible core in the Neurospora Varkud satellite ribozyme. EMBO J., 20, 5461-5469.
-
(2001)
EMBO J.
, vol.20
, pp. 5461-5469
-
-
Hiley, S.L.1
Collins, R.A.2
-
15
-
-
0035869008
-
Structure, folding and activity of the VS ribozyme: Importance of the 2-3-6 helical junction
-
Lafontaine, D. A., Norman, D. G. and Lilley, D. M. (2001) Structure, folding and activity of the VS ribozyme: importance of the 2-3-6 helical junction. EMBO J., 20, 1415-1424.
-
(2001)
EMBO J.
, vol.20
, pp. 1415-1424
-
-
Lafontaine, D.A.1
Norman, D.G.2
Lilley, D.M.3
-
16
-
-
0037093486
-
The global structure of the VS ribozyme
-
Lafontaine, D. A., Norman, D. G. and Lilley, D. M. (2002) The global structure of the VS ribozyme. EMBO J., 21, 2461-2471.
-
(2002)
EMBO J.
, vol.21
, pp. 2461-2471
-
-
Lafontaine, D.A.1
Norman, D.G.2
Lilley, D.M.3
-
17
-
-
50649108803
-
The complete VS ribozyme in solution studied by small-angle X-ray scattering
-
Lipfert, J., Ouellet, J., Norman, D. G., Doniach, S. and Lilley, D. M. (2008) The complete VS ribozyme in solution studied by small-angle X-ray scattering. Structure, 16, 1357-1367.
-
(2008)
Structure
, vol.16
, pp. 1357-1367
-
-
Lipfert, J.1
Ouellet, J.2
Norman, D.G.3
Doniach, S.4
Lilley, D.M.5
-
18
-
-
41649114425
-
Role of SLV in SLI substrate recognition by the Neurospora VS ribozyme
-
Bouchard, P., Lacroix-Labonte , J., Desjardins, G., Lampron, P., Lisi, V., Lemieux, S., Major, F. and Legault, P. (2008) Role of SLV in SLI substrate recognition by the Neurospora VS ribozyme. RNA, 14, 736-748.
-
(2008)
RNA
, vol.14
, pp. 736-748
-
-
Bouchard, P.1
Lacroix-Labonte, J.2
Desjardins, G.3
Lampron, P.4
Lisi, V.5
Lemieux, S.6
Major, F.7
Legault, P.8
-
19
-
-
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. and Lilley, D. M. (2001) The A730 loop is an important component of the active site of the VS ribozyme. J. Mol. Biol., 312, 663-674.
-
(2001)
J. Mol. Biol.
, vol.312
, pp. 663-674
-
-
Lafontaine, D.A.1
Wilson, T.J.2
Norman, D.G.3
Lilley, D.M.4
-
20
-
-
0036396544
-
Functional group requirements in the probable active site of the VS ribozyme
-
Lafontaine, D. A., Wilson, T. J., Zhao, Z.-Y. and Lilley, D. M. J. (2002) Functional group requirements in the probable active site of the VS ribozyme. J. Mol. Biol., 323, 23-34.
-
(2002)
J. Mol. Biol.
, vol.323
, pp. 23-34
-
-
Lafontaine, D.A.1
Wilson, T.J.2
Zhao, Z.-Y.3
Lilley, D.M.J.4
-
21
-
-
0036314853
-
Identification of the catalytic subdomain of the VS ribozyme and evidence for remarkable sequence tolerance in the active site loop
-
Sood, V. D. and Collins, R. A. (2002) Identification of the catalytic subdomain of the VS ribozyme and evidence for remarkable sequence tolerance in the active site loop. J. Mol. Biol., 320, 443-454.
-
(2002)
J. Mol. Biol.
, vol.320
, pp. 443-454
-
-
Sood, V.D.1
Collins, R.A.2
-
22
-
-
0037446518
-
Ionization of a critical adenosine residue in the Neurospora Varkud satellite ribozyme active site
-
Jones, F. D. and Strobel, S. A. (2003) Ionization of a critical adenosine residue in the Neurospora Varkud satellite ribozyme active site. Biochemistry, 42, 4265-4276.
-
(2003)
Biochemistry
, vol.42
, pp. 4265-4276
-
-
Jones, F.D.1
Strobel, S.A.2
-
23
-
-
17144407220
-
Nucleobase participation in ribozyme catalysis
-
Zhao, Z. Y., McLeod, A., Harusawa, S., Araki, L., Yamaguchi, M., Kurihara, T. and Lilley, D. M. (2005) Nucleobase participation in ribozyme catalysis. J. Am. Chem. Soc., 127, 5026-5027.
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 5026-5027
-
-
Zhao, Z.Y.1
McLeod, A.2
Harusawa, S.3
Araki, L.4
Yamaguchi, M.5
Kurihara, T.6
Lilley, D.M.7
-
24
-
-
34249098371
-
A guanine nucleobase important for catalysis by the VS ribozyme
-
Wilson, T. J., McLeod, A. C. and Lilley, D. M. (2007) A guanine nucleobase important for catalysis by the VS ribozyme. EMBO J., 26, 2489-2500.
-
(2007)
EMBO J.
, vol.26
, pp. 2489-2500
-
-
Wilson, T.J.1
McLeod, A.C.2
Lilley, D.M.3
-
25
-
-
34347246717
-
Evidence for proton transfer in the rate-limiting step of a fast-cleaving Varkud satellite ribozyme
-
Smith, M. D. and Collins, R. A. (2007) Evidence for proton transfer in the rate-limiting step of a fast-cleaving Varkud satellite ribozyme. Proc. Natl Acad. Sci. USA, 104, 5818-5823.
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 5818-5823
-
-
Smith, M.D.1
Collins, R.A.2
-
26
-
-
42449110782
-
An important role of G638 in the cis-cleavage reaction of the Neurospora VS ribozyme revealed by a novel nucleotide analog incorporation method
-
Jaikaran, D., Smith, M. D., Mehdizadeh, R., Olive, J. and Collins, R. A. (2008) An important role of G638 in the cis-cleavage reaction of the Neurospora VS ribozyme revealed by a novel nucleotide analog incorporation method. RNA, 14, 938-949.
-
(2008)
RNA
, vol.14
, pp. 938-949
-
-
Jaikaran, D.1
Smith, M.D.2
Mehdizadeh, R.3
Olive, J.4
Collins, R.A.5
-
27
-
-
77955394614
-
Nucleobase-mediated general acid-base catalysis in the Varkud satellite ribozyme
-
Wilson, T. J., Li, N. S., Lu, J., Frederiksen, J. K., Piccirilli, J. A. and Lilley, D. M. (2010) Nucleobase-mediated general acid-base catalysis in the Varkud satellite ribozyme. Proc. Natl Acad. Sci. USA, 107, 11751-11756.
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 11751-11756
-
-
Wilson, T.J.1
Li, N.S.2
Lu, J.3
Frederiksen, J.K.4
Piccirilli, J.A.5
Lilley, D.M.6
-
28
-
-
0032571266
-
Smaller, faster ribozymes reveal the catalytic core of Neurospora VS RNA
-
Rastogi, T. and Collins, R. A. (1998) Smaller, faster ribozymes reveal the catalytic core of Neurospora VS RNA. J. Mol. Biol., 277, 215-224.
-
(1998)
J. Mol. Biol.
, vol.277
, pp. 215-224
-
-
Rastogi, T.1
Collins, R.A.2
-
29
-
-
0028855671
-
Efficient trans-cleavage of a stem-loop RNA substrate by a ribozyme derived from Neurospora VS RNA
-
Guo, H. C. T. and Collins, R. A. (1995) Efficient trans-cleavage of a stem-loop RNA substrate by a ribozyme derived from Neurospora VS RNA. EMBO J., 14, 368-376.
-
(1995)
EMBO J.
, vol.14
, pp. 368-376
-
-
Guo, H.C.T.1
Collins, R.A.2
-
30
-
-
0026077710
-
The combination of symbolic and numerical computation for three-dimensional modeling of RNA
-
Major, F., Turcotte, M., Gautheret, D., Lapalme, G., Fillion, E. and Cedergren, R. (1991) The combination of symbolic and numerical computation for three-dimensional modeling of RNA. Science, 253, 1255-1260.
-
(1991)
Science
, vol.253
, pp. 1255-1260
-
-
Major, F.1
Turcotte, M.2
Gautheret, D.3
Lapalme, G.4
Fillion, E.5
Cedergren, R.6
-
31
-
-
33748264614
-
NMR structure of Varkud satellite ribozyme stem-loop v in the presence of magnesium ions and localization of metal-binding sites
-
Campbell, D. O., Bouchard, P., Desjardins, G. and Legault, P. (2006) NMR structure of Varkud satellite ribozyme stem-loop V in the presence of magnesium ions and localization of metal-binding sites. Biochemistry, 45, 10591-10605.
-
(2006)
Biochemistry
, vol.45
, pp. 10591-10605
-
-
Campbell, D.O.1
Bouchard, P.2
Desjardins, G.3
Legault, P.4
-
32
-
-
0038810208
-
NMR structure of the active conformation of the Varkud satellite ribozyme cleavage site
-
Hoffmann, B., Mitchell, G. T., Gendron, P., Major, F., Andersen, A. A., Collins, R. A. and Legault, P. (2003) NMR structure of the active conformation of the Varkud satellite ribozyme cleavage site. Proc. Natl Acad. Sci. USA, 100, 7003-7008.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 7003-7008
-
-
Hoffmann, B.1
Mitchell, G.T.2
Gendron, P.3
Major, F.4
Andersen, A.A.5
Collins, R.A.6
Legault, P.7
-
33
-
-
0029633186
-
Amber, a package of computer-programs for applying molecular mechanics, normal-mode analysis, molecular-dynamics and free-energy calculations to simulate the structural and energetic properties of molecules
-
Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheatham, T. E., Debolt, S., Ferguson, D., Seibel, G. and Kollman, P. (1995) Amber, a package of computer-programs for applying molecular mechanics, normal-mode analysis, molecular-dynamics and free-energy calculations to simulate the structural and energetic properties of molecules. Comput. Phys. Commun., 91, 1-41.
-
(1995)
Comput. Phys. Commun.
, vol.91
, pp. 1-41
-
-
Pearlman, D.A.1
Case, D.A.2
Caldwell, J.W.3
Ross, W.S.4
Cheatham, T.E.5
Debolt, S.6
Ferguson, D.7
Seibel, G.8
Kollman, P.9
-
34
-
-
0344778061
-
Semianalytical treatment of solvation for molecular mechanics and dynamics
-
Still, W. C., Tempczyk, A., Hawley, R. C. and Hendrickson, T. (1990) Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc., 112, 6127-6129.
-
(1990)
J. Am. Chem. Soc.
, vol.112
, pp. 6127-6129
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.C.3
Hendrickson, T.4
-
35
-
-
70450261721
-
Conformational analysis of nucleic acids revisited: Curves+
-
Lavery, R., Moakher, M., Maddocks, J. H., Petkeviciute, D. and Zakrzewska, K. (2009) Conformational analysis of nucleic acids revisited: Curves+. Nucleic Acids Res., 37, 5917-5929.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 5917-5929
-
-
Lavery, R.1
Moakher, M.2
Maddocks, J.H.3
Petkeviciute, D.4
Zakrzewska, K.5
-
36
-
-
84872636119
-
An approximate distribution of estimates of variance components
-
Satterthwaite, F. E. (1946) An approximate distribution of estimates of variance components. Biometrics, 2, 110-114.
-
(1946)
Biometrics
, vol.2
, pp. 110-114
-
-
Satterthwaite, F.E.1
-
37
-
-
0000898845
-
An analysis of variance test for normality (complete samples)
-
Shapiro, S. S. and Wilk, M. B. (1965) An analysis of variance test for normality (complete samples). Biometrika, 52, 591-611.
-
(1965)
Biometrika
, vol.52
, pp. 591-611
-
-
Shapiro, S.S.1
Wilk, M.B.2
-
38
-
-
0029011972
-
A secondary-structure model for the self-cleaving region of Neurospora VS RNA
-
Beattie, T. L., Olive, J. E. and Collins, R. A. (1995) A secondary-structure model for the self-cleaving region of Neurospora VS RNA. Proc. Natl Acad. Sci. USA, 92, 4686-4690.
-
(1995)
Proc. Natl Acad. Sci. USA
, vol.92
, pp. 4686-4690
-
-
Beattie, T.L.1
Olive, J.E.2
Collins, R.A.3
-
39
-
-
0007972388
-
RNA structure, not sequence, determines the 50 splice-site specificity of a group i intron
-
Doudna, J. A., Cormack, B. P. and Szostak, J. W. (1989) RNA structure, not sequence, determines the 50 splice-site specificity of a group I intron. Proc. Natl Acad. Sci. USA, 86, 7402-7406.
-
(1989)
Proc. Natl Acad. Sci. USA
, vol.86
, pp. 7402-7406
-
-
Doudna, J.A.1
Cormack, B.P.2
Szostak, J.W.3
-
40
-
-
77952896659
-
Compact intermediates in RNA folding
-
Woodson, S. A. (2010) Compact intermediates in RNA folding. Annu. Rev. Biophys., 39, 61-77.
-
(2010)
Annu. Rev. Biophys.
, vol.39
, pp. 61-77
-
-
Woodson, S.A.1
-
41
-
-
79958069365
-
Topological constraints: Using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation
-
Bailor, M. H., Mustoe, A. M., Brooks, C. L. 3rd and Al-Hashimi, H. M. (2011) Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation. Curr. Opin. Struct. Biol, 21, 296-305.
-
(2011)
Curr. Opin. Struct. Biol
, vol.21
, pp. 296-305
-
-
Bailor, M.H.1
Mustoe, A.M.2
Brooks III, C.L.3
Al-Hashimi, H.M.4
-
42
-
-
0030761966
-
An RNA internal loop acts as a hinge to facilitate ribozyme folding and catalysis
-
Szewczak, A. A. and Cech, T. R. (1997) An RNA internal loop acts as a hinge to facilitate ribozyme folding and catalysis. RNA, 3, 838-849.
-
(1997)
RNA
, vol.3
, pp. 838-849
-
-
Szewczak, A.A.1
Cech, T.R.2
-
43
-
-
74249115345
-
Topology links RNA secondary structure with global conformation, dynamics, and adaptation
-
Bailor, M. H., Sun, X. and Al-Hashimi, H. M. (2010) Topology links RNA secondary structure with global conformation, dynamics, and adaptation. Science, 327, 202-206.
-
(2010)
Science
, vol.327
, pp. 202-206
-
-
Bailor, M.H.1
Sun, X.2
Al-Hashimi, H.M.3
-
44
-
-
0031806709
-
Schistosome satellite DNA encodes active hammerhead ribozymes
-
Ferbeyre, G., Smith, J. M. and Cedergren, R. (1998) Schistosome satellite DNA encodes active hammerhead ribozymes. Mol. Cell. Biol., 18, 3880-3888.
-
(1998)
Mol. Cell. Biol.
, vol.18
, pp. 3880-3888
-
-
Ferbeyre, G.1
Smith, J.M.2
Cedergren, R.3
-
45
-
-
21044451884
-
A database search for hammerhead ribozyme motifs
-
Gräf, S., Przybilski, R., Steger, G. and Hamman, C. (2005) A database search for hammerhead ribozyme motifs. Biochem. Soc. Trans., 33, 477-478.
-
(2005)
Biochem. Soc. Trans.
, vol.33
, pp. 477-478
-
-
Gräf, S.1
Przybilski, R.2
Steger, G.3
Hamman, C.4
-
46
-
-
34548712632
-
Searching genomes for ribozymes and riboswitches
-
Hammann, C. and Westhof, E. (2007) Searching genomes for ribozymes and riboswitches. Genome Biol., 8, 210.
-
(2007)
Genome Biol.
, vol.8
, pp. 210
-
-
Hammann, C.1
Westhof, E.2
-
47
-
-
79952996320
-
An expanded collection and refined consensus model of glmS ribozymes
-
McCown, P. J., Roth, A. and Breaker, R. R. (2011) An expanded collection and refined consensus model of glmS ribozymes. RNA, 17, 728-736.
-
(2011)
RNA
, vol.17
, pp. 728-736
-
-
McCown, P.J.1
Roth, A.2
Breaker, R.R.3
|