-
1
-
-
0020417286
-
Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena
-
K. Kruger, P.J. Grabowski, A.J. Zaug, J. Sands, D.E. Gottschling, and T.R. Cech Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena Cell 31 1982 147 157
-
(1982)
Cell
, vol.31
, pp. 147-157
-
-
Kruger, K.1
Grabowski, P.J.2
Zaug, A.J.3
Sands, J.4
Gottschling, D.E.5
Cech, T.R.6
-
2
-
-
0036863325
-
Ribozymes, the first 20 years
-
T.R. Cech Ribozymes, the first 20 years Biochem Soc Trans 30 2002 1162 1166
-
(2002)
Biochem Soc Trans
, vol.30
, pp. 1162-1166
-
-
Cech, T.R.1
-
3
-
-
0037062949
-
The chemical repertoire of natural ribozymes
-
J.A. Doudna, and T.R. Cech The chemical repertoire of natural ribozymes Nature 418 2002 222 228
-
(2002)
Nature
, vol.418
, pp. 222-228
-
-
Doudna, J.A.1
Cech, T.R.2
-
4
-
-
0002160687
-
Building a catalytic active site using only RNA
-
R.F. Gesteland T.R. Cech J.F. Atkins edn 2 Cold Spring Harbor Laboratory Press
-
T.R. Cech, and B.L. Golden Building a catalytic active site using only RNA R.F. Gesteland T.R. Cech J.F. Atkins The RNA World edn 2 1999 Cold Spring Harbor Laboratory Press 321 349
-
(1999)
The RNA World
, pp. 321-349
-
-
Cech, T.R.1
Golden, B.L.2
-
5
-
-
3042848954
-
Crystal structure of a self-splicing group I intron with both exons
-
P.L. Adams, M.R. Stahley, A.B. Kosek, J. Wang, and S.A. Strobel Crystal structure of a self-splicing group I intron with both exons Nature 430 2004 45 50 The first structure of a bacterial group I splicing complex, including two metal ions localized to the active site. The complex was trapped in a state imitating the conformation before the second step of splicing, with four deoxyribose substitutions adjacent to splice sites.
-
(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
-
B.L. Golden, H. Kim, and E. Chase Crystal structure of a phage Twort group I ribozyme-product complex Nat Struct Mol Biol 12 2005 82 89 The structure of a 5′ exon product complex with a 3′ ribose provides additional details of intron tertiary structure, including the first detailed look at peripheral domains unique to this intron subclass.
-
(2005)
Nat Struct Mol Biol
, vol.12
, pp. 82-89
-
-
Golden, B.L.1
Kim, H.2
Chase, E.3
-
7
-
-
8644229237
-
Structure of the Tetrahymena ribozyme: Base triple sandwich and metal ion at the active site
-
F. Guo, A.R. Gooding, and T.R. Cech Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site Mol Cell 16 2004 351 362 Stabilizing mutations enabled the authors to obtain a higher resolution model of the Tetrahymena ribozyme, the group I intron that has been most studied biochemically. The new structure shows details of the guanosine-binding site and interdomain interactions.
-
(2004)
Mol Cell
, vol.16
, pp. 351-362
-
-
Guo, F.1
Gooding, A.R.2
Cech, T.R.3
-
8
-
-
0020198881
-
Comparison of fungal mitochondrial introns reveals extensive homologies in RNA secondary structure
-
F. Michel, A. Jacquier, and B. Dujon Comparison of fungal mitochondrial introns reveals extensive homologies in RNA secondary structure Biochimie 64 1982 867 881
-
(1982)
Biochimie
, vol.64
, pp. 867-881
-
-
Michel, F.1
Jacquier, A.2
Dujon, B.3
-
9
-
-
0023462809
-
Three-dimensional model of the active site of the self-splicing rRNA precursor of Tetrahymena
-
S.H. Kim, and T.R. Cech Three-dimensional model of the active site of the self-splicing rRNA precursor of Tetrahymena Proc Natl Acad Sci USA 84 1987 8788 8792
-
(1987)
Proc Natl Acad Sci USA
, vol.84
, pp. 8788-8792
-
-
Kim, S.H.1
Cech, T.R.2
-
10
-
-
0025678737
-
Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis
-
F. Michel, and E. Westhof Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis J Mol Biol 216 1990 585 610
-
(1990)
J Mol Biol
, vol.216
, pp. 585-610
-
-
Michel, F.1
Westhof, E.2
-
11
-
-
0029820625
-
Crystal structure of a group I ribozyme domain: Principles of RNA packing
-
J.H. Cate, A.R. Gooding, E. Podell, K. Zhou, B.L. Golden, C.E. Kundrot, T.R. Cech, and J.A. Doudna Crystal structure of a group I ribozyme domain: principles of RNA packing Science 273 1996 1678 1685
-
(1996)
Science
, vol.273
, pp. 1678-1685
-
-
Cate, J.H.1
Gooding, A.R.2
Podell, E.3
Zhou, K.4
Golden, B.L.5
Kundrot, C.E.6
Cech, T.R.7
Doudna, J.A.8
-
12
-
-
0035085466
-
Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA-solvent interactions
-
K. Juneau, E. Podell, D.J. Harrington, and T.R. Cech Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA-solvent interactions Structure 9 2001 221 231
-
(2001)
Structure
, vol.9
, pp. 221-231
-
-
Juneau, K.1
Podell, E.2
Harrington, D.J.3
Cech, T.R.4
-
13
-
-
0032500731
-
A preorganized active site in the crystal structure of the Tetrahymena ribozyme
-
B.L. Golden, A.R. Gooding, E.R. Podell, and T.R. Cech A preorganized active site in the crystal structure of the Tetrahymena ribozyme Science 282 1998 259 264
-
(1998)
Science
, vol.282
, pp. 259-264
-
-
Golden, B.L.1
Gooding, A.R.2
Podell, E.R.3
Cech, T.R.4
-
14
-
-
0024427177
-
The guanosine binding site of the Tetrahymena ribozyme
-
F. Michel, M. Hanna, R. Green, D.P. Bartel, and J.W. Szostak The guanosine binding site of the Tetrahymena ribozyme Nature 342 1989 391 395
-
(1989)
Nature
, vol.342
, pp. 391-395
-
-
Michel, F.1
Hanna, M.2
Green, R.3
Bartel, D.P.4
Szostak, J.W.5
-
15
-
-
0031984645
-
Complementary sets of noncanonical base pairs mediate RNA helix packing in the group I intron active site
-
S.A. Strobel, L. Ortoleva-Donnelly, S.P. Ryder, J.H. Cate, and E. Moncoeur Complementary sets of noncanonical base pairs mediate RNA helix packing in the group I intron active site Nat Struct Biol 5 1998 60 66
-
(1998)
Nat Struct Biol
, vol.5
, pp. 60-66
-
-
Strobel, S.A.1
Ortoleva-Donnelly, L.2
Ryder, S.P.3
Cate, J.H.4
Moncoeur, E.5
-
16
-
-
12044255049
-
Movement of the guide sequence during RNA catalysis by a group I ribozyme
-
J.F. Wang, W.D. Downs, and T.R. Cech Movement of the guide sequence during RNA catalysis by a group I ribozyme Science 260 1993 504 508
-
(1993)
Science
, vol.260
, pp. 504-508
-
-
Wang, J.F.1
Downs, W.D.2
Cech, T.R.3
-
18
-
-
0346422450
-
Artificial modules for enhancing rate constants of a group I intron ribozyme without a P4-P6 core element
-
S.J. Ohuchi, Y. Ikawa, H. Shiraishi, and T. Inoue Artificial modules for enhancing rate constants of a group I intron ribozyme without a P4-P6 core element J Biol Chem 279 2004 540 546 This paper, together with [17], shows that the P3-P9 domain alone retains partial catalytic activity.
-
(2004)
J Biol Chem
, vol.279
, pp. 540-546
-
-
Ohuchi, S.J.1
Ikawa, Y.2
Shiraishi, H.3
Inoue, T.4
-
19
-
-
0033607225
-
Three metal ions at the active site of the Tetrahymena group I ribozyme
-
S. Shan, A. Yoshida, S. Sun, J.A. Piccirilli, and D. Herschlag Three metal ions at the active site of the Tetrahymena group I ribozyme Proc Natl Acad Sci USA 96 1999 12299 12304
-
(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
-
20
-
-
0035340961
-
Defining the catalytic metal ion interactions in the Tetrahymena ribozyme reaction
-
S. Shan, A.V. Kravchuk, J.A. Piccirilli, and D. Herschlag Defining the catalytic metal ion interactions in the Tetrahymena ribozyme reaction Biochemistry 40 2001 5161 5171
-
(2001)
Biochemistry
, vol.40
, pp. 5161-5171
-
-
Shan, S.1
Kravchuk, A.V.2
Piccirilli, J.A.3
Herschlag, D.4
-
22
-
-
0027184481
-
A general two-metal-ion mechanism for catalytic RNA
-
T.A. Steitz, and J.A. Steitz A general two-metal-ion mechanism for catalytic RNA Proc Natl Acad Sci USA 90 1993 6498 6502
-
(1993)
Proc Natl Acad Sci USA
, vol.90
, pp. 6498-6502
-
-
Steitz, T.A.1
Steitz, J.A.2
-
23
-
-
0029985347
-
The environment of two metal ions surrounding the splice site of a group I intron
-
B. Streicher, E. Westhof, and R. Schroeder The environment of two metal ions surrounding the splice site of a group I intron EMBO J 15 1996 2556 2564
-
(1996)
EMBO J
, vol.15
, pp. 2556-2564
-
-
Streicher, B.1
Westhof, E.2
Schroeder, R.3
-
24
-
-
0027247579
-
Metal coordination sites that contribute to structure and catalysis in the group I intron from Tetrahymena
-
E.L. Christian, and M. Yarus Metal coordination sites that contribute to structure and catalysis in the group I intron from Tetrahymena Biochemistry 32 1993 4475 4480
-
(1993)
Biochemistry
, vol.32
, pp. 4475-4480
-
-
Christian, E.L.1
Yarus, M.2
-
25
-
-
0034665747
-
A chemical phylogeny of group I introns based upon interference mapping of a bacterial ribozyme
-
J.K. Strauss-Soukup, and S.A. Strobel A chemical phylogeny of group I introns based upon interference mapping of a bacterial ribozyme J Mol Biol 302 2000 339 358
-
(2000)
J Mol Biol
, vol.302
, pp. 339-358
-
-
Strauss-Soukup, J.K.1
Strobel, S.A.2
-
26
-
-
0038737980
-
2+ binding in the group I intron core
-
2+ binding in the group I intron core J Mol Biol 329 2003 229 238
-
(2003)
J Mol Biol
, vol.329
, pp. 229-238
-
-
Rangan, P.1
Woodson, S.A.2
-
27
-
-
9344232753
-
Crystal structure of a group I intron splicing intermediate
-
P.L. Adams, M.R. Stahley, M.L. Gill, A.B. Kosek, J. Wang, and S.A. Strobel Crystal structure of a group I intron splicing intermediate RNA 10 2004 1867 1887 An exquisitely detailed analysis of tertiary interactions in the bacterial splicing complex. RNA structure enthusiasts will find schematic diagrams of base hydrogen bonds and stacking interactions especially helpful.
-
(2004)
RNA
, vol.10
, pp. 1867-1887
-
-
Adams, P.L.1
Stahley, M.R.2
Gill, M.L.3
Kosek, A.B.4
Wang, J.5
Strobel, S.A.6
-
30
-
-
0026729278
-
RNA substrate binding site in the catalytic core of the Tetrahymena ribozyme
-
A.M. Pyle, F.L. Murphy, and T.R. Cech RNA substrate binding site in the catalytic core of the Tetrahymena ribozyme Nature 358 1992 123 128
-
(1992)
Nature
, vol.358
, pp. 123-128
-
-
Pyle, A.M.1
Murphy, F.L.2
Cech, T.R.3
-
31
-
-
0037143508
-
Identification of A-minor tertiary interactions within a bacterial group I intron active site by 3-deazaadenosine interference mapping
-
J.K. Soukup, N. Minakawa, A. Matsuda, and S.A. Strobel Identification of A-minor tertiary interactions within a bacterial group I intron active site by 3-deazaadenosine interference mapping Biochemistry 41 2002 10426 10438
-
(2002)
Biochemistry
, vol.41
, pp. 10426-10438
-
-
Soukup, J.K.1
Minakawa, N.2
Matsuda, A.3
Strobel, S.A.4
-
32
-
-
0025134897
-
Phylogenetic and genetic evidence for base-triples in the catalytic domain of group I introns
-
F. Michel, A.D. Ellington, S. Couture, and J.W. Szostak Phylogenetic and genetic evidence for base-triples in the catalytic domain of group I introns Nature 347 1990 578 580
-
(1990)
Nature
, vol.347
, pp. 578-580
-
-
Michel, F.1
Ellington, A.D.2
Couture, S.3
Szostak, J.W.4
-
33
-
-
0024432780
-
A conserved base pair within helix P4 of the Tetrahymena ribozyme helps to form the tertiary structure required for self-splicing
-
P.J. Flor, J.B. Flanegan, and T.R. Cech A conserved base pair within helix P4 of the Tetrahymena ribozyme helps to form the tertiary structure required for self-splicing EMBO J 8 1989 3391 3399
-
(1989)
EMBO J
, vol.8
, pp. 3391-3399
-
-
Flor, P.J.1
Flanegan, J.B.2
Cech, T.R.3
-
34
-
-
0027958767
-
In vitro genetic analysis of the hinge region between helical elements P5-P4-P6 and P7-P3-P8 in the sunY group I self-splicing intron
-
R. Green, and J.W. Szostak In vitro genetic analysis of the hinge region between helical elements P5-P4-P6 and P7-P3-P8 in the sunY group I self-splicing intron J Mol Biol 235 1994 140 155
-
(1994)
J Mol Biol
, vol.235
, pp. 140-155
-
-
Green, R.1
Szostak, J.W.2
-
35
-
-
0029258956
-
Self-assembly of a group I intron active site from its component tertiary structural domains
-
J.A. Doudna, and T.R. Cech Self-assembly of a group I intron active site from its component tertiary structural domains RNA 1 1995 36 45
-
(1995)
RNA
, vol.1
, pp. 36-45
-
-
Doudna, J.A.1
Cech, T.R.2
-
36
-
-
0029874598
-
The kinetic folding pathway of the Tetrahymena ribozyme reveals possible similarities between RNA and protein folding
-
P.P. Zarrinkar, and J.R. Williamson The kinetic folding pathway of the Tetrahymena ribozyme reveals possible similarities between RNA and protein folding Nat Struct Biol 3 1996 432 438
-
(1996)
Nat Struct Biol
, vol.3
, pp. 432-438
-
-
Zarrinkar, P.P.1
Williamson, J.R.2
-
37
-
-
0030452773
-
New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: A complete 3D model of the Tetrahymena thermophila ribozyme
-
V. Lehnert, L. Jaeger, F. Michel, and E. Westhof New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme Chem Biol 3 1996 993 1009
-
(1996)
Chem Biol
, vol.3
, pp. 993-1009
-
-
Lehnert, V.1
Jaeger, L.2
Michel, F.3
Westhof, E.4
-
38
-
-
0027433710
-
Monitoring of the cooperative unfolding of the sunY group I intron of bacteriophage T4. the active form of the sunY ribozyme is stabilized by multiple interactions with 3′ terminal intron components
-
L. Jaeger, E. Westhof, and F. Michel Monitoring of the cooperative unfolding of the sunY group I intron of bacteriophage T4. The active form of the sunY ribozyme is stabilized by multiple interactions with 3′ terminal intron components J Mol Biol 234 1993 331 346
-
(1993)
J Mol Biol
, vol.234
, pp. 331-346
-
-
Jaeger, L.1
Westhof, E.2
Michel, F.3
-
39
-
-
0036828951
-
Evolution of Tetrahymena ribozyme mutants with increased structural stability
-
F. Guo, and T.R. Cech Evolution of Tetrahymena ribozyme mutants with increased structural stability Nat Struct Biol 9 2002 855 861
-
(2002)
Nat Struct Biol
, vol.9
, pp. 855-861
-
-
Guo, F.1
Cech, T.R.2
-
40
-
-
0026770256
-
Activation of the catalytic core of a group I intron by a remote 3′ splice junction
-
F. Michel, L. Jaeger, E. Westhof, R. Kuras, F. Tihy, M.Q. Xu, and D.A. Shub Activation of the catalytic core of a group I intron by a remote 3′ splice junction Genes Dev 6 1992 1373 1385
-
(1992)
Genes Dev
, vol.6
, pp. 1373-1385
-
-
Michel, F.1
Jaeger, L.2
Westhof, E.3
Kuras, R.4
Tihy, F.5
Xu, M.Q.6
Shub, D.A.7
-
43
-
-
0347763700
-
New approaches to targeting RNA with oligonucleotides: Inhibition of group I intron self-splicing
-
M.D. Disney, J.L. Childs, and D.H. Turner New approaches to targeting RNA with oligonucleotides: inhibition of group I intron self-splicing Biopolymers 73 2004 151 161
-
(2004)
Biopolymers
, vol.73
, pp. 151-161
-
-
Disney, M.D.1
Childs, J.L.2
Turner, D.H.3
-
44
-
-
0034104321
-
Compact but disordered states of RNA
-
S.A. Woodson Compact but disordered states of RNA Nat Struct Biol 7 2000 349 352
-
(2000)
Nat Struct Biol
, vol.7
, pp. 349-352
-
-
Woodson, S.A.1
-
45
-
-
0033984264
-
Mapping local nucleotide flexibility by selective acylation of 2′-amine substituted RNA
-
S.I. Chamberlin, and K.M. Weeks Mapping local nucleotide flexibility by selective acylation of 2′-amine substituted RNA J Am Chem Soc 122 2000 216 224
-
(2000)
J Am Chem Soc
, vol.122
, pp. 216-224
-
-
Chamberlin, S.I.1
Weeks, K.M.2
-
46
-
-
0346037281
-
Differential helix stabilities and sites pre-organized for tertiary interactions revealed by monitoring local nucleotide flexibility in the bI5 group I intron RNA
-
S.I. Chamberlin, and K.M. Weeks Differential helix stabilities and sites pre-organized for tertiary interactions revealed by monitoring local nucleotide flexibility in the bI5 group I intron RNA Biochemistry 42 2003 901 909
-
(2003)
Biochemistry
, vol.42
, pp. 901-909
-
-
Chamberlin, S.I.1
Weeks, K.M.2
-
48
-
-
10044240394
-
Structural basis for the self-chaperoning function of an RNA collapsed state
-
• ], this paper shows that pre-establishment of native interactions within compact yet dynamic intermediates rapidly produces active complexes of the yeast mitochondrial bI5 intron and CBP2 protein.
-
(2004)
Biochemistry
, vol.43
, pp. 15179-15186
-
-
Garcia, I.1
Weeks, K.M.2
-
49
-
-
0037418272
-
Extraordinarily slow binding of guanosine to the Tetrahymena group I ribozyme: Implications for RNA preorganization and function
-
•,50 ] provide biochemical evidence that binding of guanosine is much slower than diffusion and requires local induced fit.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 2300-2305
-
-
Karbstein, K.1
Herschlag, D.2
-
50
-
-
0030065737
-
A mechanistic framework for the second step of splicing catalyzed by the Tetrahymena ribozyme
-
P.C. Bevilacqua, N. Sugimoto, and D.H. Turner A mechanistic framework for the second step of splicing catalyzed by the Tetrahymena ribozyme Biochemistry 35 1996 648 658
-
(1996)
Biochemistry
, vol.35
, pp. 648-658
-
-
Bevilacqua, P.C.1
Sugimoto, N.2
Turner, D.H.3
-
51
-
-
0025877764
-
Group I intron self-splicing with adenosine: Evidence for a single nucleoside-binding site
-
M.D. Been, and A.T. Perrotta Group I intron self-splicing with adenosine: evidence for a single nucleoside-binding site Science 252 1991 434 437
-
(1991)
Science
, vol.252
, pp. 434-437
-
-
Been, M.D.1
Perrotta, A.T.2
-
52
-
-
2342525139
-
Architecture and folding mechanism of the Azoarcus group I pre-tRNA
-
P. Rangan, B. Masquida, E. Westhof, and S.A. Woodson Architecture and folding mechanism of the Azoarcus group I pre-tRNA J Mol Biol 339 2004 41 51
-
(2004)
J Mol Biol
, vol.339
, pp. 41-51
-
-
Rangan, P.1
Masquida, B.2
Westhof, E.3
Woodson, S.A.4
-
53
-
-
0026678180
-
Dynamics of ribozyme binding of substrate revealed by fluorescence-detected stopped-flow methods
-
P.C. Bevilacqua, R. Kierzek, K.A. Johnson, and D.H. Turner Dynamics of ribozyme binding of substrate revealed by fluorescence-detected stopped-flow methods Science 258 1992 1355 1358
-
(1992)
Science
, vol.258
, pp. 1355-1358
-
-
Bevilacqua, P.C.1
Kierzek, R.2
Johnson, K.A.3
Turner, D.H.4
-
54
-
-
0034674420
-
A single-molecule study of RNA catalysis and folding
-
X. Zhuang, L.E. Bartley, H.P. Babcock, R. Russell, T. Ha, D. Herschlag, and S. Chu A single-molecule study of RNA catalysis and folding Science 288 2000 2048 2051
-
(2000)
Science
, vol.288
, pp. 2048-2051
-
-
Zhuang, X.1
Bartley, L.E.2
Babcock, H.P.3
Russell, R.4
Ha, T.5
Herschlag, D.6
Chu, S.7
-
55
-
-
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
-
Y. Li, P.C. Bevilacqua, D. Mathews, and D.H. Turner 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
-
(1995)
Biochemistry
, vol.34
, pp. 14394-14399
-
-
Li, Y.1
Bevilacqua, P.C.2
Mathews, D.3
Turner, D.H.4
-
56
-
-
2942571539
-
The Comparative RNA Web (CRW) site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs
-
J.J. Cannone, S. Subramanian, M.N. Schnare, J.R. Collett, L.M. D'Souza, Y. Du, B. Feng, N. Lin, L.V. Madabusi, and K.M. Muller The Comparative RNA Web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs BMC Bioinformatics 3 2002 2
-
(2002)
BMC Bioinformatics
, vol.3
, pp. 2
-
-
Cannone, J.J.1
Subramanian, S.2
Schnare, M.N.3
Collett, J.R.4
D'Souza, L.M.5
Du, Y.6
Feng, B.7
Lin, N.8
Madabusi, L.V.9
Muller, K.M.10
|