-
1
-
-
0025367254
-
Self-splicing of group I introns
-
Cech,T.R. (1990) Self-splicing of group I introns. Annu. Rev. Biochem., 59, 543-568.
-
(1990)
Annu. Rev. Biochem.
, vol.59
, pp. 543-568
-
-
Cech, T.R.1
-
2
-
-
0020417286
-
Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena
-
Kruger,K., Grabowski,P.J., Zaug,A.J., Sands,J., Gottschling,D.E. and Cech,T.R. (1982) Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell, 31, 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
-
3
-
-
0029163563
-
RNA chaperones and the RNA folding problem
-
Herschlag,D. (1995) RNA chaperones and the RNA folding problem. J. Biol. Chem., 270, 20871-20874.
-
(1995)
J. Biol. Chem.
, vol.270
, pp. 20871-20874
-
-
Herschlag, D.1
-
4
-
-
0002671710
-
Group I and group II ribozymes as RNPs: Clue to the past and guides to the future
-
Gesteland,R., Cech,T.R. and Atkins,J. (eds), 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
-
Lambowitz,A.M., Caprara,M.G., Zimmerly,S. and Perlman,P.S. (1999) Group I and group II ribozymes as RNPs: Clue to the past and guides to the future. In Gesteland,R., Cech,T.R. and Atkins,J. (eds), The RNA World, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 451-485.
-
(1999)
The RNA World
, pp. 451-485
-
-
Lambowitz, A.M.1
Caprara, M.G.2
Zimmerly, S.3
Perlman, P.S.4
-
5
-
-
8444229753
-
Strategies for RNA folding and assembly
-
Schroeder,R., Barta,A. and Semrad,K. (2004) Strategies for RNA folding and assembly. Nature Rev. Mol. Cell Biol., 5, 908-919.
-
(2004)
Nature Rev. Mol. Cell Biol.
, vol.5
, pp. 908-919
-
-
Schroeder, R.1
Barta, A.2
Semrad, K.3
-
6
-
-
0036600576
-
RNA folding in vivo
-
Schroeder,R., Grossberger,R., Pichler,A. and Waldsich,C. (2002) RNA folding in vivo. Curr. Opin. Struct. Biol., 12, 296-300.
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 296-300
-
-
Schroeder, R.1
Grossberger, R.2
Pichler, A.3
Waldsich, C.4
-
7
-
-
2942571539
-
The comparative RNA web (CRW) site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs
-
Cannone,J.J., Subramanian,S., Schnare,M.N., Collett,J.R., D'Souza,L.M., Du,Y., Feng,B., Lin,N., Madabusi,L.V., Muller,K.M. et al. (2002) The comparative RNA web (CRW) site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics, 3, 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
-
8
-
-
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
-
9
-
-
0032959496
-
A group I intron in the nuclear small subunit rRNA gene of Cryptendoxyla hypophloia, an ascomycetous fungus: Evidence for a new major class of group I introns
-
Suh,S.O., Jones,K.G. and Blackwell,M. (1999) A group I intron in the nuclear small subunit rRNA gene of Cryptendoxyla hypophloia, an ascomycetous fungus: Evidence for a new major class of group I introns. J. Mol. Evol., 48, 493-500.
-
(1999)
J. Mol. Evol.
, vol.48
, pp. 493-500
-
-
Suh, S.O.1
Jones, K.G.2
Blackwell, M.3
-
10
-
-
0023664964
-
Structural conventions for group I introns
-
Burke,J.M., Belfort,M., Cech,T.R., Davies,R.W., Schweyen,R.J., Shub,D.A., Szostak,J.W. and Tabak,H.F. (1987) Structural conventions for group I introns. Nucleic Acids Res., 15, 7217-7221.
-
(1987)
Nucleic Acids Res.
, vol.15
, pp. 7217-7221
-
-
Burke, J.M.1
Belfort, M.2
Cech, T.R.3
Davies, R.W.4
Schweyen, R.J.5
Shub, D.A.6
Szostak, J.W.7
Tabak, H.F.8
-
11
-
-
0030866522
-
Mutagenesis and comparative sequence analysis of a base triple joining the two domains of group I ribozymes
-
Tanner,M.A., Anderson,E.M., Gutell,R.R. and Cech,T.R. (1997) Mutagenesis and comparative sequence analysis of a base triple joining the two domains of group I ribozymes. RNA, 3, 1037-1051.
-
(1997)
RNA
, vol.3
, pp. 1037-1051
-
-
Tanner, M.A.1
Anderson, E.M.2
Gutell, R.R.3
Cech, T.R.4
-
12
-
-
0032500731
-
A preorganized active site in the crystal structure of the Tetrahymena ribozyme
-
Golden,B.L., Gooding,A.R., Podell,E.R. and Cech,T.R. (1998) A preorganized active site in the crystal structure of the Tetrahymena ribozyme. Science, 282, 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
-
13
-
-
0033787391
-
Ribozyme structures and mechanisms
-
Doherty,E.A. and Doudna,J.A. (2000) Ribozyme structures and mechanisms. Annu. Rev. Biochem., 69, 597-615.
-
(2000)
Annu. Rev. Biochem.
, vol.69
, pp. 597-615
-
-
Doherty, E.A.1
Doudna, J.A.2
-
14
-
-
0030452773
-
New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: A complete 3D model of the Tetrahymena thermophila ribozyme
-
Lehnert,V., Jaeger,L., Michel,F. and Westhof,E. (1996) 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, 993-1009.
-
(1996)
Chem. Biol.
, vol.3
, pp. 993-1009
-
-
Lehnert, V.1
Jaeger, L.2
Michel, F.3
Westhof, E.4
-
15
-
-
0034646209
-
The P5abc peripheral element facilitates preorganization of the Tetrahymena group I ribozyme for catalysis
-
Engelhardt,M.A., Doherty,E.A., Knitt,D.S., Doudna,J.A. and Herschlag,D. (2000) The P5abc peripheral element facilitates preorganization of the Tetrahymena group I ribozyme for catalysis. Biochemistry, 39, 2639-2651.
-
(2000)
Biochemistry
, vol.39
, pp. 2639-2651
-
-
Engelhardt, M.A.1
Doherty, E.A.2
Knitt, D.S.3
Doudna, J.A.4
Herschlag, D.5
-
16
-
-
0030831172
-
Long-range interaction between the P2.1 and P9.1 peripheral domains of the Tetrahymena ribozyme
-
Ikawa,Y., Ohta,H., Shiraishi,H. and Inoue,T. (1997) Long-range interaction between the P2.1 and P9.1 peripheral domains of the Tetrahymena ribozyme. Nucleic Acids Res., 25, 1761-1765.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 1761-1765
-
-
Ikawa, Y.1
Ohta, H.2
Shiraishi, H.3
Inoue, T.4
-
17
-
-
0035808384
-
Concerted kinetic folding of a multidomain ribozyme with a disrupted loop receptor interaction
-
Treiber,D.K. and Williamson,J.R. (2001) Concerted kinetic folding of a multidomain ribozyme with a disrupted loop receptor interaction. J. Mol. Biol., 305, 11-21.
-
(2001)
J. Mol. Biol.
, vol.305
, pp. 11-21
-
-
Treiber, D.K.1
Williamson, J.R.2
-
18
-
-
0033544723
-
The effect of long-range loop-loop interactions on folding of the Tetrahymena self-splicing RNA
-
Pan,J. and Woodson,S.A. (1999) The effect of long-range loop-loop interactions on folding of the Tetrahymena self-splicing RNA. J. Mol. Biol., 294, 955-965.
-
(1999)
J. Mol. Biol.
, vol.294
, pp. 955-965
-
-
Pan, J.1
Woodson, S.A.2
-
19
-
-
0037039464
-
Exploring the folding landscape of a structured RNA
-
Russell,R., Zhuang,X., Babcock,H.P., Millett,I.S., Doniach,S., Chu,S. and Herschlag,D. (2002) Exploring the folding landscape of a structured RNA. Proc. Natl Acad. Sci. USA, 99, 155-160.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 155-160
-
-
Russell, R.1
Zhuang, X.2
Babcock, H.P.3
Millett, I.S.4
Doniach, S.5
Chu, S.6
Herschlag, D.7
-
22
-
-
0034111513
-
Metal ions in ribozyme folding and catalysis
-
Hanna,R. and Doudna,J.A. (2000) Metal ions in ribozyme folding and catalysis. Curr. Opin. Chem. Biol., 4, 166-170.
-
(2000)
Curr. Opin. Chem. Biol.
, vol.4
, pp. 166-170
-
-
Hanna, R.1
Doudna, J.A.2
-
23
-
-
0036864241
-
Folding mechanisms of group I ribozymes: Role of stability and contact order
-
Woodson,S.A. (2002) Folding mechanisms of group I ribozymes: Role of stability and contact order. Biochem. Soc. Trans., 30, 1166-1169.
-
(2002)
Biochem. Soc. Trans.
, vol.30
, pp. 1166-1169
-
-
Woodson, S.A.1
-
24
-
-
8644229237
-
Structure of the Tetrahymena ribozyme: Base triple sandwich and metal ion at the active site
-
Guo,F., Gooding,A.R. and Cech,T.R. (2004) Structure of the Tetrahymena ribozyme: Base triple sandwich and metal ion at the active site. Mol. Cell, 16, 351-362.
-
(2004)
Mol. Cell
, vol.16
, pp. 351-362
-
-
Guo, F.1
Gooding, A.R.2
Cech, T.R.3
-
25
-
-
9344232753
-
Crystal structure of a group I intron splicing intermediate
-
Adams,P.L., Stahley,M.R., Gill,M.L., Kosek,A.B., Wang,J. and Strobel,S.A. (2004) Crystal structure of a group I intron splicing intermediate. RNA, 10, 1867-1887.
-
(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
-
26
-
-
3042848954
-
Crystal structure of a self-splicing group I intron with both exons
-
Adams,P.L., Stahley,M.R., Kosek,A.B., Wangj. 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
-
27
-
-
11444263264
-
Crystal structure of a phage Twort group I ribozyme-product complex
-
Golden,B.L., Kim,H. and Chase,E. (2005) Crystal structure of a phage Twort group I ribozyme-product complex. Nature Struct. Mol. Biol., 12,82-89.
-
(2005)
Nature Struct. Mol. Biol.
, vol.12
, pp. 82-89
-
-
Golden, B.L.1
Kim, H.2
Chase, E.3
-
28
-
-
0035875145
-
Folding of the group I intron ribozyme from the 26S rRNA gene of Candida albicans
-
Zhang,Y. and Leibowitz,M.J. (2001) Folding of the group I intron ribozyme from the 26S rRNA gene of Candida albicans. Nucleic Acids Res., 29, 2644-2653.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 2644-2653
-
-
Zhang, Y.1
Leibowitz, M.J.2
-
29
-
-
0242317691
-
Concerted folding of a Candida ribozyme into the catalytically active structure posterior to a rapid RNA compaction
-
Xiao,M., Leibowitz,M.J. and Zhang,Y. (2003) Concerted folding of a Candida ribozyme into the catalytically active structure posterior to a rapid RNA compaction. Nucleic Acids Res., 31, 3901-3908.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3901-3908
-
-
Xiao, M.1
Leibowitz, M.J.2
Zhang, Y.3
-
30
-
-
11144256451
-
Fast formation of the P3-P7 pseudoknot: A strategy for efficient folding of the catalytically active ribozyme
-
Zhang,L., Xiao,M., Lu,C. and Zhang,Y. (2005) Fast formation of the P3-P7 pseudoknot: A strategy for efficient folding of the catalytically active ribozyme. RNA, 11, 59-69.
-
(2005)
RNA
, vol.11
, pp. 59-69
-
-
Zhang, L.1
Xiao, M.2
Lu, C.3
Zhang, Y.4
-
31
-
-
0037452797
-
Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme
-
Rangan,P., Masquida,B., WesthofE. and Woodson,S.A. (2003) Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme. Proc. Natl Arad. Sci. USA, 100, 1574-1579.
-
(2003)
Proc. Natl. Arad. Sci. USA
, vol.100
, pp. 1574-1579
-
-
Rangan, P.1
Masquida, B.2
Westhof, E.3
Woodson, S.A.4
-
32
-
-
0027722247
-
Correlation between the presence of a self-splicing intron in the 25S rDNA of C.albicans and strains susceptibility to 5-fluorocytosine
-
Mercure,S., Montplaisir,S. and Lemay,G. (1993) Correlation between the presence of a self-splicing intron in the 25S rDNA of C.albicans and strains susceptibility to 5-fluorocytosine. Nucleic Acids Res., 21, 6020-6027.
-
(1993)
Nucleic Acids Res.
, vol.21
, pp. 6020-6027
-
-
Mercure, S.1
Montplaisir, S.2
Lemay, G.3
-
33
-
-
0034882882
-
A structural and phylogenetic analysis of the group IC1 introns in the order Bangiales (Rhodophyta)
-
Muller,K.M., Cannonej.J., Gutell,R.R. and Sheath,R.G. (2001) A structural and phylogenetic analysis of the group IC1 introns in the order Bangiales (Rhodophyta). Mol. Biol. Evol., 18, 1654-1667.
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 1654-1667
-
-
Muller, K.M.1
Cannone, J.J.2
Gutell, R.R.3
Sheath, R.G.4
-
34
-
-
0033591465
-
Expanded sequence dependence ofthermodynamic parameters improves prediction of RNA secondary structure
-
Mathews,D.H., Sabinaj., Zuker,M. and Turner,D.H. (1999) Expanded sequence dependence ofthermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol., 288, 911-940.
-
(1999)
J. Mol. Biol.
, vol.288
, pp. 911-940
-
-
Mathews, D.H.1
Sabina, J.2
Zuker, M.3
Turner, D.H.4
-
35
-
-
0000122573
-
-
PHYLIP-Phylogeny Inference Package (Version 3.2)
-
Felsensteinj. (1989) PHYLIP-Phylogeny Inference Package (Version 3.2). Cladistics, 5, 164-166.
-
(1989)
Cladistics
, vol.5
, pp. 164-166
-
-
Felsenstein, J.1
-
36
-
-
0026466830
-
Identifying constraints on the higher-order structure of RNA: Continued development and application ofcomparative sequence analysis methods
-
Gutell,R.R., Power,A., Hertz,G.Z., Putz,E.J. and Stormo,G.D. (1992) Identifying constraints on the higher-order structure of RNA: Continued development and application ofcomparative sequence analysis methods. Nucleic Acids Res., 20, 5785-5795.
-
(1992)
Nucleic Acids Res.
, vol.20
, pp. 5785-5795
-
-
Gutell, R.R.1
Power, A.2
Hertz, G.Z.3
Putz, E.J.4
Stormo, G.D.5
-
37
-
-
0002051540
-
BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT
-
Hall,T.A. (1999) BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids. Symp. Ser., 41, 95-98.
-
(1999)
Nucleic Acids. Symp. Ser.
, vol.41
, pp. 95-98
-
-
Hall, T.A.1
-
38
-
-
0034637111
-
The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution
-
Ban,N., Nissen,P., Hansenj., Moore,P.B. and Steitz,T.A. (2000) The complete atomic structure of the large ribosomal subunit at 2.4 Å 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
-
39
-
-
0029804920
-
Function of a pseudoknot in the suppression of an alternative splicing event in a group I intron
-
Jaeger,L., WesthofE. and Michel,F. (1996) Function of a pseudoknot in the suppression of an alternative splicing event in a group I intron. Biochimie, 78, 466-473.
-
(1996)
Biochimie
, vol.78
, pp. 466-473
-
-
Jaeger, L.1
Westhof, E.2
Michel, F.3
-
40
-
-
0034405491
-
A story: Unpaired adenosine bases in ribosomal RNAs
-
Gutell,R.R., Cannonej.J., Shang,Z., Du,Y. and Serra,M.J. (2000) A story: unpaired adenosine bases in ribosomal RNAs. J. Mol. Biol., 304, 335-354.
-
(2000)
J. Mol. Biol.
, vol.304
, pp. 335-354
-
-
Gutell, R.R.1
Cannone, J.J.2
Shang, Z.3
Du, Y.4
Serra, M.J.5
-
41
-
-
0035942248
-
RNA tertiary interactions in the large ribosomal subunit: The A-minor motif
-
Nissen,P., Ippolito,J.A., Ban,N., Moore,P.B. and Steitz,T.A. (200 1) RNA tertiary interactions in the large ribosomal subunit: The A-minor motif. Proc. Natl Arad. Sci. USA, 98, 4899-4903.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 4899-4903
-
-
Nissen, P.1
Ippolito, J.A.2
Ban, N.3
Moore, P.B.4
Steitz, T.A.5
-
42
-
-
0028294458
-
Involvement of a GNRA tetraloop in long-range RNA tertiary interactions
-
Jaeger,L., Michel,F. and WesthofE. (1994) Involvement of a GNRA tetraloop in long-range RNA tertiary interactions. J. Mol. Biol., 236, 1271-1276.
-
(1994)
J. Mol. Biol.
, vol.236
, pp. 1271-1276
-
-
Jaeger, L.1
Michel, F.2
Westhof, E.3
-
43
-
-
0028921811
-
Frequent use ofthe same tertiary motif by self-folding RNAs
-
Costa,M. and Michel,F. (1995) Frequent use ofthe same tertiary motif by self-folding RNAs. EMBO J., 14, 1276-1285.
-
(1995)
EMBO J.
, vol.14
, pp. 1276-1285
-
-
Costa, M.1
Michel, F.2
-
44
-
-
0032497521
-
Crystal structure of a hepatitis delta virus ribozyme
-
Ferre-D'Amare,A.R., Zhou,K. and Doudna,J.A. (1998) Crystal structure of a hepatitis delta virus ribozyme. Nature, 395, 567-574.
-
(1998)
Nature
, vol.395
, pp. 567-574
-
-
Ferre-D'Amare, A.R.1
Zhou, K.2
Doudna, J.A.3
-
45
-
-
0025344901
-
Base-pairing interactions involvingthe 5′ and 3′-terminal nucleotides of group 11 self-splicing introns
-
Jacquier,A. and Michel,F. (1990) Base-pairing interactions involvingthe 5′ and 3′-terminal nucleotides of group 11 self-splicing introns. J. Mol. Biol., 213, 437-447.
-
(1990)
J. Mol. Biol.
, vol.213
, pp. 437-447
-
-
Jacquier, A.1
Michel, F.2
-
46
-
-
3342969661
-
A conserved element in the yeast RNase MRP RNA subunit can participate in a long-range base-pairing interaction
-
Walker,S.C. and Avis,J.M. (2004) A conserved element in the yeast RNase MRP RNA subunit can participate in a long-range base-pairing interaction. J. Mol. Biol., 341, 375-388.
-
(2004)
J. Mol. Biol.
, vol.341
, pp. 375-388
-
-
Walker, S.C.1
Avis, J.M.2
-
47
-
-
0024214064
-
Conserved sequences and structures ofgroup I introns: Building an active site for RNA catalysis
-
Cech,T.R. (1988) Conserved sequences and structures ofgroup I introns: building an active site for RNA catalysis. Gene, 73, 259-271.
-
(1988)
Gene
, vol.73
, pp. 259-271
-
-
Cech, T.R.1
|