-
1
-
-
20444478991
-
Riboswitches as versatile gene control elements
-
Tucker B.J., Breaker R.R. Riboswitches as versatile gene control elements. Curr. Opin. Struct. Biol. 2005, 15:342-348.
-
(2005)
Curr. Opin. Struct. Biol.
, vol.15
, pp. 342-348
-
-
Tucker, B.J.1
Breaker, R.R.2
-
2
-
-
33750874085
-
From ribosome to riboswitch: control of gene expression in bacteria by RNA structural rearrangements
-
Grundy F.J., Henkin T.M. From ribosome to riboswitch: control of gene expression in bacteria by RNA structural rearrangements. Crit. Rev. Biochem. Mol. Biol. 2006, 41:329-338.
-
(2006)
Crit. Rev. Biochem. Mol. Biol.
, vol.41
, pp. 329-338
-
-
Grundy, F.J.1
Henkin, T.M.2
-
3
-
-
85011936076
-
-
Riboswitch RNAs: Regulation of gene expression by direct monitoring of a physiological signal. RNA Biol. 7.
-
Smith, A. M., Fuchs, R. T., Grundy, F. J. & Henkin, T. M. Riboswitch RNAs: Regulation of gene expression by direct monitoring of a physiological signal. RNA Biol. 7.
-
-
-
Smith, A.M.1
Fuchs, R.T.2
Grundy, F.J.3
Henkin, T.M.4
-
4
-
-
34250613153
-
Sensing metabolic signals with nascent RNA transcripts: the T box and S box riboswitches as paradigms
-
Henkin T.M., Grundy F.J. Sensing metabolic signals with nascent RNA transcripts: the T box and S box riboswitches as paradigms. Cold. Spring. Harb. Symp. Quant. Biol. 2006, 71:231-237.
-
(2006)
Cold. Spring. Harb. Symp. Quant. Biol.
, vol.71
, pp. 231-237
-
-
Henkin, T.M.1
Grundy, F.J.2
-
5
-
-
71849091911
-
Amino acid recognition and gene regulation by riboswitches
-
Serganov A., Patel D.J. Amino acid recognition and gene regulation by riboswitches. Biochim. Biophys. Acta 2009, 1789:592-611.
-
(2009)
Biochim. Biophys. Acta
, vol.1789
, pp. 592-611
-
-
Serganov, A.1
Patel, D.J.2
-
7
-
-
48249104039
-
Riboswitches: emerging themes in RNA structure and function
-
Montange R.K., Batey R.T. Riboswitches: emerging themes in RNA structure and function. Annu. Rev. Biophys. 2008, 37:117-133.
-
(2008)
Annu. Rev. Biophys.
, vol.37
, pp. 117-133
-
-
Montange, R.K.1
Batey, R.T.2
-
8
-
-
34547577434
-
Flipping off the riboswitch: RNA structures that control gene expression
-
Sashital D.G., Butcher S.E. Flipping off the riboswitch: RNA structures that control gene expression. ACS Chem. Biol. 2006, 1:341-345.
-
(2006)
ACS Chem. Biol.
, vol.1
, pp. 341-345
-
-
Sashital, D.G.1
Butcher, S.E.2
-
9
-
-
63749126957
-
Expanding roles for metabolite-sensing regulatory RNAs
-
Dambach M.D., Winkler W.C. Expanding roles for metabolite-sensing regulatory RNAs. Curr. Opin. Microbiol. 2009, 12:161-169.
-
(2009)
Curr. Opin. Microbiol.
, vol.12
, pp. 161-169
-
-
Dambach, M.D.1
Winkler, W.C.2
-
11
-
-
34249278470
-
Control of alternative RNA splicing and gene expression by eukaryotic riboswitches
-
Cheah M.T., Wachter A., Sudarsan N., Breaker R.R. Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature 2007, 447:497-500.
-
(2007)
Nature
, vol.447
, pp. 497-500
-
-
Cheah, M.T.1
Wachter, A.2
Sudarsan, N.3
Breaker, R.R.4
-
12
-
-
37849045636
-
Riboswitch control of gene expression in plants by splicing and alternative 3' end processing of mRNAs
-
Wachter A., Tunc-Ozdemir M., Grove B.C., Green P.J., Shintani D.K., Breaker R.R. Riboswitch control of gene expression in plants by splicing and alternative 3' end processing of mRNAs. Plant Cell 2007, 19:3437-3450.
-
(2007)
Plant Cell
, vol.19
, pp. 3437-3450
-
-
Wachter, A.1
Tunc-Ozdemir, M.2
Grove, B.C.3
Green, P.J.4
Shintani, D.K.5
Breaker, R.R.6
-
13
-
-
46349083026
-
The distributions, mechanisms, and structures of metabolite-binding riboswitches
-
Barrick J.E., Breaker R.R. The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biol. 2007, 8:R239.
-
(2007)
Genome Biol.
, vol.8
-
-
Barrick, J.E.1
Breaker, R.R.2
-
14
-
-
0345531094
-
Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch?
-
Rodionov D.A., Vitreschak A.G., Mironov A.A., Gelfand M.S. Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch?. Nucleic Acids Res. 2003, 31:6748-6757.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 6748-6757
-
-
Rodionov, D.A.1
Vitreschak, A.G.2
Mironov, A.A.3
Gelfand, M.S.4
-
15
-
-
0031735563
-
The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria
-
Grundy F.J., Henkin T.M. The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria. Mol. Microbiol. 1998, 30:737-749.
-
(1998)
Mol. Microbiol.
, vol.30
, pp. 737-749
-
-
Grundy, F.J.1
Henkin, T.M.2
-
16
-
-
0037453069
-
Transcription termination control of the S box system: direct measurement of S-adenosylmethionine by the leader RNA
-
McDaniel B.A., Grundy F.J., Artsimovitch I., Henkin T.M. Transcription termination control of the S box system: direct measurement of S-adenosylmethionine by the leader RNA. Proc. Natl Acad. Sci. USA 2003, 100:3083-3088.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 3083-3088
-
-
McDaniel, B.A.1
Grundy, F.J.2
Artsimovitch, I.3
Henkin, T.M.4
-
17
-
-
23744510923
-
A tertiary structural element in S box leader RNAs is required for S-adenosylmethionine-directed transcription termination
-
McDaniel B.A., Grundy F.J., Henkin T.M. A tertiary structural element in S box leader RNAs is required for S-adenosylmethionine-directed transcription termination. Mol. Microbiol. 2005, 57:1008-1021.
-
(2005)
Mol. Microbiol.
, vol.57
, pp. 1008-1021
-
-
McDaniel, B.A.1
Grundy, F.J.2
Henkin, T.M.3
-
18
-
-
0042320361
-
An mRNA structure that controls gene expression by binding S-adenosylmethionine
-
Winkler W.C., Nahvi A., Sudarsan N., Barrick J.E., Breaker R.R. An mRNA structure that controls gene expression by binding S-adenosylmethionine. Nat. Struct. Biol. 2003, 10:701-707.
-
(2003)
Nat. Struct. Biol.
, vol.10
, pp. 701-707
-
-
Winkler, W.C.1
Nahvi, A.2
Sudarsan, N.3
Barrick, J.E.4
Breaker, R.R.5
-
19
-
-
0038476616
-
The riboswitch-mediated control of sulfur metabolism in bacteria
-
Epshtein V., Mironov A.S., Nudler E. The riboswitch-mediated control of sulfur metabolism in bacteria. Proc. Natl Acad. Sci. USA 2003, 100:5052-5056.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 5052-5056
-
-
Epshtein, V.1
Mironov, A.S.2
Nudler, E.3
-
20
-
-
38649086717
-
Natural variability in S-adenosylmethionine (SAM)-dependent riboswitches: S-box elements in bacillus subtilis exhibit differential sensitivity to SAM In vivo and in vitro
-
Tomsic J., McDaniel B.A., Grundy F.J., Henkin T.M. Natural variability in S-adenosylmethionine (SAM)-dependent riboswitches: S-box elements in bacillus subtilis exhibit differential sensitivity to SAM In vivo and in vitro. J. Bacteriol. 2008, 190:823-833.
-
(2008)
J. Bacteriol.
, vol.190
, pp. 823-833
-
-
Tomsic, J.1
McDaniel, B.A.2
Grundy, F.J.3
Henkin, T.M.4
-
21
-
-
70350111141
-
A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria
-
Poiata E., Meyer M.M., Ames T.D., Breaker R.R. A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria. RNA 2009, 15:2046-2056.
-
(2009)
RNA
, vol.15
, pp. 2046-2056
-
-
Poiata, E.1
Meyer, M.M.2
Ames, T.D.3
Breaker, R.R.4
-
22
-
-
0034897731
-
The GA motif: an RNA element common to bacterial antitermination systems, rRNA, and eukaryotic RNAs
-
Winkler W.C., Grundy F.J., Murphy B.A., Henkin T.M. The GA motif: an RNA element common to bacterial antitermination systems, rRNA, and eukaryotic RNAs. RNA 2001, 7:1165-1172.
-
(2001)
RNA
, vol.7
, pp. 1165-1172
-
-
Winkler, W.C.1
Grundy, F.J.2
Murphy, B.A.3
Henkin, T.M.4
-
23
-
-
33745628336
-
Structure of the S-adenosylmethionine riboswitch regulatory mRNA element
-
Montange R.K., Batey R.T. Structure of the S-adenosylmethionine riboswitch regulatory mRNA element. Nature 2006, 441:1172-1175.
-
(2006)
Nature
, vol.441
, pp. 1172-1175
-
-
Montange, R.K.1
Batey, R.T.2
-
24
-
-
77949327506
-
Discrimination between closely related cellular metabolites by the SAM-I riboswitch
-
Montange R.K., Mondragon E., van Tyne D., Garst A.D., Ceres P., Batey R.T. Discrimination between closely related cellular metabolites by the SAM-I riboswitch. J. Mol. Biol. 2010, 396:761-772.
-
(2010)
J. Mol. Biol.
, vol.396
, pp. 761-772
-
-
Montange, R.K.1
Mondragon, E.2
van Tyne, D.3
Garst, A.D.4
Ceres, P.5
Batey, R.T.6
-
25
-
-
77954627025
-
Free state conformational sampling of the SAM-I riboswitch aptamer domain
-
Stoddard C.D., Montange R.K., Hennelly S.P., Rambo R.P., Sanbonmatsu K.Y., Batey R.T. Free state conformational sampling of the SAM-I riboswitch aptamer domain. Structure 2010, 18:787-797.
-
(2010)
Structure
, vol.18
, pp. 787-797
-
-
Stoddard, C.D.1
Montange, R.K.2
Hennelly, S.P.3
Rambo, R.P.4
Sanbonmatsu, K.Y.5
Batey, R.T.6
-
26
-
-
38849197858
-
Structure of the SAM-II riboswitch bound to S-adenosylmethionine
-
Gilbert S.D., Rambo R.P., Van Tyne D., Batey R.T. Structure of the SAM-II riboswitch bound to S-adenosylmethionine. Nat. Struct. Mol. Biol. 2008, 15:177-182.
-
(2008)
Nat. Struct. Mol. Biol.
, vol.15
, pp. 177-182
-
-
Gilbert, S.D.1
Rambo, R.P.2
Van Tyne, D.3
Batey, R.T.4
-
27
-
-
53549089576
-
Crystal structures of the SAM-III/S(MK) riboswitch reveal the SAM-dependent translation inhibition mechanism
-
Lu C., Smith A.M., Fuchs R.T., Ding F., Rajashankar K., Henkin T.M., Ke A. Crystal structures of the SAM-III/S(MK) riboswitch reveal the SAM-dependent translation inhibition mechanism. Nat. Struct. Mol. Biol 2008, 15:1076-1083.
-
(2008)
Nat. Struct. Mol. Biol
, vol.15
, pp. 1076-1083
-
-
Lu, C.1
Smith, A.M.2
Fuchs, R.T.3
Ding, F.4
Rajashankar, K.5
Henkin, T.M.6
Ke, A.7
-
28
-
-
75649088957
-
Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch
-
Kulshina N., Edwards T.E., Ferre-D'Amare A.R. Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch. RNA 2010, 16:186-196.
-
(2010)
RNA
, vol.16
, pp. 186-196
-
-
Kulshina, N.1
Edwards, T.E.2
Ferre-D'Amare, A.R.3
-
29
-
-
44149086117
-
Hinge stiffness is a barrier to RNA folding
-
Schlatterer J.C., Kwok L.W., Lamb J.S., Park H.Y., Andresen K., Brenowitz M., Pollack L. Hinge stiffness is a barrier to RNA folding. J. Mol. Biol. 2008, 379:859-870.
-
(2008)
J. Mol. Biol.
, vol.379
, pp. 859-870
-
-
Schlatterer, J.C.1
Kwok, L.W.2
Lamb, J.S.3
Park, H.Y.4
Andresen, K.5
Brenowitz, M.6
Pollack, L.7
-
30
-
-
28844509318
-
Concordant exploration of the kinetics of RNA folding from global and local perspectives
-
Kwok L.W., Shcherbakova I., Lamb J.S., Park H.Y., Andresen K., Smith H., et al. Concordant exploration of the kinetics of RNA folding from global and local perspectives. J. Mol. Biol. 2006, 355:282-293.
-
(2006)
J. Mol. Biol.
, vol.355
, pp. 282-293
-
-
Kwok, L.W.1
Shcherbakova, I.2
Lamb, J.S.3
Park, H.Y.4
Andresen, K.5
Smith, H.6
-
31
-
-
0026003204
-
RRNA transcription rate in Escherichia coli
-
Gotta S.L., Miller O.L., French S.L. rRNA transcription rate in Escherichia coli. J. Bacteriol. 1991, 173:6647-6649.
-
(1991)
J. Bacteriol.
, vol.173
, pp. 6647-6649
-
-
Gotta, S.L.1
Miller, O.L.2
French, S.L.3
-
32
-
-
16344370497
-
RNA SHAPE chemistry reveals nonhierarchical interactions dominate equilibrium structural transitions in tRNA(Asp) transcripts
-
Wilkinson K.A., Merino E.J., Weeks K.M. RNA SHAPE chemistry reveals nonhierarchical interactions dominate equilibrium structural transitions in tRNA(Asp) transcripts. J. Am. Chem. Soc. 2005, 127:4659-4667.
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 4659-4667
-
-
Wilkinson, K.A.1
Merino, E.J.2
Weeks, K.M.3
-
33
-
-
38949114262
-
Folding of the SAM aptamer is determined by the formation of a K-turn-dependent pseudoknot
-
Heppell B., Lafontaine D.A. Folding of the SAM aptamer is determined by the formation of a K-turn-dependent pseudoknot. Biochemistry 2008, 47:1490-1499.
-
(2008)
Biochemistry
, vol.47
, pp. 1490-1499
-
-
Heppell, B.1
Lafontaine, D.A.2
-
34
-
-
71049194730
-
A mechanism for S-adenosyl methionine assisted formation of a riboswitch conformation: a small molecule with a strong arm
-
Huang W., Kim J., Jha S., Aboul-ela F. A mechanism for S-adenosyl methionine assisted formation of a riboswitch conformation: a small molecule with a strong arm. Nucleic Acids Res. 2009, 37:6528-6539.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 6528-6539
-
-
Huang, W.1
Kim, J.2
Jha, S.3
Aboul-ela, F.4
-
35
-
-
38449096224
-
Molecular basis of gene regulation by the THI-box riboswitch
-
Ontiveros-Palacios N., Smith A.M., Grundy F.J., Soberon M., Henkin T.M., Miranda-Rios J. Molecular basis of gene regulation by the THI-box riboswitch. Mol. Microbiol. 2008, 67:793-803.
-
(2008)
Mol. Microbiol.
, vol.67
, pp. 793-803
-
-
Ontiveros-Palacios, N.1
Smith, A.M.2
Grundy, F.J.3
Soberon, M.4
Henkin, T.M.5
Miranda-Rios, J.6
-
36
-
-
4344596976
-
Crystallization of RNA and RNA-protein complexes
-
Ke A., Doudna J.A. Crystallization of RNA and RNA-protein complexes. Methods 2004, 34:408-414.
-
(2004)
Methods
, vol.34
, pp. 408-414
-
-
Ke, A.1
Doudna, J.A.2
-
39
-
-
3543012707
-
Crystallography & NMR system: A new software suite for macromolecular structure determination
-
Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. Sect. D: Biol. Crystallogr. 1998, 54:905-921.
-
(1998)
Acta Crystallogr. Sect. D: Biol. Crystallogr.
, vol.54
, pp. 905-921
-
-
Brunger, A.T.1
Adams, P.D.2
Clore, G.M.3
DeLano, W.L.4
Gros, P.5
Grosse-Kunstleve, R.W.6
-
40
-
-
37049014272
-
Version 1.2 of the crystallography and NMR system
-
Brunger A.T. Version 1.2 of the crystallography and NMR system. Nat. Protoc. 2007, 2:2728-2733.
-
(2007)
Nat. Protoc.
, vol.2
, pp. 2728-2733
-
-
Brunger, A.T.1
-
41
-
-
0028103275
-
The CCP4 suite: programs for protein crystallography
-
Collaborative Computational Project, N
-
Collaborative Computational Project, N The CCP4 suite: programs for protein crystallography. Acta Crystallogr. Sect. D: Biol. Crystallogr. 1994, 50:760-763.
-
(1994)
Acta Crystallogr. Sect. D: Biol. Crystallogr.
, vol.50
, pp. 760-763
-
-
-
42
-
-
33947720028
-
Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution
-
Wilkinson K.A., Merino E.J., Weeks K.M. Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution. Nat. Protoc. 2006, 1:1610-1616.
-
(2006)
Nat. Protoc.
, vol.1
, pp. 1610-1616
-
-
Wilkinson, K.A.1
Merino, E.J.2
Weeks, K.M.3
-
43
-
-
16244412610
-
RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE)
-
Merino E.J., Wilkinson K.A., Coughlan J.L., Weeks K.M. RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE). J. Am. Chem. Soc. 2005, 127:4223-4231.
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 4223-4231
-
-
Merino, E.J.1
Wilkinson, K.A.2
Coughlan, J.L.3
Weeks, K.M.4
-
44
-
-
67649371451
-
Influence of nucleotide identity on ribose 2'-hydroxyl reactivity in RNA
-
Wilkinson K.A., Vasa S.M., Deigan K.E., Mortimer S.A., Giddings M.C., Weeks K.M. Influence of nucleotide identity on ribose 2'-hydroxyl reactivity in RNA. RNA 2009, 15:1314-1321.
-
(2009)
RNA
, vol.15
, pp. 1314-1321
-
-
Wilkinson, K.A.1
Vasa, S.M.2
Deigan, K.E.3
Mortimer, S.A.4
Giddings, M.C.5
Weeks, K.M.6
-
45
-
-
52949152433
-
ShapeFinder: a software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis
-
Vasa S.M., Guex N., Wilkinson K.A., Weeks K.M., Giddings M.C. ShapeFinder: a software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis. RNA 2008, 14:1979-1990.
-
(2008)
RNA
, vol.14
, pp. 1979-1990
-
-
Vasa, S.M.1
Guex, N.2
Wilkinson, K.A.3
Weeks, K.M.4
Giddings, M.C.5
-
46
-
-
0033858359
-
Van't Hoff enthalpies without baselines
-
John D.M., Weeks K.M. van't Hoff enthalpies without baselines. Protein Sci. 2000, 9:1416-1419.
-
(2000)
Protein Sci.
, vol.9
, pp. 1416-1419
-
-
John, D.M.1
Weeks, K.M.2
|