-
1
-
-
84908067664
-
The purine riboswitch as a model system for exploring RNA biology and chemistry
-
Porter, E. B., Marcano-Velázquez, J. G., and Batey, R. T. (2014) The purine riboswitch as a model system for exploring RNA biology and chemistry. Biochim. Biophys. Acta 1839, 919-930
-
(2014)
Biochim. Biophys. Acta
, vol.1839
, pp. 919-930
-
-
Porter, E.B.1
Marcano-Velázquez, J.G.2
Batey, R.T.3
-
2
-
-
0842334528
-
Adenine riboswitches and gene activation by disruption of a transcription terminator
-
Mandal, M., and Breaker, R. R. (2004) Adenine riboswitches and gene activation by disruption of a transcription terminator. Nat. Struct. Mol. Biol. 11, 29-35
-
(2004)
Nat. Struct. Mol. Biol.
, vol.11
, pp. 29-35
-
-
Mandal, M.1
Breaker, R.R.2
-
3
-
-
84867629183
-
Direct observation of cotranscriptional folding in an adenine riboswitch
-
Frieda, K. L., and Block, S. M. (2012) Direct observation of cotranscriptional folding in an adenine riboswitch. Science 338, 397-400
-
(2012)
Science
, vol.338
, pp. 397-400
-
-
Frieda, K.L.1
Block, S.M.2
-
4
-
-
38849204944
-
Direct observation of hierarchical folding in single riboswitch aptamers
-
Greenleaf, W. J., Frieda, K. L., Foster, D. A., Woodside, M. T., and Block, S. M. (2008) Direct observation of hierarchical folding in single riboswitch aptamers. Science 319, 630-633
-
(2008)
Science
, vol.319
, pp. 630-633
-
-
Greenleaf, W.J.1
Frieda, K.L.2
Foster, D.A.3
Woodside, M.T.4
Block, S.M.5
-
5
-
-
33846898497
-
Interplay of 'induced fit' and preorganization in the ligand induced folding of the aptamer domain of the guanine binding riboswitch
-
Noeske, J., Buck, J., Fürtig, B., Nasiri, H. R., Schwalbe, H., and Wöhnert, J. (2007) Interplay of 'induced fit' and preorganization in the ligand induced folding of the aptamer domain of the guanine binding riboswitch. Nucleic Acids Res. 35, 572-583
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 572-583
-
-
Noeske, J.1
Buck, J.2
Fürtig, B.3
Nasiri, H.R.4
Schwalbe, H.5
Wöhnert, J.6
-
6
-
-
84889243990
-
The cellular environment stabilizes adenine riboswitch RNA structure
-
Tyrrell, J., McGinnis, J. L., Weeks, K. M., and Pielak, G. J. (2013) The cellular environment stabilizes adenine riboswitch RNA structure. Biochemistry 52, 8777-8785
-
(2013)
Biochemistry
, vol.52
, pp. 8777-8785
-
-
Tyrrell, J.1
McGinnis, J.L.2
Weeks, K.M.3
Pielak, G.J.4
-
7
-
-
84894281794
-
Molecular crowders and cosolutes promote folding cooperativity of RNA under physiological ionic conditions
-
Strulson, C. A., Boyer, J. A., Whitman, E. E., and Bevilacqua, P. C. (2014) Molecular crowders and cosolutes promote folding cooperativity of RNA under physiological ionic conditions. RNA 20, 331-347
-
(2014)
RNA
, vol.20
, pp. 331-347
-
-
Strulson, C.A.1
Boyer, J.A.2
Whitman, E.E.3
Bevilacqua, P.C.4
-
8
-
-
84888265981
-
Molecular crowding favors reactivity of a human ribozyme under physiological ionic conditions
-
Strulson, C. A., Yennawar, N. H., Rambo, R. P., and Bevilacqua, P. C. (2013) Molecular crowding favors reactivity of a human ribozyme under physiological ionic conditions. Biochemistry 52, 8187-8197
-
(2013)
Biochemistry
, vol.52
, pp. 8187-8197
-
-
Strulson, C.A.1
Yennawar, N.H.2
Rambo, R.P.3
Bevilacqua, P.C.4
-
9
-
-
15944382675
-
The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch
-
Wickiser, J. K., Winkler, W. C., Breaker, R. R., and Crothers, D. M. (2005) The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Mol. Cell 18, 49-60
-
(2005)
Mol. Cell
, vol.18
, pp. 49-60
-
-
Wickiser, J.K.1
Winkler, W.C.2
Breaker, R.R.3
Crothers, D.M.4
-
10
-
-
79851499341
-
Comparative study between transcriptionally- and translationally-acting adenine riboswitches reveals key differences in riboswitch regulatory mechanisms
-
Lemay, J. F., Desnoyers, G., Blouin, S., Heppell, B., Bastet, L., St-Pierre, P., Massé, E., and Lafontaine, D. A. (2011) Comparative study between transcriptionally- and translationally-acting adenine riboswitches reveals key differences in riboswitch regulatory mechanisms. PLoS Genetics 7, e1001278
-
(2011)
PLoS Genetics
, vol.7
, pp. e1001278
-
-
Lemay, J.F.1
Desnoyers, G.2
Blouin, S.3
Heppell, B.4
Bastet, L.5
St-Pierre, P.6
Massé, E.7
Lafontaine, D.A.8
-
11
-
-
21244459458
-
Kinetics and thermodynamics make different contributions to RNA folding in vitro and in yeast
-
Mahen, E. M., Harger, J. W., Calderon, E. M., and Fedor, M. J. (2005) Kinetics and thermodynamics make different contributions to RNA folding in vitro and in yeast. Mol. Cell 19, 27-37
-
(2005)
Mol. Cell
, vol.19
, pp. 27-37
-
-
Mahen, E.M.1
Harger, J.W.2
Calderon, E.M.3
Fedor, M.J.4
-
12
-
-
84882622399
-
Modularity of select riboswitch expression platforms enables facile engineering of novel genetic regulatory devices
-
Ceres, P., Garst, A. D., Marcano-Velázquez, J. G., and Batey, R. T. (2013) Modularity of select riboswitch expression platforms enables facile engineering of novel genetic regulatory devices. ACS Synth. Biol. 2, 463-472
-
(2013)
ACS Synth. Biol.
, vol.2
, pp. 463-472
-
-
Ceres, P.1
Garst, A.D.2
Marcano-Velázquez, J.G.3
Batey, R.T.4
-
13
-
-
79951565301
-
Design, construction and characterization of a set of insulated bacterial promoters
-
Davis, J. H., Rubin, A. J., and Sauer, R. T. (2011) Design, construction and characterization of a set of insulated bacterial promoters. Nucleic Acids Res. 39, 1131-1141
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 1131-1141
-
-
Davis, J.H.1
Rubin, A.J.2
Sauer, R.T.3
-
14
-
-
0003903343
-
-
Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
-
Sambrook, J., and Russell, D. W. (2001) Molecular Cloning: A Laboratory Manual, 3 Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
-
(2001)
Molecular Cloning: A Laboratory Manual, 3 Ed
-
-
Sambrook, J.1
Russell, D.W.2
-
15
-
-
31544450286
-
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: The Keio collection
-
Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K. A., Tomita, M., Wanner, B. L., and Mori, H. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2, 2006.0008
-
(2006)
Mol. Syst. Biol.
, vol.2
, pp. 20060008
-
-
Baba, T.1
Ara, T.2
Hasegawa, M.3
Takai, Y.4
Okumura, Y.5
Baba, M.6
Datsenko, K.A.7
Tomita, M.8
Wanner, B.L.9
Mori, H.10
-
16
-
-
80054074740
-
The structure of a tetrahydrofolate-sensing riboswitch reveals two ligand binding sites in a single aptamer
-
Trausch, J. J., Ceres, P., Reyes, F. E., and Batey, R. T. (2011) The structure of a tetrahydrofolate-sensing riboswitch reveals two ligand binding sites in a single aptamer. Structure 19, 1413-1423
-
(2011)
Structure
, vol.19
, pp. 1413-1423
-
-
Trausch, J.J.1
Ceres, P.2
Reyes, F.E.3
Batey, R.T.4
-
17
-
-
84866340759
-
Insights into the regulatory landscape of the lysine riboswitch
-
Garst, A. D., Porter, E. B., and Batey, R. T. (2012) Insights into the regulatory landscape of the lysine riboswitch. J. Mol. Biol. 423, 17-33
-
(2012)
J. Mol. Biol.
, vol.423
, pp. 17-33
-
-
Garst, A.D.1
Porter, E.B.2
Batey, R.T.3
-
18
-
-
69449089715
-
Determining structures of RNA aptamers and riboswitches by x-ray crystallography
-
Edwards, A. L., Garst, A. D., and Batey, R. T. (2009) Determining structures of RNA aptamers and riboswitches by x-ray crystallography. Methods Mol. Biol. 535, 135-163
-
(2009)
Methods Mol. Biol.
, vol.535
, pp. 135-163
-
-
Edwards, A.L.1
Garst, A.D.2
Batey, R.T.3
-
19
-
-
84877582071
-
Nucleotides adjacent to the ligandbinding pocket are linked to activity tuning in the purine riboswitch
-
Stoddard, C. D., Widmann, J., Trausch, J. J., Marcano-Velázquez, J. G., Knight, R., and Batey, R. T. (2013) Nucleotides adjacent to the ligandbinding pocket are linked to activity tuning in the purine riboswitch. J. Mol. Biol. 425, 1596-1611
-
(2013)
J. Mol. Biol.
, vol.425
, pp. 1596-1611
-
-
Stoddard, C.D.1
Widmann, J.2
Trausch, J.J.3
Marcano-Velázquez, J.G.4
Knight, R.5
Batey, R.T.6
-
20
-
-
36749100959
-
A new function for the Bacillus PbuE purine base efflux pump: Efflux of purine nucleosides
-
Zakataeva, N. P., Gronskiy, S. V., Sheremet, A. S., Kutukova, E. A., Novikova, A. E., and Livshits, V. A. (2007) A new function for the Bacillus PbuE purine base efflux pump: efflux of purine nucleosides. Res. Microbiol. 158, 659-665
-
(2007)
Res. Microbiol.
, vol.158
, pp. 659-665
-
-
Zakataeva, N.P.1
Gronskiy, S.V.2
Sheremet, A.S.3
Kutukova, E.A.4
Novikova, A.E.5
Livshits, V.A.6
-
21
-
-
34548726217
-
Ligand recognition determinants of guanine riboswitches
-
Mulhbacher, J., and Lafontaine, D. A. (2007) Ligand recognition determinants of guanine riboswitches. Nucleic Acids Res. 35, 5568-5580
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 5568-5580
-
-
Mulhbacher, J.1
Lafontaine, D.A.2
-
22
-
-
26444620938
-
The kinetics of ligand binding by an adenine-sensing riboswitch
-
Wickiser, J. K., Cheah, M. T., Breaker, R. R., and Crothers, D. M. (2005) The kinetics of ligand binding by an adenine-sensing riboswitch. Biochemistry 44, 13404-13414
-
(2005)
Biochemistry
, vol.44
, pp. 13404-13414
-
-
Wickiser, J.K.1
Cheah, M.T.2
Breaker, R.R.3
Crothers, D.M.4
-
23
-
-
33847308180
-
Core requirements of the adenine riboswitch aptamer for ligand binding
-
Lemay, J. F., and Lafontaine, D. A. (2007) Core requirements of the adenine riboswitch aptamer for ligand binding. RNA 13, 339-350
-
(2007)
RNA
, vol.13
, pp. 339-350
-
-
Lemay, J.F.1
Lafontaine, D.A.2
-
24
-
-
33646768226
-
Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain
-
Gilbert, S. D., Stoddard, C. D., Wise, S. J., and Batey, R. T. (2006) Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain. J. Mol. Biol. 359, 754-768
-
(2006)
J. Mol. Biol.
, vol.359
, pp. 754-768
-
-
Gilbert, S.D.1
Stoddard, C.D.2
Wise, S.J.3
Batey, R.T.4
-
25
-
-
36248982074
-
Mutational analysis of the purine riboswitch aptamer domain
-
Gilbert, S. D., Love, C. E., Edwards, A. L., and Batey, R. T. (2007) Mutational analysis of the purine riboswitch aptamer domain. Biochemistry 46, 13297-13309
-
(2007)
Biochemistry
, vol.46
, pp. 13297-13309
-
-
Gilbert, S.D.1
Love, C.E.2
Edwards, A.L.3
Batey, R.T.4
-
26
-
-
33747345020
-
Folding of the adenine riboswitch
-
Lemay, J. F., Penedo, J. C., Tremblay, R., Lilley, D. M., and Lafontaine, D. A. (2006) Folding of the adenine riboswitch. Chem. Biol. 13, 857-868
-
(2006)
Chem. Biol.
, vol.13
, pp. 857-868
-
-
Lemay, J.F.1
Penedo, J.C.2
Tremblay, R.3
Lilley, D.M.4
Lafontaine, D.A.5
-
27
-
-
84890327325
-
Engineering modular 'ON' RNA switches using biological components
-
Ceres, P., Trausch, J. J., and Batey, R. T. (2013) Engineering modular 'ON' RNA switches using biological components. Nucleic Acids Res. 41, 10449-10461
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 10449-10461
-
-
Ceres, P.1
Trausch, J.J.2
Batey, R.T.3
-
28
-
-
41649108293
-
Ligand-dependent folding of the three-way junction in the purine riboswitch
-
Stoddard, C. D., Gilbert, S. D., and Batey, R. T. (2008) Ligand-dependent folding of the three-way junction in the purine riboswitch. RNA 14, 675-684
-
(2008)
RNA
, vol.14
, pp. 675-684
-
-
Stoddard, C.D.1
Gilbert, S.D.2
Batey, R.T.3
-
29
-
-
9244225713
-
Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine
-
Batey, R. T., Gilbert, S. D., and Montange, R. K. (2004) Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature 432, 411-415
-
(2004)
Nature
, vol.432
, pp. 411-415
-
-
Batey, R.T.1
Gilbert, S.D.2
Montange, R.K.3
-
30
-
-
10644250950
-
Structural basis for discriminative regulation of gene expression by adenine-and guanine-sensing mRNAs
-
Serganov, A., Yuan, Y. R., Pikovskaya, O., Polonskaia, A., Malinina, L., Phan, A. T., Hobartner, C., Micura, R., Breaker, R. R., and Patel, D. J. (2004) Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. Chem. Biol. 11, 1729-1741
-
(2004)
Chem. Biol.
, vol.11
, pp. 1729-1741
-
-
Serganov, A.1
Yuan, Y.R.2
Pikovskaya, O.3
Polonskaia, A.4
Malinina, L.5
Phan, A.T.6
Hobartner, C.7
Micura, R.8
Breaker, R.R.9
Patel, D.J.10
-
31
-
-
0042121256
-
Mfold web server for nucleic acid folding and hybridization prediction
-
Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406-3415
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3406-3415
-
-
Zuker, M.1
-
32
-
-
84906329914
-
The importance of helix P1 stability for structural pre-organization and ligand binding affinity of the adenine riboswitch aptamer domain
-
Nozinovic, S., Reining, A., Kim, Y.-B., Noeske, J., Schlepckow, K., Wöhnert, J., and Schwalbe, H. (2014) The importance of helix P1 stability for structural pre-organization and ligand binding affinity of the adenine riboswitch aptamer domain. RNA Biol. 11, 655-666
-
(2014)
RNA Biol.
, vol.11
, pp. 655-666
-
-
Nozinovic, S.1
Reining, A.2
Kim, Y.-B.3
Noeske, J.4
Schlepckow, K.5
Wöhnert, J.6
Schwalbe, H.7
-
33
-
-
0037252684
-
Rfam: An RNA family database
-
Griffiths-Jones, S., Bateman, A., Marshall, M., Khanna, A., and Eddy, S. R. (2003) Rfam: an RNA family database. Nucleic Acids Res. 31, 439-441
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 439-441
-
-
Griffiths-Jones, S.1
Bateman, A.2
Marshall, M.3
Khanna, A.4
Eddy, S.R.5
-
34
-
-
57349085197
-
In vitro approaches to analysis of transcription termination
-
Artsimovitch, I., and Henkin, T. M. (2009) In vitro approaches to analysis of transcription termination. Methods 47, 37-43
-
(2009)
Methods
, vol.47
, pp. 37-43
-
-
Artsimovitch, I.1
Henkin, T.M.2
-
35
-
-
68049100110
-
Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli
-
Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., and Rabinowitz, J. D. (2009) Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat. Chem. Biol. 5, 593-599
-
(2009)
Nat. Chem. Biol.
, vol.5
, pp. 593-599
-
-
Bennett, B.D.1
Kimball, E.H.2
Gao, M.3
Osterhout, R.4
Van Dien, S.J.5
Rabinowitz, J.D.6
-
36
-
-
79955604950
-
Folding of the lysine riboswitch: Importance of peripheral elements for transcriptional regulation
-
Blouin, S., Chinnappan, R., and Lafontaine, D. A. (2011) Folding of the lysine riboswitch: importance of peripheral elements for transcriptional regulation. Nucleic Acids Res. 39, 3373-3387
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 3373-3387
-
-
Blouin, S.1
Chinnappan, R.2
Lafontaine, D.A.3
-
37
-
-
67650542563
-
Contribution of the closing base pair to exceptional stability in RNA tetraloops: Roles for molecular mimicry and electrostatic factors
-
Blose, J. M., Proctor, D. J., Veeraraghavan, N., Misra, V. K., and Bevilacqua, P. C. (2009) Contribution of the closing base pair to exceptional stability in RNA tetraloops: roles for molecular mimicry and electrostatic factors. J. Am. Chem. Soc. 131, 8474-8484
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 8474-8484
-
-
Blose, J.M.1
Proctor, D.J.2
Veeraraghavan, N.3
Misra, V.K.4
Bevilacqua, P.C.5
-
38
-
-
33744996366
-
Structural parameters affecting the kinetics of RNA hairpin formation
-
Nagel, J. H., Flamm, C., Hofacker, I. L., Franke, K., de Smit, M. H., Schuster, P., and Pleij, C. W. (2006) Structural parameters affecting the kinetics of RNA hairpin formation. Nucleic Acids Res. 34, 3568-3576
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 3568-3576
-
-
Nagel, J.H.1
Flamm, C.2
Hofacker, I.L.3
Franke, K.4
De Smit, M.H.5
Schuster, P.6
Pleij, C.W.7
-
39
-
-
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., and Henkin, T. M. (2003) Transcription termination control of the S box system: direct measurement of S-adenosylmethionine by the leader RNA. Proc. Natl. Acad. Sci. U.S.A. 100, 3083-3088
-
(2003)
Proc. Natl. Acad. Sci. U.S.A.
, vol.100
, pp. 3083-3088
-
-
McDaniel, B.A.1
Grundy, F.J.2
Artsimovitch, I.3
Henkin, T.M.4
-
40
-
-
77649169870
-
MRNA secondary structures fold sequentially but exchange rapidly in vivo
-
Mahen, E. M., Watson, P. Y., Cottrell, J. W., and Fedor, M. J. (2010)mRNA secondary structures fold sequentially but exchange rapidly in vivo. PLoS Biol. 8, e1000307
-
(2010)
PLoS Biol.
, vol.8
, pp. e1000307
-
-
Mahen, E.M.1
Watson, P.Y.2
Cottrell, J.W.3
Fedor, M.J.4
-
41
-
-
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., and Henkin, T. M. (2008) 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. 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
-
42
-
-
0035010211
-
Geometric nomenclature and classification of RNA base pairs
-
Leontis, N. B., and Westhof, E. (2001) Geometric nomenclature and classification of RNA base pairs. RNA 7, 499-512
-
(2001)
RNA
, vol.7
, pp. 499-512
-
-
Leontis, N.B.1
Westhof, E.2
|