-
1
-
-
0038210214
-
Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria
-
DOI 10.1016/S0092-8674(03)00391-X
-
Mandai, M., Boese, B., Barrick, J. E., Winkler, W. C., and Breaker, R. R. (2003) Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell 113, 577-586. (Pubitemid 36694183)
-
(2003)
Cell
, vol.113
, Issue.5
, pp. 577-586
-
-
Mandal, M.1
Boese, B.2
Barrick, J.E.3
Winkler, W.C.4
Breaker, R.R.5
-
2
-
-
67650713931
-
The structural and functional diversity of metabolite-binding riboswitches
-
Roth, A., and Breaker, R. R. (2009) The Structural and Functional Diversity of Metabolite-Binding Riboswitches. Annu. Rev. Biochem. 78, 305-334.
-
(2009)
Annu. Rev. Biochem.
, vol.78
, pp. 305-334
-
-
Roth, A.1
Breaker, R.R.2
-
3
-
-
48249104039
-
Riboswitches: Emerging themes in RNA structure and function
-
Montange, R. K., and Batey, R. T. (2008) Riboswitches: Emerging themes in RNA structure and function. Annu. Rev. Biophys. 37, 117-133.
-
(2008)
Annu. Rev. Biophys.
, vol.37
, pp. 117-133
-
-
Montange, R.K.1
Batey, R.T.2
-
4
-
-
60349085695
-
Riboswitches: Ancient and promising genetic regulators
-
Blouin, S., Mulhbacher, J., Penedo, J. C., and Lafontaine, D. A. (2009) Riboswitches: Ancient and Promising Genetic Regulators. ChemBioChem 10, 400-416.
-
(2009)
ChemBioChem
, vol.10
, pp. 400-416
-
-
Blouin, S.1
Mulhbacher, J.2
Penedo, J.C.3
Lafontaine, D.A.4
-
5
-
-
0042890402
-
Definition of a second Bacillus subtilis pur regulon comprising the pur and xpt-pbuX operons plus pbuG, nupG (yxjA), and pbuE (ydhL)
-
DOI 10.1128/JB.185.17.5200-5209.2003
-
Johansen, L. E., Nygaard, P., Lassen, C., Agersa, Y., and Saxild, H. H. (2003) Definition of a second Bacillus subtitis pur regulon comprising the pur and xpt-pbuX operons plus pbuG, nupG (yxjA), and pbuE (ydhL). J. Bacteriol. 185, 5200-5209. (Pubitemid 37021982)
-
(2003)
Journal of Bacteriology
, vol.185
, Issue.17
, pp. 5200-5209
-
-
Johansen, L.E.1
Nygaard, P.2
Lassen, C.3
Agerso, Y.4
Saxild, H.H.5
-
6
-
-
0842334528
-
Adenine riboswitches and gene activation by disruption of a transcription, terminator
-
Mandai, 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
-
-
Mandai, M.1
Breaker, R.R.2
-
7
-
-
34447548824
-
Ligand-induced folding of the adenosine deaminase A-riboswitch and implications on riboswitch translational control
-
DOI 10.1002/cbic.200700057
-
Rieder, R., Lang, K., Graber, D., and Micura, R. (2007) LigandInduced Folding of the Adenosine Deaminase A-Riboswitch and Implications on Riboswitch Translational Control. ChemBioChem 8, 896-902. (Pubitemid 47194838)
-
(2007)
ChemBioChem
, vol.8
, Issue.8
, pp. 896-902
-
-
Rieder, R.1
Lang, K.2
Graber, D.3
Micura, R.4
-
8
-
-
72149126118
-
A switch in time: Detailing the life of a riboswitch
-
Garst, A. D., and Batey, R. T. (2009) A switch in time: Detailing the life of a riboswitch. Biochim. Biophys. Acta 1789, 584-591.
-
(2009)
Biochim. Biophys. Acta
, vol.1789
, pp. 584-591
-
-
Garst, A.D.1
Batey, R.T.2
-
9
-
-
38849103659
-
Purine sensing by riboswitches
-
Kim, J. N., and Breaker, R. R. (2008) Purine sensing by riboswitches. Biol. Cell 100, 1-11.
-
(2008)
Biol. Cell
, vol.100
, pp. 1-11
-
-
Kim, J.N.1
Breaker, R.R.2
-
10
-
-
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
-
11
-
-
10644250950
-
Structural basis for discriminative regulation of gene expression by adenine- And guanine-sensing mRNAs
-
DOI 10.1016/j.chembiol.2004.11.018, PII S1074552104003436
-
Serganov, A., Yuan, Y. R., Pikovskaya, O., Polonskaia, A., Malinina, L., Phan, A. T., Höbartner, 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. (Pubitemid 39651306)
-
(2004)
Chemistry and Biology
, vol.11
, Issue.12
, 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
-
12
-
-
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
-
13
-
-
13444271576
-
An intermolecular base triple as the basis of ligand specificity and affinity in the guanine- And adenine-sensing riboswitch RNAs
-
DOI 10.1073/pnas.0406347102
-
Noeske, J., Richter, C., Grandi, M. A., Nasiri, H. R., Schwalbe, H., and Wöhnert, J. (2005) An intermolecular base triple as the basis of ligand specificity and affinity in the guanine- and adenine-sensing riboswitch RNAs. Proc. Natl. Acad. Sci. U.S.A. 102, 1372-1377. (Pubitemid 40209177)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.5
, pp. 1372-1377
-
-
Noeske, J.1
Richter, C.2
Grundl, M.A.3
Nasiri, H.R.4
Schwalbe, H.5
Wohnert, J.6
-
14
-
-
34548726217
-
Ligand recognition determinants of guanine riboswitches
-
DOI 10.1093/nar/gkm572
-
Mulhbacher, J., and Lafontaine, D. A. (2007) Ligand recognition determinants of guanine riboswitches. Nucleic Acids Res. 35, 5568-5580. (Pubitemid 47423928)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.16
, pp. 5568-5580
-
-
Mulhbacher, J.1
Lafontaine, D.A.2
-
15
-
-
66349133602
-
Adaptive ligand binding by the purine riboswitch in the recognition of guanine and adenine analogs
-
Gilbert, S. D., Reyes, F. E., Edwards, A. L., and Batey, R. T. (2009) Adaptive ligand binding by the purine riboswitch in the recognition of guanine and adenine analogs. Structure 17, 857-868.
-
(2009)
Structure
, vol.17
, pp. 857-868
-
-
Gilbert, S.D.1
Reyes, F.E.2
Edwards, A.L.3
Batey, R.T.4
-
16
-
-
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. Biochimistry 46, 13297-13309.
-
(2007)
Biochimistry
, vol.46
, pp. 13297-13309
-
-
Gilbert, S.D.1
Love, C.E.2
Edwards, A.L.3
Batey, R.T.4
-
17
-
-
33747345020
-
Folding of the adenine riboswitch
-
Lemay, J. F., Penedo, J. C., Tremblay, R., Lilley, D. M. J., 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.J.4
Lafontaine, D.A.5
-
18
-
-
41649108293
-
Liganddependent folding of the three-way junction in the purine riboswitch
-
Stoddard, C. D., Gilbert, S. D., and Batey, R. T. (2008) Liganddependent 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
-
19
-
-
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
-
20
-
-
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
-
21
-
-
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
-
22
-
-
40749138645
-
A forced march across an RNA folding landscape
-
Silverman, S. K. (2008) A Forced March across an RNA Folding Landscape. Chem. Biol. 15, 211-213.
-
(2008)
Chem. Biol.
, vol.15
, pp. 211-213
-
-
Silverman, S.K.1
-
23
-
-
0033776960
-
Fluorescence resonance energy transfer as a structural tool for nucleic acids
-
DOI 10.1016/S1367-5931(00)00124-1
-
Lilley, D. M. J., and Wilson, T. J. (2000) Fluorescence resonance energy transfer as a structural tool for nucleic acids. Curr. Opin. Chem. Biol. 4, 507-517. (Pubitemid 30781272)
-
(2000)
Current Opinion in Chemical Biology
, vol.4
, Issue.5
, pp. 507-517
-
-
Lilley, D.M.J.1
Wilson, T.J.2
-
24
-
-
2442519939
-
Time-resolved fluorescence resonance energy transfer: A versatile tool for the analysis of nucleic acids
-
DOI 10.1002/bip.10146
-
Kiostermeier, D., and Millar, D. P. (2001) Time-resolved fluorescence resonance energy transfer: A versatile tool for the analysis of nucleic acids. Biopolymers 61, 159-179. (Pubitemid 34496055)
-
(2001)
Biopolymers
, vol.61
, Issue.3
, pp. 159-179
-
-
Klostermeier, D.1
Millar, D.P.2
-
25
-
-
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
-
26
-
-
0033529972
-
Ligand-induced conformational changes observed in single RNA molecules
-
DOI 10.1073/pnas.96.16.9077
-
Ha, T., Zhuang, X., Kim, H. D., Orr, J. W.; Williamson, J. R., and Chu, S. (1999) Ligand-induced conformational changes observed in single RNA molecules, Proc. Natl. Acad. Sci. U.S.A. 96, 9077-9082. (Pubitemid 29374710)
-
(1999)
Proceedings of the National Academy of Sciences of the United States of America
, vol.96
, Issue.16
, pp. 9077-9082
-
-
Ha, T.1
Zhuang, X.2
Kim, H.D.3
Orr, J.W.4
Williamson, J.R.5
Chu, S.6
-
27
-
-
0034674420
-
A single-molecule study of RNA catalysis and folding
-
DOI 10.1126/science.288.5473.2048
-
Zhuang, X., Bartley, L. E., Babcock, H. P., Russell, R., Ha, T., Herschlag, D., and Chu, S. (2000) A single-molecule study of RNA catalysis and folding. Science 288, 2048-2051. (Pubitemid 30397686)
-
(2000)
Science
, vol.288
, Issue.5473
, 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
-
28
-
-
0037165996
-
Correlating structural dynamics and function in single ribozyme molecules
-
DOI 10.1126/science.1069013
-
Zhuang, X., Kim, H., Pereira, M. J., Babcock, H. P., Walter, N. G., and Chu, S. (2002) Correlating structural dynamics and function in single ribozyme molecules, Science 296, 1473-1476. (Pubitemid 34553093)
-
(2002)
Science
, vol.296
, Issue.5572
, pp. 1473-1476
-
-
Zhuang, X.1
Kim, H.2
Pereira, M.J.B.3
Babcock, H.P.4
Walter, N.G.5
Chu, S.6
-
29
-
-
0043009768
-
A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate
-
DOI 10.1073/pnas.1233536100
-
Tan, E., Wilson, T. J., Nahas, M. K., Clegg, R. M., Lilley, D. M., and Ha, T. (2003) A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate, Proc. Natl. Acad. Sci. U.S.A. 100, 9308-9313. (Pubitemid 37038088)
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.16
, pp. 9308-9313
-
-
Tan, E.1
Wilson, T.J.2
Nahas, M.K.3
Clegg, R.M.4
Lilley, D.M.J.5
Ha, T.6
-
30
-
-
0347004715
-
Single-molecule studies highlight conformational heterogeneity in the early folding steps of a large ribozyme
-
DOI 10.1073/pnas.2636333100
-
Xie, Z., Srividya, N., Sosnick, T. R., Pan, T., and Scherer, N. F. (2004) Single-molecule studies highlight conformational heterogeneity in the early folding steps of a large ribozyme. Proc. Natl. Acad. Sci. U.S.A. 101, 534-539. (Pubitemid 38084671)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.2
, pp. 534-539
-
-
Xie, Z.1
Srividya, N.2
Sosnick, T.R.3
Pan, T.4
Scherer, N.F.5
-
31
-
-
23044431628
-
Docking kinetics and equilibrium of a GAAA tetraloop-receptor motif probed by single-molecule FRET
-
DOI 10.1073/pnas.0408645102
-
Hodak, J. H., Downey, C. D., Fiore, J. L., Pardi, A., and Nesbitt, D. J. (2005) Docking kinetics and equilibrium of a GAAA tetraloopreceptor motif probed by single-molecule FRET. Proc. Natl. Acad. Sci. U.S.A. 102, 10505-10510. (Pubitemid 41061584)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.30
, pp. 10505-10510
-
-
Hodak, J.H.1
Fiore, J.L.2
Nesbitt, D.J.3
Downey, C.D.4
Pardi, A.5
-
33
-
-
50049086369
-
Single VS ribozyme molecules reveal dynamic and hierarchical folding toward catalysis
-
Pereira, M. J., Nikolova, E. N., Hiley, S. L., Jaikaran, D., Collins, R. A., and Walter, N. G. (2008) Single VS ribozyme molecules reveal dynamic and hierarchical folding toward catalysis. J. Biol. Biol. 382, 496-509.
-
(2008)
J. Biol. Biol.
, vol.382
, pp. 496-509
-
-
Pereira, M.J.1
Nikolova, E.N.2
Hiley, S.L.3
Jaikaran, D.4
Collins, R.A.5
Walter, N.G.6
-
34
-
-
52949084315
-
Single-molecule studies of group II intron ribozymes
-
Steiner, M., Karunatilaka, K. S., Sigel, R. K., and Rueda, D. (2008) Single-molecule studies of group II intron ribozymes. Proc. Natl. Acad. Sci. U.S.A. 105, 13853-13858.
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.105
, pp. 13853-13858
-
-
Steiner, M.1
Karunatilaka, K.S.2
Sigel, R.K.3
Rueda, D.4
-
35
-
-
35048838732
-
Ligand-directed dynamics of adenine riboswitch conformers
-
DOI 10.1021/ja073159l
-
Eskandari, S., Prychyna, O., Leung, J., Avdic, D., and O'Neill, M. A. (2007) Ligand-directed dynamics of adenine riboswitch conformers. J. Am. Chem. Soc. 129, 11308-11309. (Pubitemid 47555530)
-
(2007)
Journal of the American Chemical Society
, vol.129
, Issue.37
, pp. 11308-11309
-
-
Eskandari, S.1
Prychyna, O.2
Leung, J.3
Avdic, D.4
O'Neill, M.A.5
-
37
-
-
84897585709
-
In-line probing analysis of riboswitches
-
Regulski, E. E., and Breaker, R. R. (2008) In-line probing analysis of riboswitches. Methods Mol. Biol. 419, 53-67.
-
(2008)
Methods Mol. Biol.
, vol.419
, pp. 53-67
-
-
Regulski, E.E.1
Breaker, R.R.2
-
38
-
-
0026687952
-
Fluorescence resonance energy transfer and nucleic acids, Methods
-
Clegg, R. M. (1992) Fluorescence resonance energy transfer and nucleic acids, Methods Enzymol. 211, 353-388.
-
(1992)
Enzymol.
, vol.211
, pp. 353-388
-
-
Clegg, R.M.1
-
39
-
-
0033607150
-
RNA tertiary folding monitored by fluorescence of covalently attached pyrene
-
Silverman, S. K., and Cech, T. R. (1999) RNA. Tertiary Folding Monitored by Fluorescence of Covalently Attached Pyrene. Biochemistry 38, 14224-14237. (Pubitemid 129520302)
-
(1999)
Biochemistry
, vol.38
, Issue.43
, pp. 14224-14237
-
-
Silverman, S.K.1
Cech, T.R.2
-
40
-
-
44449134820
-
A practical guide to singlemolecule FRET
-
Roy, R., Hohng, S., and Ha, T. (2008) A practical guide to singlemolecule FRET, Nat. Methods 5, 507-516.
-
(2008)
Nat. Methods
, vol.5
, pp. 507-516
-
-
Roy, R.1
Hohng, S.2
Ha, T.3
-
41
-
-
33750295496
-
Nonblinking and long-lasting single-molecule fluorescence imaging
-
DOI 10.1038/nmeth934, PII NMETH934
-
Rasnik, I., McKinney, S. A., and Ha, T. (2006) Nonblinking and longlasting single-molecule fluorescence imaging. Ngt. Methods 3, 891-893. (Pubitemid 44614723)
-
(2006)
Nature Methods
, vol.3
, Issue.11
, pp. 891-893
-
-
Rasnik, I.1
McKinney, S.A.2
Ha, T.3
-
42
-
-
0037315675
-
Structural dynamics of individual Holliday junctions
-
McKinney, S. A., Declais, A. C., Lilley, D. M., and Ha, T. (2003) Structural dynamics of individual Holliday junctions. Ngt. Struct. Biol. 10, 93-97.
-
(2003)
Ngt. Struct. Biol.
, vol.10
, pp. 93-97
-
-
McKinney, S.A.1
Declais, A.C.2
Lilley, D.M.3
Ha, T.4
-
43
-
-
0026699945
-
Regulation, of cell magnesium
-
Romani, A., and Scarpa, A. (1992) Regulation, of cell magnesium. Arch. Biochem. Biophys. 298, 1-12.
-
(1992)
Arch. Biochem. Biophys.
, vol.298
, pp. 1-12
-
-
Romani, A.1
Scarpa, A.2
-
44
-
-
33846898497
-
Interplay of 'induced fit' and preorganization in the ligand induced folding of the aptamer domain of the guanine binding riboswitch
-
DOI 10.1093/nar/gkl1094
-
Noeske, J., Buck, J., Fürtig, B., Nasiri, H. R., Schwalbe, H., and Wöhnert, J. (2007) Interplay of 'induced fit' and preorganizaron in the ligand induced folding of the aptamer domain of the guanine binding riboswitch. Nucleic Acids Res. 35, 572-583. (Pubitemid 46232073)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.2
, pp. 572-583
-
-
Noeske, J.1
Buck, J.2
Furtig, B.3
Nasiri, H.R.4
Schwalbe, H.5
Wohnert, J.6
|