-
1
-
-
84872517135
-
Modulation of quaternary structure and enhancement of ligand binding by the k-turn of tandem glycine riboswitches
-
Baird NJ, Ferré-D'Amaré AR. 2013. Modulation of quaternary structure and enhancement of ligand binding by the K-turn of tandem glycine riboswitches. RNA 19: 167-176.
-
(2013)
RNA
, vol.19
, pp. 167-176
-
-
Baird, N.J.1
Ferré-D'amaré, A.R.2
-
2
-
-
46349083026
-
The distributions, mechanisms, and structures of metabolite-binding riboswitches
-
Barrick JE, Breaker RR. 2007. The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biol 8: R239.
-
(2007)
Genome Biol
, vol.8
, pp. R239
-
-
Barrick, J.E.1
Breaker, R.R.2
-
3
-
-
2342511433
-
New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control
-
Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, Lee M, Roth A, Sudarsan N, Jona I, et al. 2004. New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc Natl Acad Sci 101: 6421-6426.
-
(2004)
Proc Natl Acad Sci
, vol.101
, pp. 6421-6426
-
-
Barrick, J.E.1
Corbino, K.A.2
Winkler, W.C.3
Nahvi, A.4
Mandal, M.5
Collins, J.6
Lee, M.7
Roth, A.8
Sudarsan, N.9
Jona, I.10
-
4
-
-
80052973462
-
Prospects for riboswitch discovery and analysis
-
Breaker RR. 2011. Prospects for riboswitch discovery and analysis. Mol Cell 43: 867-879.
-
(2011)
Mol Cell
, vol.43
, pp. 867-879
-
-
Breaker, R.R.1
-
5
-
-
77749304812
-
Multivector fluorescence analysis of the xpt guanine riboswitch aptamer domain and the conformational role of guanine
-
Brenner MD, Scanlan MS, Nahas MK, Ha T, Silverman SK. 2010. Multivector fluorescence analysis of the xpt guanine riboswitch aptamer domain and the conformational role of guanine. Biochemistry 49: 1596-1605.
-
(2010)
Biochemistry
, vol.49
, pp. 1596-1605
-
-
Brenner, M.D.1
Scanlan, M.S.2
Nahas, M.K.3
Ha, T.4
Silverman, S.K.5
-
6
-
-
79953052076
-
Structural basis of cooperative ligand binding by the glycine riboswitch
-
Butler EB, Xiong Y, Wang J, Strobel SA. 2011. Structural basis of cooperative ligand binding by the glycine riboswitch. Chem Biol 18: 293-298.
-
(2011)
Chem Biol
, vol.18
, pp. 293-298
-
-
Butler, E.B.1
Xiong, Y.2
Wang, J.3
Strobel, S.A.4
-
7
-
-
17444453249
-
Revised UV extinction coefficients for nucleoside-5′-monophosphates and unpaired DNA and RNA
-
Cavaluzzi MJ, Borer PN. 2004. Revised UV extinction coefficients for nucleoside-5′-monophosphates and unpaired DNA and RNA. Nucleic Acids Res 32: E13.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. e13
-
-
Cavaluzzi, M.J.1
Borer, P.N.2
-
9
-
-
78650424317
-
Identification of a tertiary interaction important for cooperative ligand binding by the glycine riboswitch
-
Erion TV, Strobel SA. 2011. Identification of a tertiary interaction important for cooperative ligand binding by the glycine riboswitch. RNA 17: 74-84.
-
(2011)
RNA
, vol.17
, pp. 74-84
-
-
Erion, T.V.1
Strobel, S.A.2
-
10
-
-
84902197971
-
Characterizing the dynamics of the leader-linker interaction in the glycine riboswitch with site-directed spin labeling
-
Esquiaqui JM, Sherman EM, Ionescu SA, Ye J-D, Fanucci GE. 2014. Characterizing the dynamics of the leader-linker interaction in the glycine riboswitch with site-directed spin labeling. Biochemistry 53: 3526-3528.
-
(2014)
Biochemistry
, vol.53
, pp. 3526-3528
-
-
Esquiaqui, J.M.1
Sherman, E.M.2
Ionescu, S.A.3
Ye, J.-D.4
Fanucci, G.E.5
-
11
-
-
79956072525
-
Conformational capture of the SAM-II riboswitch
-
Haller A, Rieder U, Aigner M, Blanchard SC, Micura R. 2011. Conformational capture of the SAM-II riboswitch. Nat Chem Biol 7: 393-400.
-
(2011)
Nat Chem Biol
, vol.7
, pp. 393-400
-
-
Haller, A.1
Rieder, U.2
Aigner, M.3
Blanchard, S.C.4
Micura, R.5
-
12
-
-
79956101942
-
Molecular insights into the ligand- controlled organization of the SAM-I riboswitch
-
Heppell B, Blouin S, Dussault A-M, Mulhbacher J, Ennifar E, Penedo JC, Lafontaine DA. 2011. Molecular insights into the ligand- controlled organization of the SAM-I riboswitch. Nat Chem Biol 7: 384-392.
-
(2011)
Nat Chem Biol
, vol.7
, pp. 384-392
-
-
Heppell, B.1
Blouin, S.2
Dussault, A.-M.3
Mulhbacher, J.4
Ennifar, E.5
Penedo, J.C.6
Lafontaine, D.A.7
-
13
-
-
78649970557
-
Structural insights into ligand recognition by a sensing domain of the cooperative glycine riboswitch
-
Huang L, Serganov A, Patel DJ. 2010. Structural insights into ligand recognition by a sensing domain of the cooperative glycine riboswitch. Mol Cell 40: 774-786.
-
(2010)
Mol Cell
, vol.40
, pp. 774-786
-
-
Huang, L.1
Serganov, A.2
Patel, D.J.3
-
14
-
-
38549119502
-
Abundance and functional diversity of riboswitches in microbial communities
-
Kazanov MD, Vitreschak AG, Gelfand MS. 2007. Abundance and functional diversity of riboswitches in microbial communities. BMC Genomics 8: 347.
-
(2007)
BMC Genomics
, vol.8
, pp. 347
-
-
Kazanov, M.D.1
Vitreschak, A.G.2
Gelfand, M.S.3
-
15
-
-
84856246110
-
Automated RNA structure prediction uncovers a kink-turn linker in double glycine riboswitches
-
Kladwang W, Chou F-C, Das R. 2012. Automated RNA structure prediction uncovers a kink-turn linker in double glycine riboswitches. J Am Chem Soc 134: 1404-1407.
-
(2012)
J Am Chem Soc
, vol.134
, pp. 1404-1407
-
-
Kladwang, W.1
Chou, F.-C.2
Das, R.3
-
16
-
-
38049025288
-
Chemical basis of glycine riboswitch cooperativity
-
Kwon M, Strobel SA. 2008. Chemical basis of glycine riboswitch cooperativity. RNA 14: 25-34.
-
(2008)
RNA
, vol.14
, pp. 25-34
-
-
Kwon, M.1
Strobel, S.A.2
-
17
-
-
33747345020
-
Folding of the adenine riboswitch
-
Lemay J-F, Penedo JC, Tremblay R, Lilley DMJ, Lafontaine DA. 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
-
-
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, Lafontaine DA. 2011. Comparative study between transcriptionally- And translationally-acting adenine riboswitches reveals key differences in riboswitch regulatory mechanisms. PLoS Genet 7: E1001278.
-
(2011)
PLoS Genet
, 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
-
19
-
-
33845971464
-
Structural transitions and thermodynamics of a glycine- dependent riboswitch from vibrio cholerae
-
Lipfert J, Das R, Chu VB, Kudaravalli M, Boyd N, Herschlag D, Doniach S. 2007. Structural transitions and thermodynamics of a glycine- dependent riboswitch from Vibrio cholerae. J Mol Biol 365: 1393-1406.
-
(2007)
J Mol Biol
, vol.365
, pp. 1393-1406
-
-
Lipfert, J.1
Das, R.2
Chu, V.B.3
Kudaravalli, M.4
Boyd, N.5
Herschlag, D.6
Doniach, S.7
-
20
-
-
5044234799
-
A glycine-dependent riboswitch that uses cooperative binding to control gene expression
-
Mandal M, Lee M, Barrick JE, Weinberg Z, Emilsson GM, Ruzzo WL, Breaker RR. 2004. A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science 306: 275-279.
-
(2004)
Science
, vol.306
, pp. 275-279
-
-
Mandal, M.1
Lee, M.2
Barrick, J.E.3
Weinberg, Z.4
Emilsson, G.M.5
Ruzzo, W.L.6
Breaker, R.R.7
-
21
-
-
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, 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
-
22
-
-
34447548824
-
Ligand-induced folding of the adenosine deaminase a-riboswitch and implications on riboswitch translational control
-
Rieder R, Lang K, Graber D, Micura R. 2007. Ligand-induced folding of the adenosine deaminase A-riboswitch and implications on riboswitch translational control. Chembiochem 8: 896-902.
-
(2007)
Chembiochem
, vol.8
, pp. 896-902
-
-
Rieder, R.1
Lang, K.2
Graber, D.3
Micura, R.4
-
23
-
-
0032860382
-
Nucleotide analog interference mapping
-
Ryder SP, Strobel SA. 1999. Nucleotide analog interference mapping. Methods 18: 38-50.
-
(1999)
Methods
, vol.18
, pp. 38-50
-
-
Ryder, S.P.1
Strobel, S.A.2
-
24
-
-
84872543206
-
A decade of riboswitches
-
Serganov A, Nudler E. 2013. A decade of riboswitches. Cell 152: 17-24.
-
(2013)
Cell
, vol.152
, pp. 17-24
-
-
Serganov, A.1
Nudler, E.2
-
25
-
-
84861405805
-
Metabolite recognition principles and molecular mechanisms underlying riboswitch function
-
Serganov A, Patel DJ. 2012. Metabolite recognition principles and molecular mechanisms underlying riboswitch function. Annu Rev Biophys 41: 343-370.
-
(2012)
Annu Rev Biophys
, vol.41
, pp. 343-370
-
-
Serganov, A.1
Patel, D.J.2
-
26
-
-
84857438025
-
An energetically beneficial leader-linker interaction abolishes ligand-binding cooperativity in glycine riboswitches
-
Sherman EM, Esquiaqui J, Elsayed G, Ye J-D. 2012. An energetically beneficial leader-linker interaction abolishes ligand-binding cooperativity in glycine riboswitches. RNA 18: 496-507.
-
(2012)
RNA
, vol.18
, pp. 496-507
-
-
Sherman, E.M.1
Esquiaqui, J.2
Elsayed, G.3
Ye, J.-D.4
-
27
-
-
84941026253
-
Dna-rescuable allosteric inhibition of aptamer II ligand affinity by aptamer I element in the shortened vibrio cholerae glycine riboswitch
-
Sherman EM, Elsayed G, Esquiaqui JM, Elsayed M, Brinda B, Ye J-D. 2014. DNA-rescuable allosteric inhibition of aptamer II ligand affinity by aptamer I element in the shortened Vibrio cholerae glycine riboswitch. J Biochem doi: 10.1093/jb/mvu048.
-
(2014)
J Biochem
-
-
Sherman, E.M.1
Elsayed, G.2
Esquiaqui, J.M.3
Elsayed, M.4
Brinda, B.5
Ye, J.-D.6
-
28
-
-
84883432280
-
Tuning a riboswitch response through structural extension of a pseudoknot
-
Soulière MF, Altman RB, Schwarz V, Haller A, Blanchard SC, Micura R. 2013. Tuning a riboswitch response through structural extension of a pseudoknot. Proc Natl Acad Sci 110: E3256-E3264.
-
(2013)
Proc Natl Acad Sci
, vol.110
, pp. E3256-E3264
-
-
Soulière, M.F.1
Altman, R.B.2
Schwarz, V.3
Haller, A.4
Blanchard, S.C.5
Micura, R.6
-
29
-
-
33749986680
-
Tandem riboswitch architectures exhibit complex gene control functions
-
Sudarsan N, Hammond MC, Block KF, Welz R, Barrick JE, Roth A, Breaker RR. 2006. Tandem riboswitch architectures exhibit complex gene control functions. Science 314: 300-304.
-
(2006)
Science
, vol.314
, pp. 300-304
-
-
Sudarsan, N.1
Hammond, M.C.2
Block, K.F.3
Welz, R.4
Barrick, J.E.5
Roth, A.6
Breaker, R.R.7
-
30
-
-
84895737813
-
Two glycine riboswitches activate the glycine cleavage system essential for glycine detoxification in streptomyces griseus
-
Tezuka T, Ohnishi Y. 2014. Two glycine riboswitches activate the glycine cleavage system essential for glycine detoxification in Streptomyces griseus. J Bacteriol 196: 1369-1376.
-
(2014)
J Bacteriol
, vol.196
, pp. 1369-1376
-
-
Tezuka, T.1
Ohnishi, Y.2
-
31
-
-
84894462887
-
A disconnect between high-affinity binding and efficient regulation by antifolates and purines in the tetrahydrofolate riboswitch
-
Trausch JJ, Batey RT. 2014. A disconnect between high-affinity binding and efficient regulation by antifolates and purines in the tetrahydrofolate riboswitch. Chem Biol 21: 205-216.
-
(2014)
Chem Biol
, vol.21
, pp. 205-216
-
-
Trausch, J.J.1
Batey, R.T.2
-
32
-
-
80054074740
-
The structure of a tetrahydrofolate- sensing riboswitch reveals two ligand binding sites in a single aptamer
-
Trausch JJ, Ceres P, Reyes FE, Batey RT. 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
-
33
-
-
79960991166
-
Constitutive regulatory activity of an evolutionarily excluded riboswitch variant
-
Tremblay R, Lemay J-F, Blouin S, Mulhbacher J, Bonneau É, Legault P, Dupont P, Penedo JC, Lafontaine DA. 2011. Constitutive regulatory activity of an evolutionarily excluded riboswitch variant. J Biol Chem 286: 27406-27415.
-
(2011)
J Biol Chem
, vol.286
, pp. 27406-27415
-
-
Tremblay, R.1
Lemay, J.-F.2
Blouin, S.3
Mulhbacher, J.4
Bonneau É.5
Legault, P.6
Dupont, P.7
Penedo, J.C.8
Lafontaine, D.A.9
-
34
-
-
33947714417
-
Ligand binding and gene control characteristics of tandem riboswitches in bacillus anthracis
-
Welz R, Breaker RR. 2007. Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis. RNA 13: 573-582.
-
(2007)
RNA
, vol.13
, pp. 573-582
-
-
Welz, R.1
Breaker, R.R.2
-
36
-
-
15944382675
-
The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch
-
Wickiser JK, Winkler WC, Breaker RR, Crothers DM. 2005b. 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
-
37
-
-
84902688021
-
A neutral ph thermal hydrolysis method for quantification of structured RNAs
-
Wilson SC, Cohen DT, Wang XC, Hammond MC. 2014. A neutral pH thermal hydrolysis method for quantification of structured RNAs. RNA 20: 1153-1160.
-
(2014)
RNA
, vol.20
, pp. 1153-1160
-
-
Wilson, S.C.1
Cohen, D.T.2
Wang, X.C.3
Hammond, M.C.4
-
38
-
-
84862109207
-
Allosteric tertiary interactions preorganize the c-di-GMP riboswitch and accelerate ligand binding
-
Wood S, Ferré-D'Amaré AR, Rueda D. 2012. Allosteric tertiary interactions preorganize the c-di-GMP riboswitch and accelerate ligand binding. ACS Chem Biol 7: 920-927.
-
(2012)
ACS Chem Biol
, vol.7
, pp. 920-927
-
-
Wood, S.1
Ferré-D'amaré, A.R.2
Rueda, D.3
-
39
-
-
84908321643
-
Global analysis of riboswitches by small-angle X-ray scattering and calorimetry
-
Zhang J, Jones CP, Ferré-D'Amaré AR. 2014. Global analysis of riboswitches by small-angle X-ray scattering and calorimetry. Biochim Biophys Acta doi: 10.1016/j.bbagrm.2014.04.014.
-
(2014)
Biochim Biophys Acta
-
-
Zhang, J.1
Jones, C.P.2
Ferré-D'Amaré, A.R.3
-
40
-
-
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
|