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For: Breaker RR. Prospects for riboswitch discovery and analysis. Mol Cell 2011;43:867-79. [PMID: 21925376 DOI: 10.1016/j.molcel.2011.08.024] [Citation(s) in RCA: 385] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 08/15/2011] [Accepted: 08/22/2011] [Indexed: 11/23/2022]
Number Cited by Other Article(s)
201
Strobel EJ, Watters KE, Loughrey D, Lucks JB. RNA systems biology: uniting functional discoveries and structural tools to understand global roles of RNAs. Curr Opin Biotechnol 2016;39:182-191. [PMID: 27132125 DOI: 10.1016/j.copbio.2016.03.019] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 03/24/2016] [Accepted: 03/31/2016] [Indexed: 12/11/2022]
202
Furukawa K, Ramesh A, Zhou Z, Weinberg Z, Vallery T, Winkler WC, Breaker RR. Bacterial riboswitches cooperatively bind Ni(2+) or Co(2+) ions and control expression of heavy metal transporters. Mol Cell 2016;57:1088-1098. [PMID: 25794617 DOI: 10.1016/j.molcel.2015.02.009] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/17/2014] [Accepted: 02/03/2015] [Indexed: 11/19/2022]
203
Mn(2+)-sensing mechanisms of yybP-ykoY orphan riboswitches. Mol Cell 2016;57:1110-1123. [PMID: 25794619 DOI: 10.1016/j.molcel.2015.02.016] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 01/30/2015] [Accepted: 02/09/2015] [Indexed: 02/05/2023]
204
Dambach M, Sandoval M, Updegrove TB, Anantharaman V, Aravind L, Waters LS, Storz G. The ubiquitous yybP-ykoY riboswitch is a manganese-responsive regulatory element. Mol Cell 2016;57:1099-1109. [PMID: 25794618 DOI: 10.1016/j.molcel.2015.01.035] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/17/2014] [Accepted: 01/23/2015] [Indexed: 11/18/2022]
205
Lorenz R, Hofacker IL, Stadler PF. RNA folding with hard and soft constraints. Algorithms Mol Biol 2016;11:8. [PMID: 27110276 PMCID: PMC4842303 DOI: 10.1186/s13015-016-0070-z] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 04/01/2016] [Indexed: 12/21/2022]  Open
206
Litke JL, You M, Jaffrey SR. Developing Fluorogenic Riboswitches for Imaging Metabolite Concentration Dynamics in Bacterial Cells. Methods Enzymol 2016;572:315-33. [PMID: 27241761 DOI: 10.1016/bs.mie.2016.03.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
207
Hull CM, Anmangandla A, Bevilacqua PC. Bacterial Riboswitches and Ribozymes Potently Activate the Human Innate Immune Sensor PKR. ACS Chem Biol 2016;11:1118-27. [PMID: 27011290 DOI: 10.1021/acschembio.6b00081] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
208
Rewiring Riboswitches to Create New Genetic Circuits in Bacteria. Methods Enzymol 2016;575:319-48. [PMID: 27417935 DOI: 10.1016/bs.mie.2016.02.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
209
Li S, Hwang XY, Stav S, Breaker RR. The yjdF riboswitch candidate regulates gene expression by binding diverse azaaromatic compounds. RNA (NEW YORK, N.Y.) 2016;22:530-41. [PMID: 26843526 PMCID: PMC4793209 DOI: 10.1261/rna.054890.115] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/10/2015] [Indexed: 05/21/2023]
210
Inuzuka S, Nishimura KI, Kakizawa H, Fujita Y, Furuta H, Matsumura S, Ikawa Y. Mutational analysis of structural elements in a class-I cyclic di-GMP riboswitch to elucidate its regulatory mechanism. J Biochem 2016;160:153-62. [PMID: 27033943 DOI: 10.1093/jb/mvw026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 02/21/2016] [Indexed: 12/23/2022]  Open
211
Frener M, Micura R. Conformational Rearrangements of Individual Nucleotides during RNA-Ligand Binding Are Rate-Differentiated. J Am Chem Soc 2016;138:3627-30. [PMID: 26974261 PMCID: PMC4959565 DOI: 10.1021/jacs.5b11876] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
212
Inuzuka S, Matsumura S, Ikawa Y. Optimization of RNA-based c-di-GMP fluorescent sensors through tuning their structural modules. J Biosci Bioeng 2016;122:183-7. [PMID: 26968125 DOI: 10.1016/j.jbiosc.2016.01.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 01/25/2016] [Accepted: 01/26/2016] [Indexed: 01/31/2023]
213
van der Meulen SB, de Jong A, Kok J. Transcriptome landscape of Lactococcus lactis reveals many novel RNAs including a small regulatory RNA involved in carbon uptake and metabolism. RNA Biol 2016;13:353-66. [PMID: 26950529 PMCID: PMC4829306 DOI: 10.1080/15476286.2016.1146855] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]  Open
214
Zhou H, Zheng C, Su J, Chen B, Fu Y, Xie Y, Tang Q, Chou SH, He J. Characterization of a natural triple-tandem c-di-GMP riboswitch and application of the riboswitch-based dual-fluorescence reporter. Sci Rep 2016;6:20871. [PMID: 26892868 PMCID: PMC4759541 DOI: 10.1038/srep20871] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 01/11/2016] [Indexed: 12/22/2022]  Open
215
Linc-ROR induces epithelial-mesenchymal transition and contributes to drug resistance and invasion of breast cancer cells. Tumour Biol 2016;37:10861-70. [DOI: 10.1007/s13277-016-4909-1] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 01/22/2016] [Indexed: 10/22/2022]  Open
216
Ribozymes and the mechanisms that underlie RNA catalysis. Front Chem Sci Eng 2016. [DOI: 10.1007/s11705-016-1558-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
217
Banerjee C, Singh PK, Shukla P. Microalgal bioengineering for sustainable energy development: Recent transgenesis and metabolic engineering strategies. Biotechnol J 2016;11:303-14. [DOI: 10.1002/biot.201500284] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 09/15/2015] [Accepted: 01/05/2016] [Indexed: 12/11/2022]
218
Small molecule fluoride toxicity agonists. ACTA ACUST UNITED AC 2016;22:527-534. [PMID: 25910244 DOI: 10.1016/j.chembiol.2015.03.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 03/09/2015] [Accepted: 03/16/2015] [Indexed: 12/15/2022]
219
Duchardt-Ferner E, Gottstein-Schmidtke SR, Weigand JE, Ohlenschläger O, Wurm JP, Hammann C, Suess B, Wöhnert J. Eine OH-Gruppe ändert alles: konformative Dynamik als Grundlage für die Ligandenspezifität des Neomycin-bindenden RNA-Schalters. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201507365] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
220
Chen B, LeBlanc R, Dayie TK. SAM-II Riboswitch Samples at least Two Conformations in Solution in the Absence of Ligand: Implications for Recognition. Angew Chem Int Ed Engl 2016;55:2724-7. [PMID: 26800479 DOI: 10.1002/anie.201509997] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 12/18/2015] [Indexed: 11/10/2022]
221
Chen B, LeBlanc R, Dayie TK. SAM‐II Riboswitch Samples at least Two Conformations in Solution in the Absence of Ligand: Implications for Recognition. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509997] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
222
Rinaldi AJ, Lund PE, Blanco MR, Walter NG. The Shine-Dalgarno sequence of riboswitch-regulated single mRNAs shows ligand-dependent accessibility bursts. Nat Commun 2016;7:8976. [PMID: 26781350 PMCID: PMC4735710 DOI: 10.1038/ncomms9976] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 10/21/2015] [Indexed: 01/20/2023]  Open
223
The unmasking of 'junk' RNA reveals novel sRNAs: from processed RNA fragments to marooned riboswitches. Curr Opin Microbiol 2016;30:16-21. [PMID: 26771674 DOI: 10.1016/j.mib.2015.12.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/17/2015] [Accepted: 12/09/2015] [Indexed: 11/22/2022]
224
Valadkhan S, Valencia-Hipólito A. lncRNAs in Stress Response. Curr Top Microbiol Immunol 2016;394:203-36. [PMID: 26658944 PMCID: PMC11293874 DOI: 10.1007/82_2015_489] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
225
Ohbayashi R, Akai H, Yoshikawa H, Hess WR, Watanabe S. A tightly inducible riboswitch system in Synechocystis sp. PCC 6803. J GEN APPL MICROBIOL 2016;62:154-9. [DOI: 10.2323/jgam.2016.02.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
226
Preparation and Crystallization of Riboswitches. Methods Mol Biol 2016;1320:21-36. [PMID: 26227035 DOI: 10.1007/978-1-4939-2763-0_3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
227
Zhou LB, Zeng AP. Engineering a Lysine-ON Riboswitch for Metabolic Control of Lysine Production in Corynebacterium glutamicum. ACS Synth Biol 2015;4:1335-40. [PMID: 26300047 DOI: 10.1021/acssynbio.5b00075] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
228
Wachsmuth M, Domin G, Lorenz R, Serfling R, Findeiß S, Stadler PF, Mörl M. Design criteria for synthetic riboswitches acting on transcription. RNA Biol 2015;12:221-31. [PMID: 25826571 DOI: 10.1080/15476286.2015.1017235] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
229
Whisper mutations: cryptic messages within the genetic code. Oncogene 2015;35:3753-9. [PMID: 26657150 DOI: 10.1038/onc.2015.454] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 10/28/2015] [Accepted: 10/28/2015] [Indexed: 01/17/2023]
230
Duchardt-Ferner E, Gottstein-Schmidtke SR, Weigand JE, Ohlenschläger O, Wurm JP, Hammann C, Suess B, Wöhnert J. What a Difference an OH Makes: Conformational Dynamics as the Basis for the Ligand Specificity of the Neomycin-Sensing Riboswitch. Angew Chem Int Ed Engl 2015;55:1527-30. [PMID: 26661511 DOI: 10.1002/anie.201507365] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Indexed: 01/13/2023]
231
Identification of RNA Oligonucleotides Binding to Several Proteins from Potential G-Quadruplex Forming Regions in Transcribed Pre-mRNA. Molecules 2015;20:20832-40. [PMID: 26610452 PMCID: PMC6332122 DOI: 10.3390/molecules201119733] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/06/2015] [Accepted: 11/12/2015] [Indexed: 11/16/2022]  Open
232
Ren A, Xue Y, Peselis A, Serganov A, Al-Hashimi HM, Patel DJ. Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch. Cell Rep 2015;13:1800-13. [PMID: 26655897 DOI: 10.1016/j.celrep.2015.10.062] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 08/17/2015] [Accepted: 10/20/2015] [Indexed: 12/24/2022]  Open
233
Regulated Control of the Assembly and Diversity of LPS by Noncoding sRNAs. BIOMED RESEARCH INTERNATIONAL 2015;2015:153561. [PMID: 26618164 PMCID: PMC4651636 DOI: 10.1155/2015/153561] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/07/2015] [Accepted: 10/13/2015] [Indexed: 01/31/2023]
234
Ramesh A. Second messenger - Sensing riboswitches in bacteria. Semin Cell Dev Biol 2015;47-48:3-8. [PMID: 26493703 DOI: 10.1016/j.semcdb.2015.10.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
235
Yuan X, Khokhani D, Wu X, Yang F, Biener G, Koestler BJ, Raicu V, He C, Waters CM, Sundin GW, Tian F, Yang CH. Cross-talk between a regulatory small RNA, cyclic-di-GMP signalling and flagellar regulator FlhDC for virulence and bacterial behaviours. Environ Microbiol 2015;17:4745-63. [PMID: 26462993 DOI: 10.1111/1462-2920.13029] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 08/14/2015] [Accepted: 08/15/2015] [Indexed: 12/01/2022]
236
Salmon L, Giambaşu GM, Nikolova EN, Petzold K, Bhattacharya A, Case DA, Al-Hashimi HM. Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings. J Am Chem Soc 2015;137:12954-65. [PMID: 26306428 PMCID: PMC4748170 DOI: 10.1021/jacs.5b07229] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
237
Apostolidi M, Saad NY, Drainas D, Pournaras S, Becker HD, Stathopoulos C. A glyS T-box riboswitch with species-specific structural features responding to both proteinogenic and nonproteinogenic tRNAGly isoacceptors. RNA (NEW YORK, N.Y.) 2015;21:1790-806. [PMID: 26276802 PMCID: PMC4574755 DOI: 10.1261/rna.052712.115] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 07/13/2015] [Indexed: 06/04/2023]
238
Lussier A, Bastet L, Chauvier A, Lafontaine DA. A kissing loop is important for btuB riboswitch ligand sensing and regulatory control. J Biol Chem 2015;290:26739-51. [PMID: 26370077 DOI: 10.1074/jbc.m115.684134] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Indexed: 12/18/2022]  Open
239
FASTR: A novel data format for concomitant representation of RNA sequence and secondary structure information. J Biosci 2015;40:571-7. [PMID: 26333403 DOI: 10.1007/s12038-015-9546-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
240
Genomes by design. Nat Rev Genet 2015;16:501-16. [PMID: 26260262 DOI: 10.1038/nrg3956] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
241
Neuner S, Santner T, Kreutz C, Micura R. The "Speedy" Synthesis of Atom-Specific (15)N Imino/Amido-Labeled RNA. Chemistry 2015;21:11634-11643. [PMID: 26237536 PMCID: PMC4946632 DOI: 10.1002/chem.201501275] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
242
Dutta D, Wedekind JE. Gene Regulation Gets in Tune: How Riboswitch Tertiary-Structure Networks Adapt to Meet the Needs of Their Transcription Units. J Mol Biol 2015;427:3469-3472. [PMID: 26255959 DOI: 10.1016/j.jmb.2015.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
243
Venayak N, Anesiadis N, Cluett WR, Mahadevan R. Engineering metabolism through dynamic control. Curr Opin Biotechnol 2015;34:142-52. [DOI: 10.1016/j.copbio.2014.12.022] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 12/22/2014] [Accepted: 12/22/2014] [Indexed: 11/30/2022]
244
Drory Retwitzer M, Kifer I, Sengupta S, Yakhini Z, Barash D. An Efficient Minimum Free Energy Structure-Based Search Method for Riboswitch Identification Based on Inverse RNA Folding. PLoS One 2015;10:e0134262. [PMID: 26230932 PMCID: PMC4521916 DOI: 10.1371/journal.pone.0134262] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 07/07/2015] [Indexed: 11/22/2022]  Open
245
Gong S, Wang Y, Zhang W. The regulation mechanism ofyitJandmetFriboswitches. J Chem Phys 2015;143:045103. [DOI: 10.1063/1.4927390] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]  Open
246
Okui S, Kawai G. In NMR tube transcription for rapid screening of RNA conformation. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015;34:103-13. [PMID: 25621704 DOI: 10.1080/15257770.2014.964412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
247
Novel riboswitch-binding flavin analog that protects mice against Clostridium difficile infection without inhibiting cecal flora. Antimicrob Agents Chemother 2015;59:5736-46. [PMID: 26169403 DOI: 10.1128/aac.01282-15] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 07/03/2015] [Indexed: 01/08/2023]  Open
248
Wunderlich CH, Juen MA, LeBlanc RM, Longhini AP, Dayie TK, Kreutz C. Stable isotope-labeled RNA phosphoramidites to facilitate dynamics by NMR. Methods Enzymol 2015;565:461-94. [PMID: 26577742 DOI: 10.1016/bs.mie.2015.06.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
249
Peselis A, Gao A, Serganov A. Cooperativity, allostery and synergism in ligand binding to riboswitches. Biochimie 2015;117:100-9. [PMID: 26143008 DOI: 10.1016/j.biochi.2015.06.028] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 06/29/2015] [Indexed: 01/04/2023]
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Duss O, Diarra Dit Konté N, Allain FHT. Cut and paste RNA for nuclear magnetic resonance, paramagnetic resonance enhancement, and electron paramagnetic resonance structural studies. Methods Enzymol 2015;565:537-62. [PMID: 26577744 DOI: 10.1016/bs.mie.2015.05.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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