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Volumn 56, Issue 9, 2017, Pages 1181-1198

Synthetic Riboswitches: From Plug and Pray toward Plug and Play

Author keywords

[No Author keywords available]

Indexed keywords

BIOSYNTHESIS; GENE EXPRESSION REGULATION; GENE THERAPY; GENES; METABOLIC ENGINEERING; NUCLEIC ACIDS; PROTEINS; RNA; TRANSCRIPTION;

EID: 85014820996     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/acs.biochem.6b01218     Document Type: Article
Times cited : (74)

References (189)
  • 1
    • 20444382737 scopus 로고    scopus 로고
    • Regulation of transcription: From lambda to eukaryotes
    • Ptashne, M. (2005) Regulation of transcription: from lambda to eukaryotes Trends Biochem. Sci. 30, 275-279 10.1016/j.tibs.2005.04.003
    • (2005) Trends Biochem. Sci. , vol.30 , pp. 275-279
    • Ptashne, M.1
  • 2
    • 33846516797 scopus 로고    scopus 로고
    • The lactose repressor system: Paradigms for regulation, allosteric behavior and protein folding
    • Wilson, C. J., Zhan, H., Swint-Kruse, L., and Matthews, K. S. (2007) The lactose repressor system: paradigms for regulation, allosteric behavior and protein folding Cell. Mol. Life Sci. 64, 3-16 10.1007/s00018-006-6296-z
    • (2007) Cell. Mol. Life Sci. , vol.64 , pp. 3-16
    • Wilson, C.J.1    Zhan, H.2    Swint-Kruse, L.3    Matthews, K.S.4
  • 3
    • 85010992233 scopus 로고    scopus 로고
    • Thirty-five years of research into ribozymes and nucleic acid catalysis: Where do we stand today?
    • Muller, S., Appel, B., Balke, D., Hieronymus, R., and Nubel, C. (2016) Thirty-five years of research into ribozymes and nucleic acid catalysis: where do we stand today? F1000Research 5, 1511 10.12688/f1000research.8601.1
    • (2016) F1000Research , vol.5 , pp. 1511
    • Muller, S.1    Appel, B.2    Balke, D.3    Hieronymus, R.4    Nubel, C.5
  • 4
    • 84943398217 scopus 로고    scopus 로고
    • The RNA World as a Model System to Study the Origin of Life
    • Pressman, A., Blanco, C., and Chen, I. A. (2015) The RNA World as a Model System to Study the Origin of Life Curr. Biol. 25, R953 10.1016/j.cub.2015.06.016
    • (2015) Curr. Biol. , vol.25 , pp. R953
    • Pressman, A.1    Blanco, C.2    Chen, I.A.3
  • 5
    • 0019856947 scopus 로고
    • In vitro splicing of the ribosomal RNA precursor of Tetrahymena: Involvement of a guanosine nucleotide in the excision of the intervening sequence
    • Cech, T. R., Zaug, A. J., and Grabowski, P. J. (1981) In vitro splicing of the ribosomal RNA precursor of Tetrahymena: Involvement of a guanosine nucleotide in the excision of the intervening sequence Cell 27, 487-496 10.1016/0092-8674(81)90390-1
    • (1981) Cell , vol.27 , pp. 487-496
    • Cech, T.R.1    Zaug, A.J.2    Grabowski, P.J.3
  • 6
    • 0021013526 scopus 로고
    • The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme
    • Guerrier-Takada, C., Gardiner, K., Marsh, T., Pace, N., and Altman, S. (1983) The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme Cell 35, 849-857 10.1016/0092-8674(83)90117-4
    • (1983) Cell , vol.35 , pp. 849-857
    • Guerrier-Takada, C.1    Gardiner, K.2    Marsh, T.3    Pace, N.4    Altman, S.5
  • 7
    • 0025074907 scopus 로고
    • In vitro selection of RNA molecules that bind specific ligands
    • Ellington, A. D. and Szostak, J. W. (1990) In vitro selection of RNA molecules that bind specific ligands Nature 346, 818-822 10.1038/346818a0
    • (1990) Nature , vol.346 , pp. 818-822
    • Ellington, A.D.1    Szostak, J.W.2
  • 8
    • 0025194307 scopus 로고
    • Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase
    • Tuerk, C. and Gold, L. (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase Science 249, 505-510 10.1126/science.2200121
    • (1990) Science , vol.249 , pp. 505-510
    • Tuerk, C.1    Gold, L.2
  • 9
    • 0031570666 scopus 로고    scopus 로고
    • A biopolymer by any other name would bind as well. A comparison of the ligand-binding pockets of nucleic acids and proteins
    • Marshall, K. A., Robertson, M. P., and Ellington, A. D. (1997) A biopolymer by any other name would bind as well. A comparison of the ligand-binding pockets of nucleic acids and proteins Structure 5, 729-734 10.1016/S0969-2126(97)00227-X
    • (1997) Structure , vol.5 , pp. 729-734
    • Marshall, K.A.1    Robertson, M.P.2    Ellington, A.D.3
  • 10
    • 84055193858 scopus 로고    scopus 로고
    • RNA aptamer evolution: Two decades of SELEction
    • Aquino-Jarquin, G. and Toscano-Garibay, J. D. (2011) RNA aptamer evolution: two decades of SELEction Int. J. Mol. Sci. 12, 9155-9171 10.3390/ijms12129155
    • (2011) Int. J. Mol. Sci. , vol.12 , pp. 9155-9171
    • Aquino-Jarquin, G.1    Toscano-Garibay, J.D.2
  • 12
    • 0037206833 scopus 로고    scopus 로고
    • Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression
    • Winkler, W., Nahvi, A., and Breaker, R. R. (2002) Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression Nature 419, 952-956 10.1038/nature01145
    • (2002) Nature , vol.419 , pp. 952-956
    • Winkler, W.1    Nahvi, A.2    Breaker, R.R.3
  • 13
    • 18744396047 scopus 로고    scopus 로고
    • Sensing Small Molecules by Nascent RNA: A Mechanism to Control Transcription in Bacteria
    • Mironov, A. S., Gusarov, I., Rafikov, R., Lopez, L. E., Shatalin, K., Kreneva, R. A., Perumov, D. A., and Nudler, E. (2002) Sensing Small Molecules by Nascent RNA: A Mechanism to Control Transcription in Bacteria Cell 111, 747-756 10.1016/S0092-8674(02)01134-0
    • (2002) Cell , vol.111 , pp. 747-756
    • Mironov, A.S.1    Gusarov, I.2    Rafikov, R.3    Lopez, L.E.4    Shatalin, K.5    Kreneva, R.A.6    Perumov, D.A.7    Nudler, E.8
  • 14
    • 46349083026 scopus 로고    scopus 로고
    • The distributions, mechanisms, and structures of metabolite-binding riboswitches
    • Barrick, J. E. and Breaker, R. R. (2007) The distributions, mechanisms, and structures of metabolite-binding riboswitches Genome Biol. 8, R239 10.1186/gb-2007-8-11-r239
    • (2007) Genome Biol. , vol.8 , pp. R239
    • Barrick, J.E.1    Breaker, R.R.2
  • 16
    • 80052973462 scopus 로고    scopus 로고
    • Prospects for riboswitch discovery and analysis
    • Breaker, R. R. (2011) Prospects for riboswitch discovery and analysis Mol. Cell 43, 867-879 10.1016/j.molcel.2011.08.024
    • (2011) Mol. Cell , vol.43 , pp. 867-879
    • Breaker, R.R.1
  • 17
    • 84872543206 scopus 로고    scopus 로고
    • A decade of riboswitches
    • Serganov, A. and Nudler, E. (2013) A decade of riboswitches Cell 152, 17-24 10.1016/j.cell.2012.12.024
    • (2013) Cell , vol.152 , pp. 17-24
    • Serganov, A.1    Nudler, E.2
  • 20
    • 84906052564 scopus 로고    scopus 로고
    • Riboswitch engineering - Making the all-important second and third steps
    • Berens, C. and Suess, B. (2015) Riboswitch engineering-making the all-important second and third steps Curr. Opin. Biotechnol. 31, 10-15 10.1016/j.copbio.2014.07.014
    • (2015) Curr. Opin. Biotechnol. , vol.31 , pp. 10-15
    • Berens, C.1    Suess, B.2
  • 21
    • 84922652279 scopus 로고    scopus 로고
    • RNA aptamers as genetic control devices: The potential of riboswitches as synthetic elements for regulating gene expression
    • Berens, C., Groher, F., and Suess, B. (2015) RNA aptamers as genetic control devices: the potential of riboswitches as synthetic elements for regulating gene expression Biotechnol. J. 10, 246-257 10.1002/biot.201300498
    • (2015) Biotechnol. J. , vol.10 , pp. 246-257
    • Berens, C.1    Groher, F.2    Suess, B.3
  • 22
    • 84863617223 scopus 로고    scopus 로고
    • Engineered riboswitches: Expanding researchers' toolbox with synthetic RNA regulators
    • Wittmann, A. and Suess, B. (2012) Engineered riboswitches: Expanding researchers' toolbox with synthetic RNA regulators FEBS Lett. 586, 2076-2083 10.1016/j.febslet.2012.02.038
    • (2012) FEBS Lett. , vol.586 , pp. 2076-2083
    • Wittmann, A.1    Suess, B.2
  • 23
    • 79955613663 scopus 로고    scopus 로고
    • Mechanistic insights into an engineered riboswitch: A switching element which confers riboswitch activity
    • Weigand, J. E., Schmidtke, S. R., Will, T. J., Duchardt-Ferner, E., Hammann, C., Wöhnert, J., and Suess, B. (2011) Mechanistic insights into an engineered riboswitch: a switching element which confers riboswitch activity Nucleic Acids Res. 39, 3363-3372 10.1093/nar/gkq946
    • (2011) Nucleic Acids Res. , vol.39 , pp. 3363-3372
    • Weigand, J.E.1    Schmidtke, S.R.2    Will, T.J.3    Duchardt-Ferner, E.4    Hammann, C.5    Wöhnert, J.6    Suess, B.7
  • 25
    • 38049004429 scopus 로고    scopus 로고
    • Screening for engineered neomycin riboswitches that control translation initiation
    • Weigand, J. E., Sanchez, M., Gunnesch, E.-B., Zeiher, S., Schroeder, R., and Suess, B. (2008) Screening for engineered neomycin riboswitches that control translation initiation RNA 14, 89-97 10.1261/rna.772408
    • (2008) RNA , vol.14 , pp. 89-97
    • Weigand, J.E.1    Sanchez, M.2    Gunnesch, E.-B.3    Zeiher, S.4    Schroeder, R.5    Suess, B.6
  • 26
    • 0032500736 scopus 로고    scopus 로고
    • Controlling Gene Expression in Living Cells Through Small Molecule-RNA Interactions
    • Werstuck, G. and Green, M. R. (1998) Controlling Gene Expression in Living Cells Through Small Molecule-RNA Interactions Science 282, 296-298 10.1126/science.282.5387.296
    • (1998) Science , vol.282 , pp. 296-298
    • Werstuck, G.1    Green, M.R.2
  • 27
    • 0141677751 scopus 로고    scopus 로고
    • Tetracycline-aptamer-mediated translational regulation in yeast
    • Hanson, S., Berthelot, K., Fink, B., McCarthy, J. E. G., and Suess, B. (2003) Tetracycline-aptamer-mediated translational regulation in yeast Mol. Microbiol. 49, 1627-1637 10.1046/j.1365-2958.2003.03656.x
    • (2003) Mol. Microbiol. , vol.49 , pp. 1627-1637
    • Hanson, S.1    Berthelot, K.2    Fink, B.3    McCarthy, J.E.G.4    Suess, B.5
  • 28
    • 0034853943 scopus 로고    scopus 로고
    • A tetracycline-binding RNA aptamer
    • Berens, C., Thain, A., and Schroeder, R. (2001) A tetracycline-binding RNA aptamer Bioorg. Med. Chem. 9, 2549-2556 10.1016/S0968-0896(01)00063-3
    • (2001) Bioorg. Med. Chem. , vol.9 , pp. 2549-2556
    • Berens, C.1    Thain, A.2    Schroeder, R.3
  • 29
    • 53649104514 scopus 로고    scopus 로고
    • Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch
    • Xiao, H., Edwards, T. E., and Ferré-D'Amaré, A. R. (2008) Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch Chem. Biol. 15, 1125-1137 10.1016/j.chembiol.2008.09.004
    • (2008) Chem. Biol. , vol.15 , pp. 1125-1137
    • Xiao, H.1    Edwards, T.E.2    Ferré-D'Amaré, A.R.3
  • 30
    • 15444379109 scopus 로고    scopus 로고
    • Molecular analysis of a synthetic tetracycline-binding riboswitch
    • Hanson, S., Bauer, G., Fink, B., and Suess, B. (2005) Molecular analysis of a synthetic tetracycline-binding riboswitch RNA 11, 503-511 10.1261/rna.7251305
    • (2005) RNA , vol.11 , pp. 503-511
    • Hanson, S.1    Bauer, G.2    Fink, B.3    Suess, B.4
  • 31
    • 78650475424 scopus 로고    scopus 로고
    • Ligand-induced conformational capture of a synthetic tetracycline riboswitch revealed by pulse EPR
    • Wunnicke, D., Strohbach, D., Weigand, J. E., Appel, B., Feresin, E., Suess, B., Muller, S., and Steinhoff, H.-J. (2011) Ligand-induced conformational capture of a synthetic tetracycline riboswitch revealed by pulse EPR RNA 17, 182-188 10.1261/rna.2222811
    • (2011) RNA , vol.17 , pp. 182-188
    • Wunnicke, D.1    Strohbach, D.2    Weigand, J.E.3    Appel, B.4    Feresin, E.5    Suess, B.6    Muller, S.7    Steinhoff, H.-J.8
  • 33
    • 33646909444 scopus 로고    scopus 로고
    • Thermodynamic characterization of an engineered tetracycline-binding riboswitch
    • Muller, M., Weigand, J. E., Weichenrieder, O., and Suess, B. (2006) Thermodynamic characterization of an engineered tetracycline-binding riboswitch Nucleic Acids Res. 34, 2607-2617 10.1093/nar/gkl347
    • (2006) Nucleic Acids Res. , vol.34 , pp. 2607-2617
    • Muller, M.1    Weigand, J.E.2    Weichenrieder, O.3    Suess, B.4
  • 34
    • 0037388001 scopus 로고    scopus 로고
    • Conditional gene expression by controlling translation with tetracycline-binding aptamers
    • Suess, B., Hanson, S., Berens, C., Fink, B., Schroeder, R., and Hillen, W. (2003) Conditional gene expression by controlling translation with tetracycline-binding aptamers Nucleic Acids Res. 31, 1853-1858 10.1093/nar/gkg285
    • (2003) Nucleic Acids Res. , vol.31 , pp. 1853-1858
    • Suess, B.1    Hanson, S.2    Berens, C.3    Fink, B.4    Schroeder, R.5    Hillen, W.6
  • 35
    • 79960372206 scopus 로고    scopus 로고
    • Selection of tetracycline inducible self-cleaving ribozymes as synthetic devices for gene regulation in yeast
    • Wittmann, A. and Suess, B. (2011) Selection of tetracycline inducible self-cleaving ribozymes as synthetic devices for gene regulation in yeast Mol. BioSyst. 7, 2419-2427 10.1039/c1mb05070b
    • (2011) Mol. BioSyst. , vol.7 , pp. 2419-2427
    • Wittmann, A.1    Suess, B.2
  • 36
    • 34547639506 scopus 로고    scopus 로고
    • Tetracycline aptamer-controlled regulation of pre-mRNA splicing in yeast
    • Weigand, J. E. and Suess, B. (2007) Tetracycline aptamer-controlled regulation of pre-mRNA splicing in yeast Nucleic Acids Res. 35, 4179-4185 10.1093/nar/gkm425
    • (2007) Nucleic Acids Res. , vol.35 , pp. 4179-4185
    • Weigand, J.E.1    Suess, B.2
  • 37
    • 0029347016 scopus 로고
    • A novel RNA motif for neomycin recognition
    • Wallis, M. G., von Ahsen, U., Schroeder, R., and Famulok, M. (1995) A novel RNA motif for neomycin recognition Chem. Biol. 2, 543-552 10.1016/1074-5521(95)90188-4
    • (1995) Chem. Biol. , vol.2 , pp. 543-552
    • Wallis, M.G.1    Von Ahsen, U.2    Schroeder, R.3    Famulok, M.4
  • 40
    • 0028224199 scopus 로고
    • High-resolution molecular discrimination by RNA
    • Jenison, R. D., Gill, S. C., Pardi, A., and Polisky, B. (1994) High-resolution molecular discrimination by RNA Science 263, 1425-1429 10.1126/science.7510417
    • (1994) Science , vol.263 , pp. 1425-1429
    • Jenison, R.D.1    Gill, S.C.2    Pardi, A.3    Polisky, B.4
  • 41
    • 0030752211 scopus 로고    scopus 로고
    • Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA
    • Zimmermann, G. R., Jenison, R. D., Wick, C. L., Simorre, J. P., and Pardi, A. (1997) Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA Nat. Struct. Biol. 4, 644-649 10.1038/nsb0897-644
    • (1997) Nat. Struct. Biol. , vol.4 , pp. 644-649
    • Zimmermann, G.R.1    Jenison, R.D.2    Wick, C.L.3    Simorre, J.P.4    Pardi, A.5
  • 42
    • 77950423140 scopus 로고    scopus 로고
    • Ultrafast dynamics show that the theophylline and 3-methylxanthine aptamers employ a conformational capture mechanism for binding their ligands
    • Lee, S. W., Zhao, L., Pardi, A., and Xia, T. (2010) Ultrafast dynamics show that the theophylline and 3-methylxanthine aptamers employ a conformational capture mechanism for binding their ligands Biochemistry 49, 2943-2951 10.1021/bi100106c
    • (2010) Biochemistry , vol.49 , pp. 2943-2951
    • Lee, S.W.1    Zhao, L.2    Pardi, A.3    Xia, T.4
  • 43
    • 67849097652 scopus 로고    scopus 로고
    • NMR chemical exchange as a probe for ligand-binding kinetics in a theophylline-binding RNA aptamer
    • Latham, M. P., Zimmermann, G. R., and Pardi, A. (2009) NMR chemical exchange as a probe for ligand-binding kinetics in a theophylline-binding RNA aptamer J. Am. Chem. Soc. 131, 5052-5053 10.1021/ja900695m
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 5052-5053
    • Latham, M.P.1    Zimmermann, G.R.2    Pardi, A.3
  • 44
    • 0037432340 scopus 로고    scopus 로고
    • Role of a heterogeneous free state in the formation of a specific RNA-theophylline complex
    • Jucker, F. M., Phillips, R. M., McCallum, S. A., and Pardi, A. (2003) Role of a heterogeneous free state in the formation of a specific RNA-theophylline complex Biochemistry 42, 2560-2567 10.1021/bi027103+
    • (2003) Biochemistry , vol.42 , pp. 2560-2567
    • Jucker, F.M.1    Phillips, R.M.2    McCallum, S.A.3    Pardi, A.4
  • 45
    • 0022412762 scopus 로고
    • Theophylline toxicity
    • Ellis, E. F. (1985) Theophylline toxicity J. Allergy Clin. Immunol. 76, 297-301 10.1016/0091-6749(85)90645-1
    • (1985) J. Allergy Clin. Immunol. , vol.76 , pp. 297-301
    • Ellis, E.F.1
  • 46
    • 0036235684 scopus 로고    scopus 로고
    • Inhibition of translation by RNA-small molecule interactions
    • Harvey, I., Garneau, P., and Pelletier, J. (2002) Inhibition of translation by RNA-small molecule interactions RNA 8, 452-463 10.1017/S135583820202633X
    • (2002) RNA , vol.8 , pp. 452-463
    • Harvey, I.1    Garneau, P.2    Pelletier, J.3
  • 47
    • 6044261460 scopus 로고    scopus 로고
    • Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation
    • Desai, S. K. and Gallivan, J. P. (2004) Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation J. Am. Chem. Soc. 126, 13247-13254 10.1021/ja048634j
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 13247-13254
    • Desai, S.K.1    Gallivan, J.P.2
  • 48
    • 2542601538 scopus 로고    scopus 로고
    • A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo
    • Suess, B., Fink, B., Berens, C., Stentz, R., and Hillen, W. (2004) A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo Nucleic Acids Res. 32, 1610-1614 10.1093/nar/gkh321
    • (2004) Nucleic Acids Res. , vol.32 , pp. 1610-1614
    • Suess, B.1    Fink, B.2    Berens, C.3    Stentz, R.4    Hillen, W.5
  • 49
    • 54349119816 scopus 로고    scopus 로고
    • A FACS-based approach to engineering artificial riboswitches
    • Fowler, C. C., Brown, E. D., and Li, Y. (2008) A FACS-based approach to engineering artificial riboswitches ChemBioChem 9, 1906-1911 10.1002/cbic.200700713
    • (2008) ChemBioChem , vol.9 , pp. 1906-1911
    • Fowler, C.C.1    Brown, E.D.2    Li, Y.3
  • 50
    • 27144526390 scopus 로고    scopus 로고
    • An artificial riboswitch for controlling pre-mRNA splicing
    • Kim, D.-S., Gusti, V., Pillai, S. G., and Gaur, R. K. (2005) An artificial riboswitch for controlling pre-mRNA splicing RNA 11, 1667-1677 10.1261/rna.2162205
    • (2005) RNA , vol.11 , pp. 1667-1677
    • Kim, D.-S.1    Gusti, V.2    Pillai, S.G.3    Gaur, R.K.4
  • 51
    • 35448990907 scopus 로고    scopus 로고
    • A modular and extensible RNA-based gene-regulatory platform for engineering cellular function
    • Win, M. N. and Smolke, C. D. (2007) A modular and extensible RNA-based gene-regulatory platform for engineering cellular function Proc. Natl. Acad. Sci. U. S. A. 104, 14283-14288 10.1073/pnas.0703961104
    • (2007) Proc. Natl. Acad. Sci. U. S. A. , vol.104 , pp. 14283-14288
    • Win, M.N.1    Smolke, C.D.2
  • 53
    • 79960206790 scopus 로고    scopus 로고
    • Engineering ligand-responsive RNA controllers in yeast through the assembly of RNase III tuning modules
    • Babiskin, A. H. and Smolke, C. D. (2011) Engineering ligand-responsive RNA controllers in yeast through the assembly of RNase III tuning modules Nucleic Acids Res. 39, 5299-5311 10.1093/nar/gkr090
    • (2011) Nucleic Acids Res. , vol.39 , pp. 5299-5311
    • Babiskin, A.H.1    Smolke, C.D.2
  • 54
    • 33646183047 scopus 로고    scopus 로고
    • Artificial control of gene expression in mammalian cells by modulating RNA interference through aptamer-small molecule interaction
    • An, C.-I., Trinh, V. B., and Yokobayashi, Y. (2006) Artificial control of gene expression in mammalian cells by modulating RNA interference through aptamer-small molecule interaction RNA 12, 710-716 10.1261/rna.2299306
    • (2006) RNA , vol.12 , pp. 710-716
    • An, C.-I.1    Trinh, V.B.2    Yokobayashi, Y.3
  • 55
    • 41949098095 scopus 로고    scopus 로고
    • Improved aptazyme design and in vivo screening enable riboswitching in bacteria
    • Wieland, M. and Hartig, J. S. (2008) Improved aptazyme design and in vivo screening enable riboswitching in bacteria Angew. Chem., Int. Ed. 47, 2604-2607 10.1002/anie.200703700
    • (2008) Angew. Chem., Int. Ed. , vol.47 , pp. 2604-2607
    • Wieland, M.1    Hartig, J.S.2
  • 56
    • 70349995081 scopus 로고    scopus 로고
    • Small-molecule-dependent regulation of transfer RNA in bacteria
    • Berschneider, B., Wieland, M., Rubini, M., and Hartig, J. S. (2009) Small-molecule-dependent regulation of transfer RNA in bacteria Angew. Chem., Int. Ed. 48, 7564-7567 10.1002/anie.200900851
    • (2009) Angew. Chem., Int. Ed. , vol.48 , pp. 7564-7567
    • Berschneider, B.1    Wieland, M.2    Rubini, M.3    Hartig, J.S.4
  • 58
    • 84876376374 scopus 로고    scopus 로고
    • De novo design of a synthetic riboswitch that regulates transcription termination
    • Wachsmuth, M., Findeiss, S., Weissheimer, N., Stadler, P. F., and Morl, M. (2013) De novo design of a synthetic riboswitch that regulates transcription termination Nucleic Acids Res. 41, 2541-2551 10.1093/nar/gks1330
    • (2013) Nucleic Acids Res. , vol.41 , pp. 2541-2551
    • Wachsmuth, M.1    Findeiss, S.2    Weissheimer, N.3    Stadler, P.F.4    Morl, M.5
  • 60
    • 84872590874 scopus 로고    scopus 로고
    • Development of a 2,4-dinitrotoluene-responsive synthetic riboswitch in E. Coli cells
    • Davidson, M. E., Harbaugh, S. V., Chushak, Y. G., Stone, M. O., and Kelley-Loughnane, N. (2013) Development of a 2,4-dinitrotoluene-responsive synthetic riboswitch in E. coli cells ACS Chem. Biol. 8, 234-241 10.1021/cb300274g
    • (2013) ACS Chem. Biol. , vol.8 , pp. 234-241
    • Davidson, M.E.1    Harbaugh, S.V.2    Chushak, Y.G.3    Stone, M.O.4    Kelley-Loughnane, N.5
  • 61
    • 84903163650 scopus 로고    scopus 로고
    • A family of synthetic riboswitches adopts a kinetic trapping mechanism
    • Mishler, D. M. and Gallivan, J. P. (2014) A family of synthetic riboswitches adopts a kinetic trapping mechanism Nucleic Acids Res. 42, 6753-6761 10.1093/nar/gku262
    • (2014) Nucleic Acids Res. , vol.42 , pp. 6753-6761
    • Mishler, D.M.1    Gallivan, J.P.2
  • 62
    • 15944382675 scopus 로고    scopus 로고
    • 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 10.1016/j.molcel.2005.02.032
    • (2005) Mol. Cell , vol.18 , pp. 49-60
    • Wickiser, J.K.1    Winkler, W.C.2    Breaker, R.R.3    Crothers, D.M.4
  • 63
    • 26444620938 scopus 로고    scopus 로고
    • 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 10.1021/bi051008u
    • (2005) Biochemistry , vol.44 , pp. 13404-13414
    • Wickiser, J.K.1    Cheah, M.T.2    Breaker, R.R.3    Crothers, D.M.4
  • 64
    • 80052982281 scopus 로고    scopus 로고
    • The dynamic nature of RNA as key to understanding riboswitch mechanisms
    • Haller, A., Souliere, M. F., and Micura, R. (2011) The dynamic nature of RNA as key to understanding riboswitch mechanisms Acc. Chem. Res. 44, 1339-1348 10.1021/ar200035g
    • (2011) Acc. Chem. Res. , vol.44 , pp. 1339-1348
    • Haller, A.1    Souliere, M.F.2    Micura, R.3
  • 65
    • 79851499341 scopus 로고    scopus 로고
    • 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., Masse, E., and Lafontaine, D. A. (2011) Comparative study between transcriptionally- and translationally-acting adenine riboswitches reveals key differences in riboswitch regulatory mechanisms PLoS Genet. 7, e1001278 10.1371/journal.pgen.1001278
    • (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    Masse, E.7    Lafontaine, D.A.8
  • 66
    • 34447548824 scopus 로고    scopus 로고
    • Ligand-induced folding of the adenosine deaminase A-riboswitch and implications on riboswitch translational control
    • Rieder, R., Lang, K., Graber, D., and Micura, R. (2007) Ligand-induced folding of the adenosine deaminase A-riboswitch and implications on riboswitch translational control ChemBioChem 8, 896-902 10.1002/cbic.200700057
    • (2007) ChemBioChem , vol.8 , pp. 896-902
    • Rieder, R.1    Lang, K.2    Graber, D.3    Micura, R.4
  • 68
    • 78049276834 scopus 로고    scopus 로고
    • Ribozymes and riboswitches: Modulation of RNA function by small molecules
    • Zhang, J., Lau, M. W., and Ferre-D'Amare, A. R. (2010) Ribozymes and riboswitches: modulation of RNA function by small molecules Biochemistry 49, 9123-9131 10.1021/bi1012645
    • (2010) Biochemistry , vol.49 , pp. 9123-9131
    • Zhang, J.1    Lau, M.W.2    Ferre-D'Amare, A.R.3
  • 69
    • 40349114389 scopus 로고    scopus 로고
    • In vitro selection of RNA aptamers to a protein target by filter immobilization
    • Chapter 24, Unit 24.3, Wiley, New York
    • Jhaveri, S. D. and Ellington, A. D. (2001) In vitro selection of RNA aptamers to a protein target by filter immobilization. In Current Protocols in Molecular Biology, Chapter 24, Unit 24.3, Wiley, New York.
    • (2001) Current Protocols in Molecular Biology
    • Jhaveri, S.D.1    Ellington, A.D.2
  • 70
    • 84948383640 scopus 로고    scopus 로고
    • The Effects of SELEX Conditions on the Resultant Aptamer Pools in the Selection of Aptamers Binding to Bacterial Cells
    • Hamula, C. L. A., Peng, H., Wang, Z., Newbigging, A. M., Tyrrell, G. J., Li, X.-F., and Le, X. C. (2015) The Effects of SELEX Conditions on the Resultant Aptamer Pools in the Selection of Aptamers Binding to Bacterial Cells J. Mol. Evol. 81, 194-209 10.1007/s00239-015-9711-y
    • (2015) J. Mol. Evol. , vol.81 , pp. 194-209
    • Hamula, C.L.A.1    Peng, H.2    Wang, Z.3    Newbigging, A.M.4    Tyrrell, G.J.5    Li, X.-F.6    Le, X.C.7
  • 71
    • 24344447533 scopus 로고    scopus 로고
    • Low-magnesium, trans-cleavage activity by type III, tertiary stabilized hammerhead ribozymes with stem 1 discontinuities
    • Burke, D. H. and Greathouse, S. T. (2005) Low-magnesium, trans-cleavage activity by type III, tertiary stabilized hammerhead ribozymes with stem 1 discontinuities BMC Biochem. 6, 14 10.1186/1471-2091-6-14
    • (2005) BMC Biochem. , vol.6 , pp. 14
    • Burke, D.H.1    Greathouse, S.T.2
  • 73
    • 77952499429 scopus 로고    scopus 로고
    • Selecting RNA aptamers for synthetic biology: Investigating magnesium dependence and predicting binding affinity
    • Carothers, J. M., Goler, J. A., Kapoor, Y., Lara, L., and Keasling, J. D. (2010) Selecting RNA aptamers for synthetic biology: investigating magnesium dependence and predicting binding affinity Nucleic Acids Res. 38, 2736-2747 10.1093/nar/gkq082
    • (2010) Nucleic Acids Res. , vol.38 , pp. 2736-2747
    • Carothers, J.M.1    Goler, J.A.2    Kapoor, Y.3    Lara, L.4    Keasling, J.D.5
  • 74
    • 84937160252 scopus 로고    scopus 로고
    • Tetracycline determines the conformation of its aptamer at physiological magnesium concentrations
    • Reuss, A. J., Vogel, M., Weigand, J. E., Suess, B., and Wachtveitl, J. (2014) Tetracycline determines the conformation of its aptamer at physiological magnesium concentrations Biophys. J. 107, 2962-2971 10.1016/j.bpj.2014.11.001
    • (2014) Biophys. J. , vol.107 , pp. 2962-2971
    • Reuss, A.J.1    Vogel, M.2    Weigand, J.E.3    Suess, B.4    Wachtveitl, J.5
  • 75
    • 0036316773 scopus 로고    scopus 로고
    • Magnesium chemistry and biochemistry
    • Maguire, M. E. and Cowan, J. A. (2002) Magnesium chemistry and biochemistry BioMetals 15, 203-210 10.1023/A:1016058229972
    • (2002) BioMetals , vol.15 , pp. 203-210
    • Maguire, M.E.1    Cowan, J.A.2
  • 78
    • 84940916425 scopus 로고
    • Creating Vast Peptide Expression Libraries: Electroporation as a Tool to Construct Plasmid Libraries of Greater than 109 Recombinants
    • (Chang, D. C. Ed.) pp, Academic Press Inc. San Diego
    • Dower, W. J. and Cwirla, S. E. (1992) Creating Vast Peptide Expression Libraries: Electroporation as a Tool to Construct Plasmid Libraries of Greater than 109 Recombinants. In Guide to electroporation and electrofusion (Chang, D. C., Ed.) pp 291-301, Academic Press Inc., San Diego.
    • (1992) Guide to Electroporation and Electrofusion , pp. 291-301
    • Dower, W.J.1    Cwirla, S.E.2
  • 79
    • 1942489258 scopus 로고    scopus 로고
    • Informational complexity and functional activity of RNA structures
    • Carothers, J. M., Oestreich, S. C., Davis, J. H., and Szostak, J. W. (2004) Informational complexity and functional activity of RNA structures J. Am. Chem. Soc. 126, 5130-5137 10.1021/ja031504a
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 5130-5137
    • Carothers, J.M.1    Oestreich, S.C.2    Davis, J.H.3    Szostak, J.W.4
  • 80
    • 0032853242 scopus 로고    scopus 로고
    • In vitro selection of functional nucleic acids
    • Wilson, D. S. and Szostak, J. W. (1999) In vitro selection of functional nucleic acids Annu. Rev. Biochem. 68, 611-647 10.1146/annurev.biochem.68.1.611
    • (1999) Annu. Rev. Biochem. , vol.68 , pp. 611-647
    • Wilson, D.S.1    Szostak, J.W.2
  • 81
    • 84965158377 scopus 로고    scopus 로고
    • Opportunities in the design and application of RNA for gene expression control
    • McKeague, M., Wong, R. S., and Smolke, C. D. (2016) Opportunities in the design and application of RNA for gene expression control Nucleic Acids Res. 44, 2987-2999 10.1093/nar/gkw151
    • (2016) Nucleic Acids Res. , vol.44 , pp. 2987-2999
    • McKeague, M.1    Wong, R.S.2    Smolke, C.D.3
  • 82
    • 67651154401 scopus 로고    scopus 로고
    • In silico selection of RNA aptamers
    • Chushak, Y. and Stone, M. O. (2009) In silico selection of RNA aptamers Nucleic Acids Res. 37, e87 10.1093/nar/gkp408
    • (2009) Nucleic Acids Res. , vol.37 , pp. e87
    • Chushak, Y.1    Stone, M.O.2
  • 88
    • 84875129451 scopus 로고    scopus 로고
    • The current status of vertebrate cellular mRNA IRESs
    • Jackson, R. J. (2013) The current status of vertebrate cellular mRNA IRESs Cold Spring Harbor Perspect. Biol. 5 (5) a011569 10.1101/cshperspect.a011569
    • (2013) Cold Spring Harbor Perspect. Biol. , vol.5 , Issue.5 , pp. a011569
    • Jackson, R.J.1
  • 89
    • 84890327325 scopus 로고    scopus 로고
    • 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 10.1093/nar/gkt787
    • (2013) Nucleic Acids Res. , vol.41 , pp. 10449-10461
    • Ceres, P.1    Trausch, J.J.2    Batey, R.T.3
  • 90
    • 84921261966 scopus 로고    scopus 로고
    • Design of modular ″plug-and-play″ expression platforms derived from natural riboswitches for engineering novel genetically encodable RNA regulatory devices
    • Trausch, J. J. and Batey, R. T. (2015) Design of modular ″plug-and-play″ expression platforms derived from natural riboswitches for engineering novel genetically encodable RNA regulatory devices Methods Enzymol. 550, 41-71 10.1016/bs.mie.2014.10.031
    • (2015) Methods Enzymol. , vol.550 , pp. 41-71
    • Trausch, J.J.1    Batey, R.T.2
  • 91
    • 33847039871 scopus 로고    scopus 로고
    • A high-throughput screen for synthetic riboswitches reveals mechanistic insights into their function
    • Lynch, S. A., Desai, S. K., Sajja, H. K., and Gallivan, J. P. (2007) A high-throughput screen for synthetic riboswitches reveals mechanistic insights into their function Chem. Biol. 14, 173-184 10.1016/j.chembiol.2006.12.008
    • (2007) Chem. Biol. , vol.14 , pp. 173-184
    • Lynch, S.A.1    Desai, S.K.2    Sajja, H.K.3    Gallivan, J.P.4
  • 92
    • 57049095908 scopus 로고    scopus 로고
    • Riboswitches in unexpected places-a synthetic riboswitch in a protein coding region
    • Topp, S. and Gallivan, J. P. (2008) Riboswitches in unexpected places-a synthetic riboswitch in a protein coding region RNA 14, 2498-2503 10.1261/rna.1269008
    • (2008) RNA , vol.14 , pp. 2498-2503
    • Topp, S.1    Gallivan, J.P.2
  • 93
    • 36148970816 scopus 로고    scopus 로고
    • Reengineering a natural riboswitch by dual genetic selection
    • Nomura, Y. and Yokobayashi, Y. (2007) Reengineering a natural riboswitch by dual genetic selection J. Am. Chem. Soc. 129, 13814-13815 10.1021/ja076298b
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 13814-13815
    • Nomura, Y.1    Yokobayashi, Y.2
  • 94
    • 0142075327 scopus 로고    scopus 로고
    • Genetic control by metabolite-binding riboswitches
    • Winkler, W. C. and Breaker, R. R. (2003) Genetic control by metabolite-binding riboswitches ChemBioChem 4, 1024-1032 10.1002/cbic.200300685
    • (2003) ChemBioChem , vol.4 , pp. 1024-1032
    • Winkler, W.C.1    Breaker, R.R.2
  • 95
    • 63249090231 scopus 로고    scopus 로고
    • An efficient platform for genetic selection and screening of gene switches in Escherichia coli
    • Muranaka, N., Sharma, V., Nomura, Y., and Yokobayashi, Y. (2009) An efficient platform for genetic selection and screening of gene switches in Escherichia coli Nucleic Acids Res. 37, e39 10.1093/nar/gkp039
    • (2009) Nucleic Acids Res. , vol.37 , pp. e39
    • Muranaka, N.1    Sharma, V.2    Nomura, Y.3    Yokobayashi, Y.4
  • 96
    • 70350523604 scopus 로고    scopus 로고
    • Mechanism-guided library design and dual genetic selection of synthetic off riboswitches
    • Muranaka, N., Abe, K., and Yokobayashi, Y. (2009) Mechanism-guided library design and dual genetic selection of synthetic OFF riboswitches ChemBioChem 10, 2375-2381 10.1002/cbic.200900313
    • (2009) ChemBioChem , vol.10 , pp. 2375-2381
    • Muranaka, N.1    Abe, K.2    Yokobayashi, Y.3
  • 97
    • 33745635350 scopus 로고    scopus 로고
    • Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch
    • Serganov, A., Polonskaia, A., Phan, A. T., Breaker, R. R., and Patel, D. J. (2006) Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch Nature 441, 1167-1171 10.1038/nature04740
    • (2006) Nature , vol.441 , pp. 1167-1171
    • Serganov, A.1    Polonskaia, A.2    Phan, A.T.3    Breaker, R.R.4    Patel, D.J.5
  • 98
  • 99
    • 84864694015 scopus 로고    scopus 로고
    • Post-transcriptional Boolean computation by combining aptazymes controlling mRNA translation initiation and tRNA activation
    • Klauser, B., Saragliadis, A., Ausländer, S., Wieland, M., Berthold, M. R., and Hartig, J. S. (2012) Post-transcriptional Boolean computation by combining aptazymes controlling mRNA translation initiation and tRNA activation Mol. BioSyst. 8, 2242-2248 10.1039/c2mb25091h
    • (2012) Mol. BioSyst. , vol.8 , pp. 2242-2248
    • Klauser, B.1    Saragliadis, A.2    Ausländer, S.3    Wieland, M.4    Berthold, M.R.5    Hartig, J.S.6
  • 100
    • 0031171217 scopus 로고    scopus 로고
    • Rational design of allosteric ribozymes
    • Tang, J. and Breaker, R. R. (1997) Rational design of allosteric ribozymes Chem. Biol. 4, 453-459 10.1016/S1074-5521(97)90197-6
    • (1997) Chem. Biol. , vol.4 , pp. 453-459
    • Tang, J.1    Breaker, R.R.2
  • 101
    • 65249122814 scopus 로고    scopus 로고
    • Artificial ribozyme switches containing natural riboswitch aptamer domains
    • Wieland, M., Benz, A., Klauser, B., and Hartig, J. S. (2009) Artificial ribozyme switches containing natural riboswitch aptamer domains Angew. Chem., Int. Ed. 48, 2715-2718 10.1002/anie.200805311
    • (2009) Angew. Chem., Int. Ed. , vol.48 , pp. 2715-2718
    • Wieland, M.1    Benz, A.2    Klauser, B.3    Hartig, J.S.4
  • 102
    • 35148840942 scopus 로고    scopus 로고
    • Functional aptamers and aptazymes in biotechnology, diagnostics, and therapy
    • Famulok, M., Hartig, J. S., and Mayer, G. (2007) Functional aptamers and aptazymes in biotechnology, diagnostics, and therapy Chem. Rev. 107, 3715-3743 10.1021/cr0306743
    • (2007) Chem. Rev. , vol.107 , pp. 3715-3743
    • Famulok, M.1    Hartig, J.S.2    Mayer, G.3
  • 105
    • 33646768226 scopus 로고    scopus 로고
    • 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 10.1016/j.jmb.2006.04.003
    • (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
  • 106
    • 79953178284 scopus 로고    scopus 로고
    • Interactions of the c-di-GMP riboswitch with its second messenger ligand
    • Smith, K. D. and Strobel, S. A. (2011) Interactions of the c-di-GMP riboswitch with its second messenger ligand Biochem. Soc. Trans. 39, 647-651 10.1042/BST0390647
    • (2011) Biochem. Soc. Trans. , vol.39 , pp. 647-651
    • Smith, K.D.1    Strobel, S.A.2
  • 107
    • 84941595614 scopus 로고    scopus 로고
    • Linking aptamer-ligand binding and expression platform folding in riboswitches: Prospects for mechanistic modeling and design
    • Aboul-ela, F., Huang, W., Abd Elrahman, M., Boyapati, V., and Li, P. (2015) Linking aptamer-ligand binding and expression platform folding in riboswitches: prospects for mechanistic modeling and design Wiley Interdisc. Rev. RNA 6, 631-650 10.1002/wrna.1300
    • (2015) Wiley Interdisc. Rev. RNA , vol.6 , pp. 631-650
    • Aboul-Ela, F.1    Huang, W.2    Abd Elrahman, M.3    Boyapati, V.4    Li, P.5
  • 108
    • 84882622399 scopus 로고    scopus 로고
    • Modularity of select riboswitch expression platforms enables facile engineering of novel genetic regulatory devices
    • Ceres, P., Garst, A. D., Marcano-Velazquez, 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 10.1021/sb4000096
    • (2013) ACS Synth. Biol. , vol.2 , pp. 463-472
    • Ceres, P.1    Garst, A.D.2    Marcano-Velazquez, J.G.3    Batey, R.T.4
  • 109
    • 79951519285 scopus 로고    scopus 로고
    • Rational design of artificial riboswitches based on ligand-dependent modulation of internal ribosome entry in wheat germ extract and their applications as label-free biosensors
    • Ogawa, A. (2011) Rational design of artificial riboswitches based on ligand-dependent modulation of internal ribosome entry in wheat germ extract and their applications as label-free biosensors RNA 17, 478-488 10.1261/rna.2433111
    • (2011) RNA , vol.17 , pp. 478-488
    • Ogawa, A.1
  • 110
    • 0034652349 scopus 로고    scopus 로고
    • Methionine-independent initiation of translation in the capsid protein of an insect RNA virus
    • Sasaki, J. and Nakashima, N. (2000) Methionine-independent initiation of translation in the capsid protein of an insect RNA virus Proc. Natl. Acad. Sci. U. S. A. 97, 1512-1515 10.1073/pnas.010426997
    • (2000) Proc. Natl. Acad. Sci. U. S. A. , vol.97 , pp. 1512-1515
    • Sasaki, J.1    Nakashima, N.2
  • 111
    • 0242331742 scopus 로고    scopus 로고
    • Conditional rather than absolute requirements of the capsid coding sequence for initiation of methionine-independent translation in Plautia stali intestine virus
    • Shibuya, N., Nishiyama, T., Kanamori, Y., Saito, H., and Nakashima, N. (2003) Conditional rather than absolute requirements of the capsid coding sequence for initiation of methionine-independent translation in Plautia stali intestine virus J. Virol. 77, 12002-12010 10.1128/JVI.77.22.12002-12010.2003
    • (2003) J. Virol. , vol.77 , pp. 12002-12010
    • Shibuya, N.1    Nishiyama, T.2    Kanamori, Y.3    Saito, H.4    Nakashima, N.5
  • 112
    • 14944346224 scopus 로고    scopus 로고
    • Cell-free synthesis of polypeptides lacking an amino-terminal methionine by using a dicistroviral intergenic internal ribosome entry site
    • Shibuya, N., Nishiyama, T., and Nakashima, N. (2004) Cell-free synthesis of polypeptides lacking an amino-terminal methionine by using a dicistroviral intergenic internal ribosome entry site J. Biochem. 136, 601-606 10.1093/jb/mvh167
    • (2004) J. Biochem. , vol.136 , pp. 601-606
    • Shibuya, N.1    Nishiyama, T.2    Nakashima, N.3
  • 113
    • 33845335508 scopus 로고    scopus 로고
    • Structural basis for ribosome recruitment and manipulation by a viral IRES RNA
    • Pfingsten, J. S., Costantino, D. A., and Kieft, J. S. (2006) Structural basis for ribosome recruitment and manipulation by a viral IRES RNA Science 314, 1450-1454 10.1126/science.1133281
    • (2006) Science , vol.314 , pp. 1450-1454
    • Pfingsten, J.S.1    Costantino, D.A.2    Kieft, J.S.3
  • 114
    • 84856634400 scopus 로고    scopus 로고
    • Rational construction of eukaryotic OFF-riboswitches that downregulate internal ribosome entry site-mediated translation in response to their ligands
    • Ogawa, A. (2012) Rational construction of eukaryotic OFF-riboswitches that downregulate internal ribosome entry site-mediated translation in response to their ligands Bioorg. Med. Chem. Lett. 22, 1639-1642 10.1016/j.bmcl.2011.12.118
    • (2012) Bioorg. Med. Chem. Lett. , vol.22 , pp. 1639-1642
    • Ogawa, A.1
  • 115
    • 0034625442 scopus 로고    scopus 로고
    • Role of a short open reading frame in ribosome shunt on the cauliflower mosaic virus RNA leader
    • Pooggin, M. M., Hohn, T., and Futterer, J. (2000) Role of a short open reading frame in ribosome shunt on the cauliflower mosaic virus RNA leader J. Biol. Chem. 275, 17288-17296 10.1074/jbc.M001143200
    • (2000) J. Biol. Chem. , vol.275 , pp. 17288-17296
    • Pooggin, M.M.1    Hohn, T.2    Futterer, J.3
  • 116
    • 84934437422 scopus 로고    scopus 로고
    • Rational design of artificial ON-riboswitches
    • Ogawa, A. (2014) Rational design of artificial ON-riboswitches Methods Mol. Biol. 1111, 165-181 10.1007/978-1-62703-755-6-12
    • (2014) Methods Mol. Biol. , vol.1111 , pp. 165-181
    • Ogawa, A.1
  • 117
    • 84992411938 scopus 로고    scopus 로고
    • Rational design of a synthetic mammalian riboswitch as a ligand-responsive 1 ribosomal frame-shifting stimulator
    • Lin, Y.-H. and Chang, K.-Y. (2016) Rational design of a synthetic mammalian riboswitch as a ligand-responsive 1 ribosomal frame-shifting stimulator Nucleic Acids Res. 44, 9005-9015 10.1093/nar/gkw718
    • (2016) Nucleic Acids Res. , vol.44 , pp. 9005-9015
    • Lin, Y.-H.1    Chang, K.-Y.2
  • 118
    • 23044450885 scopus 로고    scopus 로고
    • An atypical RNA pseudoknot stimulator and an upstream attenuation signal for 1 ribosomal frameshifting of SARS coronavirus
    • Su, M.-C., Chang, C.-T., Chu, C.-H., Tsai, C.-H., and Chang, K.-Y. (2005) An atypical RNA pseudoknot stimulator and an upstream attenuation signal for 1 ribosomal frameshifting of SARS coronavirus Nucleic Acids Res. 33, 4265-4275 10.1093/nar/gki731
    • (2005) Nucleic Acids Res. , vol.33 , pp. 4265-4275
    • Su, M.-C.1    Chang, C.-T.2    Chu, C.-H.3    Tsai, C.-H.4    Chang, K.-Y.5
  • 119
    • 0042121256 scopus 로고    scopus 로고
    • 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 10.1093/nar/gkg595
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3406-3415
    • Zuker, M.1
  • 121
    • 77949447172 scopus 로고    scopus 로고
    • RNAstructure: Software for RNA secondary structure prediction and analysis
    • Reuter, J. S. and Mathews, D. H. (2010) RNAstructure: software for RNA secondary structure prediction and analysis BMC Bioinf. 11, 129 10.1186/1471-2105-11-129
    • (2010) BMC Bioinf. , vol.11 , pp. 129
    • Reuter, J.S.1    Mathews, D.H.2
  • 122
    • 84921024045 scopus 로고    scopus 로고
    • Design of transcription regulating riboswitches
    • Findeiss, S., Wachsmuth, M., Morl, M., and Stadler, P. F. (2015) Design of transcription regulating riboswitches Methods Enzymol. 550, 1-22 10.1016/bs.mie.2014.10.029
    • (2015) Methods Enzymol. , vol.550 , pp. 1-22
    • Findeiss, S.1    Wachsmuth, M.2    Morl, M.3    Stadler, P.F.4
  • 124
    • 84923537508 scopus 로고    scopus 로고
    • Thermodynamic and kinetic folding of riboswitches
    • Badelt, S., Hammer, S., Flamm, C., and Hofacker, I. L. (2015) Thermodynamic and kinetic folding of riboswitches Methods Enzymol. 553, 193-213 10.1016/bs.mie.2014.10.060
    • (2015) Methods Enzymol. , vol.553 , pp. 193-213
    • Badelt, S.1    Hammer, S.2    Flamm, C.3    Hofacker, I.L.4
  • 125
    • 84455174703 scopus 로고    scopus 로고
    • Model-Driven Engineering of RNA Devices to Quantitatively Program Gene Expression
    • Carothers, J. M., Goler, J. A., Juminaga, D., and Keasling, J. D. (2011) Model-Driven Engineering of RNA Devices to Quantitatively Program Gene Expression Science 334, 1716-1719 10.1126/science.1212209
    • (2011) Science , vol.334 , pp. 1716-1719
    • Carothers, J.M.1    Goler, J.A.2    Juminaga, D.3    Keasling, J.D.4
  • 126
    • 84938651163 scopus 로고    scopus 로고
    • Rational Design and Tuning of Functional RNA Switch to Control an Allosteric Intermolecular Interaction
    • Endoh, T. and Sugimoto, N. (2015) Rational Design and Tuning of Functional RNA Switch to Control an Allosteric Intermolecular Interaction Anal. Chem. 87, 7628-7635 10.1021/acs.analchem.5b00765
    • (2015) Anal. Chem. , vol.87 , pp. 7628-7635
    • Endoh, T.1    Sugimoto, N.2
  • 127
    • 84959135708 scopus 로고    scopus 로고
    • High-throughput cellular RNA device engineering
    • Townshend, B., Kennedy, A. B., Xiang, J. S., and Smolke, C. D. (2015) High-throughput cellular RNA device engineering Nat. Methods 12, 989-994 10.1038/nmeth.3486
    • (2015) Nat. Methods , vol.12 , pp. 989-994
    • Townshend, B.1    Kennedy, A.B.2    Xiang, J.S.3    Smolke, C.D.4
  • 128
    • 84861152754 scopus 로고    scopus 로고
    • Dynamic energy landscapes of riboswitches help interpret conformational rearrangements and function
    • Quarta, G., Sin, K., and Schlick, T. (2012) Dynamic energy landscapes of riboswitches help interpret conformational rearrangements and function PLoS Comput. Biol. 8, e1002368 10.1371/journal.pcbi.1002368
    • (2012) PLoS Comput. Biol. , vol.8 , pp. e1002368
    • Quarta, G.1    Sin, K.2    Schlick, T.3
  • 129
    • 66249084560 scopus 로고    scopus 로고
    • Design principles for riboswitch function
    • Beisel, C. L. and Smolke, C. D. (2009) Design principles for riboswitch function PLoS Comput. Biol. 5, e1000363 10.1371/journal.pcbi.1000363
    • (2009) PLoS Comput. Biol. , vol.5 , pp. e1000363
    • Beisel, C.L.1    Smolke, C.D.2
  • 130
    • 84959368267 scopus 로고    scopus 로고
    • Automated physics-based design of synthetic riboswitches from diverse RNA aptamers
    • Espah Borujeni, A., Mishler, D. M., Wang, J., Huso, W., and Salis, H. M. (2016) Automated physics-based design of synthetic riboswitches from diverse RNA aptamers Nucleic Acids Res. 44, 1-13 10.1093/nar/gkv1289
    • (2016) Nucleic Acids Res. , vol.44 , pp. 1-13
    • Espah Borujeni, A.1    Mishler, D.M.2    Wang, J.3    Huso, W.4    Salis, H.M.5
  • 131
    • 84880512394 scopus 로고    scopus 로고
    • Three-state mechanism couples ligand and temperature sensing in riboswitches
    • Reining, A., Nozinovic, S., Schlepckow, K., Buhr, F., Furtig, B., and Schwalbe, H. (2013) Three-state mechanism couples ligand and temperature sensing in riboswitches Nature 499, 355-359 10.1038/nature12378
    • (2013) Nature , vol.499 , pp. 355-359
    • Reining, A.1    Nozinovic, S.2    Schlepckow, K.3    Buhr, F.4    Furtig, B.5    Schwalbe, H.6
  • 132
    • 84923601441 scopus 로고    scopus 로고
    • Multiple conformational states of riboswitches fine-tune gene regulation
    • Furtig, B., Nozinovic, S., Reining, A., and Schwalbe, H. (2015) Multiple conformational states of riboswitches fine-tune gene regulation Curr. Opin. Struct. Biol. 30, 112-124 10.1016/j.sbi.2015.02.007
    • (2015) Curr. Opin. Struct. Biol. , vol.30 , pp. 112-124
    • Furtig, B.1    Nozinovic, S.2    Reining, A.3    Schwalbe, H.4
  • 134
    • 0031663369 scopus 로고    scopus 로고
    • The green fluorescent protein
    • Tsien, R. Y. (1998) The green fluorescent protein Annu. Rev. Biochem. 67, 509-544 10.1146/annurev.biochem.67.1.509
    • (1998) Annu. Rev. Biochem. , vol.67 , pp. 509-544
    • Tsien, R.Y.1
  • 135
    • 79960959180 scopus 로고    scopus 로고
    • RNA Mimics of Green Fluorescent Protein
    • Paige, J. S., Wu, K. Y., and Jaffrey, S. R. (2011) RNA Mimics of Green Fluorescent Protein Science 333, 642-646 10.1126/science.1207339
    • (2011) Science , vol.333 , pp. 642-646
    • Paige, J.S.1    Wu, K.Y.2    Jaffrey, S.R.3
  • 136
    • 84921417907 scopus 로고    scopus 로고
    • Using Spinach aptamer to correlate mRNA and protein levels in Escherichia coli
    • Pothoulakis, G. and Ellis, T. (2015) Using Spinach aptamer to correlate mRNA and protein levels in Escherichia coli Methods Enzymol. 550, 173-185 10.1016/bs.mie.2014.10.047
    • (2015) Methods Enzymol. , vol.550 , pp. 173-185
    • Pothoulakis, G.1    Ellis, T.2
  • 137
    • 84888883550 scopus 로고    scopus 로고
    • A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat-containing RNA
    • Strack, R. L., Disney, M. D., and Jaffrey, S. R. (2013) A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat-containing RNA Nat. Methods 10, 1219-1224 10.1038/nmeth.2701
    • (2013) Nat. Methods , vol.10 , pp. 1219-1224
    • Strack, R.L.1    Disney, M.D.2    Jaffrey, S.R.3
  • 139
    • 84930198598 scopus 로고    scopus 로고
    • In-gel imaging of RNA processing using broccoli reveals optimal aptamer expression strategies
    • Filonov, G. S., Kam, C. W., Song, W., and Jaffrey, S. R. (2015) In-gel imaging of RNA processing using broccoli reveals optimal aptamer expression strategies Chem. Biol. 22, 649-660 10.1016/j.chembiol.2015.04.018
    • (2015) Chem. Biol. , vol.22 , pp. 649-660
    • Filonov, G.S.1    Kam, C.W.2    Song, W.3    Jaffrey, S.R.4
  • 140
    • 84992751988 scopus 로고    scopus 로고
    • RNA Fluorescence with Light-Up Aptamers
    • Ouellet, J. (2016) RNA Fluorescence with Light-Up Aptamers Front. Chem. 4, 29 10.3389/fchem.2016.00029
    • (2016) Front. Chem. , vol.4 , pp. 29
    • Ouellet, J.1
  • 141
    • 34547659860 scopus 로고    scopus 로고
    • Recombinant RNA technology: The tRNA scaffold
    • Ponchon, L. and Dardel, F. (2007) Recombinant RNA technology: the tRNA scaffold Nat. Methods 4, 571-576 10.1038/nmeth1058
    • (2007) Nat. Methods , vol.4 , pp. 571-576
    • Ponchon, L.1    Dardel, F.2
  • 142
    • 84913570361 scopus 로고    scopus 로고
    • Broccoli: Rapid selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution
    • Filonov, G. S., Moon, J. D., Svensen, N., and Jaffrey, S. R. (2014) Broccoli: rapid selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution J. Am. Chem. Soc. 136, 16299-16308 10.1021/ja508478x
    • (2014) J. Am. Chem. Soc. , vol.136 , pp. 16299-16308
    • Filonov, G.S.1    Moon, J.D.2    Svensen, N.3    Jaffrey, S.R.4
  • 143
    • 84948471468 scopus 로고    scopus 로고
    • Tandem Spinach Array for mRNA Imaging in Living Bacterial Cells
    • Zhang, J., Fei, J., Leslie, B. J., Han, K. Y., Kuhlman, T. E., and Ha, T. (2015) Tandem Spinach Array for mRNA Imaging in Living Bacterial Cells Sci. Rep. 5, 17295 10.1038/srep17295
    • (2015) Sci. Rep. , vol.5 , pp. 17295
    • Zhang, J.1    Fei, J.2    Leslie, B.J.3    Han, K.Y.4    Kuhlman, T.E.5    Ha, T.6
  • 144
    • 84889649107 scopus 로고    scopus 로고
    • Contact-mediated quenching for RNA imaging in bacteria with a fluorophore-binding aptamer
    • Sunbul, M. and Jaschke, A. (2013) Contact-mediated quenching for RNA imaging in bacteria with a fluorophore-binding aptamer Angew. Chem., Int. Ed. 52, 13401-13404 10.1002/anie.201306622
    • (2013) Angew. Chem., Int. Ed. , vol.52 , pp. 13401-13404
    • Sunbul, M.1    Jaschke, A.2
  • 145
    • 84983770697 scopus 로고    scopus 로고
    • Dual-colour imaging of RNAs using quencher- and fluorophore-binding aptamers
    • Arora, A., Sunbul, M., and Jaschke, A. (2015) Dual-colour imaging of RNAs using quencher- and fluorophore-binding aptamers Nucleic Acids Res. 43, e144 10.1093/nar/gkv718
    • (2015) Nucleic Acids Res. , vol.43 , pp. e144
    • Arora, A.1    Sunbul, M.2    Jaschke, A.3
  • 146
    • 0032437793 scopus 로고    scopus 로고
    • Isolation and characterization of fluorophore-binding RNA aptamers
    • Holeman, L. A., Robinson, S. L., Szostak, J. W., and Wilson, C. (1998) Isolation and characterization of fluorophore-binding RNA aptamers Folding Des. 3, 423-431 10.1016/S1359-0278(98)00059-5
    • (1998) Folding Des. , vol.3 , pp. 423-431
    • Holeman, L.A.1    Robinson, S.L.2    Szostak, J.W.3    Wilson, C.4
  • 148
    • 84858030373 scopus 로고    scopus 로고
    • Fluorescence imaging of cellular metabolites with RNA
    • Paige, J. S., Nguyen-Duc, T., Song, W., and Jaffrey, S. R. (2012) Fluorescence imaging of cellular metabolites with RNA Science 335, 1194 10.1126/science.1218298
    • (2012) Science , vol.335 , pp. 1194
    • Paige, J.S.1    Nguyen-Duc, T.2    Song, W.3    Jaffrey, S.R.4
  • 149
    • 84930227077 scopus 로고    scopus 로고
    • Imaging metabolite dynamics in living cells using a Spinach-based riboswitch
    • You, M., Litke, J. L., and Jaffrey, S. R. (2015) Imaging metabolite dynamics in living cells using a Spinach-based riboswitch Proc. Natl. Acad. Sci. U. S. A. 112, E2756 10.1073/pnas.1504354112
    • (2015) Proc. Natl. Acad. Sci. U. S. A. , vol.112 , pp. E2756
    • You, M.1    Litke, J.L.2    Jaffrey, S.R.3
  • 150
    • 84963815342 scopus 로고    scopus 로고
    • Developing Fluorogenic Riboswitches for Imaging Metabolite Concentration Dynamics in Bacterial Cells
    • Litke, J. L., You, M., and Jaffrey, S. R. (2016) Developing Fluorogenic Riboswitches for Imaging Metabolite Concentration Dynamics in Bacterial Cells Methods Enzymol. 572, 315-333 10.1016/bs.mie.2016.03.021
    • (2016) Methods Enzymol. , vol.572 , pp. 315-333
    • Litke, J.L.1    You, M.2    Jaffrey, S.R.3
  • 151
    • 84979257985 scopus 로고    scopus 로고
    • Engineering and characterization of fluorogenic glycine riboswitches
    • Ketterer, S., Gladis, L., Kozica, A., and Meier, M. (2016) Engineering and characterization of fluorogenic glycine riboswitches Nucleic Acids Res. 44, 5983-5992 10.1093/nar/gkw465
    • (2016) Nucleic Acids Res. , vol.44 , pp. 5983-5992
    • Ketterer, S.1    Gladis, L.2    Kozica, A.3    Meier, M.4
  • 152
    • 84891715447 scopus 로고    scopus 로고
    • Using Spinach-based sensors for fluorescence imaging of intracellular metabolites and proteins in living bacteria
    • Strack, R. L., Song, W., and Jaffrey, S. R. (2014) Using Spinach-based sensors for fluorescence imaging of intracellular metabolites and proteins in living bacteria Nat. Protoc. 9, 146-155 10.1038/nprot.2014.001
    • (2014) Nat. Protoc. , vol.9 , pp. 146-155
    • Strack, R.L.1    Song, W.2    Jaffrey, S.R.3
  • 153
    • 84875784381 scopus 로고    scopus 로고
    • RNA-based fluorescent biosensors for live cell imaging of second messengers cyclic di-GMP and cyclic AMP-GMP
    • Kellenberger, C. A., Wilson, S. C., Sales-Lee, J., and Hammond, M. C. (2013) RNA-based fluorescent biosensors for live cell imaging of second messengers cyclic di-GMP and cyclic AMP-GMP J. Am. Chem. Soc. 135, 4906-4909 10.1021/ja311960g
    • (2013) J. Am. Chem. Soc. , vol.135 , pp. 4906-4909
    • Kellenberger, C.A.1    Wilson, S.C.2    Sales-Lee, J.3    Hammond, M.C.4
  • 154
    • 84930227399 scopus 로고    scopus 로고
    • RNA-Based Fluorescent Biosensors for Live Cell Imaging of Second Messenger Cyclic di-AMP
    • Kellenberger, C. A., Chen, C., Whiteley, A. T., Portnoy, D. A., and Hammond, M. C. (2015) RNA-Based Fluorescent Biosensors for Live Cell Imaging of Second Messenger Cyclic di-AMP J. Am. Chem. Soc. 137, 6432-6435 10.1021/jacs.5b00275
    • (2015) J. Am. Chem. Soc. , vol.137 , pp. 6432-6435
    • Kellenberger, C.A.1    Chen, C.2    Whiteley, A.T.3    Portnoy, D.A.4    Hammond, M.C.5
  • 155
    • 84877582071 scopus 로고    scopus 로고
    • Nucleotides adjacent to the ligand-binding pocket are linked to activity tuning in the purine riboswitch
    • Stoddard, C. D., Widmann, J., Trausch, J. J., Marcano-Velazquez, J. G., Knight, R., and Batey, R. T. (2013) Nucleotides adjacent to the ligand-binding pocket are linked to activity tuning in the purine riboswitch J. Mol. Biol. 425, 1596-1611 10.1016/j.jmb.2013.02.023
    • (2013) J. Mol. Biol. , vol.425 , pp. 1596-1611
    • Stoddard, C.D.1    Widmann, J.2    Trausch, J.J.3    Marcano-Velazquez, J.G.4    Knight, R.5    Batey, R.T.6
  • 156
    • 0025663103 scopus 로고
    • Prediction of rho-independent Escherichia coli transcription terminators
    • Carafa, Y. d., Brody, E., and Thermes, C. (1990) Prediction of rho-independent Escherichia coli transcription terminators J. Mol. Biol. 216, 835-858 10.1016/S0022-2836(99)80005-9
    • (1990) J. Mol. Biol. , vol.216 , pp. 835-858
    • Carafa, Y.D.1    Brody, E.2    Thermes, C.3
  • 157
  • 158
    • 5044234799 scopus 로고    scopus 로고
    • A glycine-dependent riboswitch that uses cooperative binding to control gene expression
    • Mandal, M., Lee, M., Barrick, J. E., Weinberg, Z., Emilsson, G. M., Ruzzo, W. L., and Breaker, R. R. (2004) A glycine-dependent riboswitch that uses cooperative binding to control gene expression Science 306, 275-279 10.1126/science.1100829
    • (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
  • 160
    • 84863923278 scopus 로고    scopus 로고
    • Riboswitches and the RNA world
    • Breaker, R. R. (2012) Riboswitches and the RNA world Cold Spring Harbor Perspect. Biol. 4, a003566 10.1101/cshperspect.a003566
    • (2012) Cold Spring Harbor Perspect. Biol. , vol.4 , pp. a003566
    • Breaker, R.R.1
  • 161
    • 84856246110 scopus 로고    scopus 로고
    • Automated RNA structure prediction uncovers a kink-turn linker in double glycine riboswitches
    • Kladwang, W., Chou, F.-C., and Das, R. (2012) Automated RNA structure prediction uncovers a kink-turn linker in double glycine riboswitches J. Am. Chem. Soc. 134, 1404-1407 10.1021/ja2093508
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 1404-1407
    • Kladwang, W.1    Chou, F.-C.2    Das, R.3
  • 162
    • 84857438025 scopus 로고    scopus 로고
    • An energetically beneficial leader-linker interaction abolishes ligand-binding cooperativity in glycine riboswitches
    • Sherman, E. M., Esquiaqui, J., Elsayed, G., and Ye, J.-D. (2012) An energetically beneficial leader-linker interaction abolishes ligand-binding cooperativity in glycine riboswitches RNA 18, 496-507 10.1261/rna.031286.111
    • (2012) RNA , vol.18 , pp. 496-507
    • Sherman, E.M.1    Esquiaqui, J.2    Elsayed, G.3    Ye, J.-D.4
  • 163
    • 22544432327 scopus 로고    scopus 로고
    • Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria
    • Rodionov, D. A., Dubchak, I., Arkin, A., Alm, E., and Gelfand, M. S. (2004) Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria Genome Biol. 5, R90 10.1186/gb-2004-5-11-r90
    • (2004) Genome Biol. , vol.5 , pp. R90
    • Rodionov, D.A.1    Dubchak, I.2    Arkin, A.3    Alm, E.4    Gelfand, M.S.5
  • 164
    • 33947714417 scopus 로고    scopus 로고
    • Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis
    • Welz, R. and Breaker, R. R. (2007) Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis RNA 13, 573-582 10.1261/rna.407707
    • (2007) RNA , vol.13 , pp. 573-582
    • Welz, R.1    Breaker, R.R.2
  • 165
    • 77956324713 scopus 로고    scopus 로고
    • A synthetic riboswitch with chemical band-pass response
    • Muranaka, N. and Yokobayashi, Y. (2010) A synthetic riboswitch with chemical band-pass response Chem. Commun. 46, 6825-6827 10.1039/c0cc01438a
    • (2010) Chem. Commun. , vol.46 , pp. 6825-6827
    • Muranaka, N.1    Yokobayashi, Y.2
  • 166
    • 77953920382 scopus 로고    scopus 로고
    • Posttranscriptional signal integration of engineered riboswitches yields band-pass output
    • Muranaka, N. and Yokobayashi, Y. (2010) Posttranscriptional signal integration of engineered riboswitches yields band-pass output Angew. Chem., Int. Ed. 49, 4653-4655 10.1002/anie.201001482
    • (2010) Angew. Chem., Int. Ed. , vol.49 , pp. 4653-4655
    • Muranaka, N.1    Yokobayashi, Y.2
  • 167
    • 13244296604 scopus 로고    scopus 로고
    • Protein tagging and detection with engineered self-assembling fragments of green fluorescent protein
    • Cabantous, S., Terwilliger, T. C., and Waldo, G. S. (2005) Protein tagging and detection with engineered self-assembling fragments of green fluorescent protein Nat. Biotechnol. 23, 102-107 10.1038/nbt1044
    • (2005) Nat. Biotechnol. , vol.23 , pp. 102-107
    • Cabantous, S.1    Terwilliger, T.C.2    Waldo, G.S.3
  • 168
    • 33749986680 scopus 로고    scopus 로고
    • Tandem Riboswitch Architectures Exhibit Complex Gene Control Functions
    • Sudarsan, N., Hammond, M. C., Block, K. F., Welz, R., Barrick, J. E., Roth, A., and Breaker, R. R. (2006) Tandem Riboswitch Architectures Exhibit Complex Gene Control Functions Science 314, 300-304 10.1126/science.1130716
    • (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
  • 169
    • 84976344650 scopus 로고    scopus 로고
    • Exploring the modular nature of riboswitches and RNA thermometers
    • Roßmanith, J. and Narberhaus, F. (2016) Exploring the modular nature of riboswitches and RNA thermometers Nucleic Acids Res. 44, 5410-5423 10.1093/nar/gkw232
    • (2016) Nucleic Acids Res. , vol.44 , pp. 5410-5423
    • Roßmanith, J.1    Narberhaus, F.2
  • 170
    • 57149117140 scopus 로고    scopus 로고
    • Engineering complex riboswitch regulation by dual genetic selection
    • Sharma, V., Nomura, Y., and Yokobayashi, Y. (2008) Engineering complex riboswitch regulation by dual genetic selection J. Am. Chem. Soc. 130, 16310-16315 10.1021/ja805203w
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 16310-16315
    • Sharma, V.1    Nomura, Y.2    Yokobayashi, Y.3
  • 171
    • 0035312243 scopus 로고    scopus 로고
    • Cooperative binding of effectors by an allosteric ribozyme
    • Jose, A. M., Soukup, G. A., and Breaker, R. R. (2001) Cooperative binding of effectors by an allosteric ribozyme Nucleic Acids Res. 29, 1631-1637 10.1093/nar/29.7.1631
    • (2001) Nucleic Acids Res. , vol.29 , pp. 1631-1637
    • Jose, A.M.1    Soukup, G.A.2    Breaker, R.R.3
  • 172
    • 54249113318 scopus 로고    scopus 로고
    • Higher-Order Cellular Information Processing with Synthetic RNA Devices
    • Win, M. N. and Smolke, C. D. (2008) Higher-Order Cellular Information Processing with Synthetic RNA Devices Science 322, 456-460 10.1126/science.1160311
    • (2008) Science , vol.322 , pp. 456-460
    • Win, M.N.1    Smolke, C.D.2
  • 173
    • 84862167101 scopus 로고    scopus 로고
    • High-throughput enzyme evolution in Saccharomyces cerevisiae using a synthetic RNA switch
    • Michener, J. K. and Smolke, C. D. (2012) High-throughput enzyme evolution in Saccharomyces cerevisiae using a synthetic RNA switch Metab. Eng. 14, 306-316 10.1016/j.ymben.2012.04.004
    • (2012) Metab. Eng. , vol.14 , pp. 306-316
    • Michener, J.K.1    Smolke, C.D.2
  • 174
    • 0347457063 scopus 로고    scopus 로고
    • The regulatory cascade that activates the Hrp regulon in Erwinia herbicola pv. Gypsophilae
    • Nizan-Koren, R., Manulis, S., Mor, H., Iraki, N. M., and Barash, I. (2003) The regulatory cascade that activates the Hrp regulon in Erwinia herbicola pv. gypsophilae Mol. Plant-Microbe Interact. 16, 249-260 10.1094/MPMI.2003.16.3.249
    • (2003) Mol. Plant-Microbe Interact. , vol.16 , pp. 249-260
    • Nizan-Koren, R.1    Manulis, S.2    Mor, H.3    Iraki, N.M.4    Barash, I.5
  • 175
  • 176
    • 77953642931 scopus 로고    scopus 로고
    • High-throughput metabolic engineering: Advances in small-molecule screening and selection
    • Dietrich, J. A., McKee, A. E., and Keasling, J. D. (2010) High-throughput metabolic engineering: advances in small-molecule screening and selection Annu. Rev. Biochem. 79, 563-590 10.1146/annurev-biochem-062608-095938
    • (2010) Annu. Rev. Biochem. , vol.79 , pp. 563-590
    • Dietrich, J.A.1    McKee, A.E.2    Keasling, J.D.3
  • 177
    • 84879164975 scopus 로고    scopus 로고
    • Synthetic RNA devices to expedite the evolution of metabolite-producing microbes
    • Yang, J., Seo, S. W., Jang, S., Shin, S.-I., Lim, C. H., Roh, T.-Y., and Jung, G. Y. (2013) Synthetic RNA devices to expedite the evolution of metabolite-producing microbes Nat. Commun. 4, 1413 10.1038/ncomms2404
    • (2013) Nat. Commun. , vol.4 , pp. 1413
    • Yang, J.1    Seo, S.W.2    Jang, S.3    Shin, S.-I.4    Lim, C.H.5    Roh, T.-Y.6    Jung, G.Y.7
  • 178
    • 84921395718 scopus 로고    scopus 로고
    • Riboselector: Riboswitch-based synthetic selection device to expedite evolution of metabolite-producing microorganisms
    • Jang, S., Yang, J., Seo, S. W., and Jung, G. Y. (2015) Riboselector: riboswitch-based synthetic selection device to expedite evolution of metabolite-producing microorganisms Methods Enzymol. 550, 341-362 10.1016/bs.mie.2014.10.039
    • (2015) Methods Enzymol. , vol.550 , pp. 341-362
    • Jang, S.1    Yang, J.2    Seo, S.W.3    Jung, G.Y.4
  • 180
    • 84455174703 scopus 로고    scopus 로고
    • Model-driven engineering of RNA devices to quantitatively program gene expression
    • Carothers, J. M., Goler, J. A., Juminaga, D., and Keasling, J. D. (2011) Model-driven engineering of RNA devices to quantitatively program gene expression Science 334, 1716-1719 10.1126/science.1212209
    • (2011) Science , vol.334 , pp. 1716-1719
    • Carothers, J.M.1    Goler, J.A.2    Juminaga, D.3    Keasling, J.D.4
  • 181
    • 84924258069 scopus 로고    scopus 로고
    • Designing RNA-based genetic control systems for efficient production from engineered metabolic pathways
    • Stevens, J. T. and Carothers, J. M. (2015) Designing RNA-based genetic control systems for efficient production from engineered metabolic pathways ACS Synth. Biol. 4, 107-115 10.1021/sb400201u
    • (2015) ACS Synth. Biol. , vol.4 , pp. 107-115
    • Stevens, J.T.1    Carothers, J.M.2
  • 182
  • 183
    • 84870601954 scopus 로고    scopus 로고
    • Synthetic riboswitches for external regulation of genes transferred by replication-deficient and oncolytic adenoviruses
    • Ketzer, P., Haas, S. F., Engelhardt, S., Hartig, J. S., and Nettelbeck, D. M. (2012) Synthetic riboswitches for external regulation of genes transferred by replication-deficient and oncolytic adenoviruses Nucleic Acids Res. 40, e167 10.1093/nar/gks734
    • (2012) Nucleic Acids Res. , vol.40 , pp. e167
    • Ketzer, P.1    Haas, S.F.2    Engelhardt, S.3    Hartig, J.S.4    Nettelbeck, D.M.5
  • 185
    • 77952679687 scopus 로고    scopus 로고
    • Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems
    • Chen, Y. Y., Jensen, M. C., and Smolke, C. D. (2010) Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems Proc. Natl. Acad. Sci. U. S. A. 107, 8531-8536 10.1073/pnas.1001721107
    • (2010) Proc. Natl. Acad. Sci. U. S. A. , vol.107 , pp. 8531-8536
    • Chen, Y.Y.1    Jensen, M.C.2    Smolke, C.D.3
  • 186
    • 79954610188 scopus 로고    scopus 로고
    • Design of small molecule-responsive microRNAs based on structural requirements for Drosha processing
    • Beisel, C. L., Chen, Y. Y., Culler, S. J., Hoff, K. G., and Smolke, C. D. (2011) Design of small molecule-responsive microRNAs based on structural requirements for Drosha processing Nucleic Acids Res. 39, 2981-2994 10.1093/nar/gkq954
    • (2011) Nucleic Acids Res. , vol.39 , pp. 2981-2994
    • Beisel, C.L.1    Chen, Y.Y.2    Culler, S.J.3    Hoff, K.G.4    Smolke, C.D.5
  • 187
    • 52249103283 scopus 로고    scopus 로고
    • Modulating endogenous gene expression of mammalian cells via RNA-small molecule interaction
    • Tuleuova, N., An, C.-I., Ramanculov, E., Revzin, A., and Yokobayashi, Y. (2008) Modulating endogenous gene expression of mammalian cells via RNA-small molecule interaction Biochem. Biophys. Res. Commun. 376, 169-173 10.1016/j.bbrc.2008.08.112
    • (2008) Biochem. Biophys. Res. Commun. , vol.376 , pp. 169-173
    • Tuleuova, N.1    An, C.-I.2    Ramanculov, E.3    Revzin, A.4    Yokobayashi, Y.5
  • 188
    • 84863171531 scopus 로고    scopus 로고
    • Hepatitis C virus replication-specific inhibition of microRNA activity with self-cleavable allosteric ribozyme
    • Lee, C. H., Kim, J. H., Kim, H. W., Myung, H., and Lee, S.-W. (2012) Hepatitis C virus replication-specific inhibition of microRNA activity with self-cleavable allosteric ribozyme Nucleic Acid Ther. 22, 17-29 10.1089/nat.2011.0326
    • (2012) Nucleic Acid Ther. , vol.22 , pp. 17-29
    • Lee, C.H.1    Kim, J.H.2    Kim, H.W.3    Myung, H.4    Lee, S.-W.5
  • 189
    • 67650727366 scopus 로고    scopus 로고
    • VARNA: Interactive drawing and editing of the RNA secondary structure
    • Darty, K., Denise, A., and Ponty, Y. (2009) VARNA: Interactive drawing and editing of the RNA secondary structure Bioinformatics 25, 1974-1975 10.1093/bioinformatics/btp250
    • (2009) Bioinformatics , vol.25 , pp. 1974-1975
    • Darty, K.1    Denise, A.2    Ponty, Y.3


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