Opportunities in the design and application of RNA for gene expression control

Nucleic Acids Research

Volumn 44, Issue 7, 2016, Pages 2987-2999

  McKeague, Maureen ^a   Wong, Remus S ^a   Smolke, Christina D ^a  

^a Stanford University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APTAMER; RNA; REGULATORY RNA SEQUENCE; RIBOSWITCH;

CELL FUNCTION; COMPUTER MODEL; EQUIPMENT DESIGN; GENE EXPRESSION REGULATION; GENERAL MEDICAL DEVICE; GENETIC ENGINEERING; IN VIVO STUDY; LIGAND BINDING; METABOLITE; MOLECULAR PROBE; PRIORITY JOURNAL; PROTEIN INTERACTION; QUANTITATIVE ANALYSIS; REGULATORY SEQUENCE; REVIEW; RIBOSWITCH; RNA BINDING; RNA DEVICE; RNA INTERFERENCE; RNA SEQUENCE; RNA TRANSLATION; STRUCTURE ACTIVITY RELATION; COMPUTER SIMULATION; METABOLIC ENGINEERING; PROCEDURES; REGULATORY RNA SEQUENCE; SYSTEMATIC EVOLUTION OF LIGANDS BY EXPONENTIAL ENRICHMENT APTAMER TECHNIQUE;

APTAMERS, NUCLEOTIDE; COMPUTER SIMULATION; GENE EXPRESSION REGULATION; GENETIC ENGINEERING; METABOLIC ENGINEERING; REGULATORY SEQUENCES, RIBONUCLEIC ACID; RIBOSWITCH; SELEX APTAMER TECHNIQUE;

EID: 84965158377     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw151     Document Type: Review

References (126)

1. Drubin, D.A., Way, J.C., Silver, P.A. (2007) Designing biological systems. Genes Dev., 21, 242-254.
2. Chen, Y.Y., Galloway, K.E., Smolke, C.D. (2012) Synthetic biology: advancing biological frontiers by building synthetic systems. Genome Biol., 13, 1-10.
3. Purnick, P.E., Weiss, R. (2009) The second wave of synthetic biology: from modules to systems. Nat. Rev. Mol. Cell Biol., 10, 410-422.
4. Khalil, A.S., Collins, J.J. (2010) Synthetic biology: applications come of age. Nat. Rev. Genet., 11, 367-379.
5. Wang, Y.H., Wei, K.Y., Smolke, C.D. (2013) Synthetic biology: advancing the design of diverse genetic systems. Annu. Rev. Chem. Biomol. Eng., 4, 69-102.
6. Qi, L.S., Arkin, A.P. (2014) A versatile framework for microbial engineering using synthetic non-coding RNAs. Nat. Rev. Microbiol., 12, 341-354.
7. Isaacs, F.J., Dwyer, D.J., Collins, J.J. (2006) RNA synthetic biology. Nat. Biotechnol., 24, 545-554.
8. Cho, E.J., Lee, J.W., Ellington, A.D. (2009) Applications of aptamers as sensors. Annu. Rev. Anal. Chem. (Palo Alto Calif.), 2, 241-264.
9. Chang, A.L., Wolf, J.J., Smolke, C.D. (2012) Synthetic RNA switches as a tool for temporal and spatial control over gene expression. Curr. Opin. Biotechnol., 23, 679-688.
10. Liang, J.C., Bloom, R.J., Smolke, C.D. (2011) Engineering biological systems with synthetic RNA molecules. Mol. Cell, 43, 915-926.
11. Chappell, J., Watters, K.E., Takahashi, M.K., Lucks, J.B. (2015) A renaissance in RNA synthetic biology: new mechanisms, applications and tools for the future. Curr. Opin. Chem. Biol., 28, 47-56.
12. Auslander, S., Stucheli, P., Rehm, C., Auslander, D., Hartig, J.S., Fussenegger, M. (2014) A general design strategy for protein-responsive riboswitches in mammalian cells. Nat. Methods, 11, 1154-1160.
13. Barrick, J.E., Breaker, R.R. (2007) The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biol., 8, R239.
14. Winkler, W.C., Cohen-Chalamish, S., Breaker, R.R. (2002) An mRNA structure that controls gene expression by binding FMN. Proc. Natl. Acad. Sci. U.S.A., 99, 15908-15913.
15. Ceres, P., Trausch, J.J., Batey, R.T. (2013) Engineering modular 'ON' RNA switches using biological components. Nucleic Acids Res., 41, 10449-10461.
16. Ceres, P., Garst, A.D., Marcano-Velazquez, J.G., Batey, R.T. (2013) Modularity of select riboswitch expression platforms enables facile engineering of novel genetic regulatory devices. ACS Synth. Biol., 2, 463-472.
17. Nomura, Y., Kumar, D., Yokobayashi, Y. (2012) Synthetic mammalian riboswitches based on guanine aptazyme. Chem. Commun., 48, 7215-7217.
18. Nomura, Y., Zhou, L., Miu, A., Yokobayashi, Y. (2013) Controlling mammalian gene expression by allosteric hepatitis delta virus ribozymes. ACS Synth. Biol., 2, 684-689.
19. Serganov, A., Nudler, E. (2013) A decade of riboswitches. Cell, 152, 17-24.
20. Rosinski-Chupin, I., Soutourina, O., Martin-Verstraete, I. (2014) Riboswitch discovery by combining RNA-seq and genome-wide identification of transcriptional start sites. Methods Enzymol., 549, 3-27.
21. Peselis, A., Serganov, A. (2014) Themes and variations in riboswitch structure and function. Biochim. Biophys. Acta, 1839, 908-918.
22. Robinson, C.J., Vincent, H.A., Wu, M.C., Lowe, P.T., Dunstan, M.S., Leys, D., Micklefield, J. (2014) Modular riboswitch toolsets for synthetic genetic control in diverse bacterial species. J. Am. Chem. Soc., 136, 10615-10624.
23. McKeague, M., Wang, Y.H., Smolke, C.D. (2015) In vitro screening and in silico modeling of RNA-based gene expression control. ACS Chem. Biol., 10, 2463-2467.
24. Tuerk, C., Gold, L. (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science, 249, 505-510.
25. Ellington, A.D., Szostak, J.W. (1990) In vitro selection of RNA molecules that bind specific ligands. Nature, 346, 818-822.
26. Robertson, D.L., Joyce, G.F. (1990) Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature, 344, 467-468.
27. Cruz-Toledo, J., McKeague, M., Zhang, X., Giamberardino, A., McConnell, E., Francis, T., Derosa, M.C., Dumontier, M. (2012) Aptamer base: a collaborative knowledge base to describe aptamers and SELEX experiments. Database, bas006.
28. McKeague, M., Derosa, M.C. (2012) Challenges and opportunities for small molecule aptamer development. J. Nucleic Acids, 2012, 748913.
29. Jenison, R.D., Gill, S.C., Pardi, A., Polisky, B. (1994) High-resolution molecular discrimination by RNA. Science, 263, 1425-1429.
30. Berens, C., Groher, F., 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.
31. Carothers, J.M., Goler, J.A., Kapoor, Y., Lara, L., Keasling, J.D. (2010) Selecting RNA aptamers for synthetic biology: investigating magnesium dependence and predicting binding affinity. Nucleic Acids Res., 38, 2736-2747.
32. Kennedy, A.B., Vowles, J.V., d'Espaux, L., Smolke, C.D. (2014) Protein-responsive ribozyme switches in eukaryotic cells. Nucleic Acids Res., 42, 12306-12321.
33. Cheng, C., Chen, Y.H., Lennox, K.A., Behlke, M.A., Davidson, B.L. (2013) In vivo SELEX for identification of brain-penetrating aptamers. Mol. Ther. Nucleic Acids, 2, e67.
34. Levay, A., Brenneman, R., Hoinka, J., Sant, D., Cardone, M., Trinchieri, G., Przytycka, T.M., Berezhnoy, A. (2015) Identifying high-affinity aptamer ligands with defined cross-reactivity using high-throughput guided systematic evolution of ligands by exponential enrichment. Nucleic Acids Res., 43, e82.
35. Ozer, A., Pagano, J.M., Lis, J.T. (2014) New technologies provide quantum changes in the scale, speed, and success of SELEX methods and aptamer characterization. Mole. Ther. Nucleic Acids, 3, e183.
36. Sun, H., Zu, Y. (2015) A highlight of recent advances in aptamer technology and its application. Molecules, 20, 11959-11980.
37. Darmostuk, M., Rimpelova, S., Gbelcova, H., Ruml, T. (2015) Current approaches in SELEX: an update to aptamer selection technology. Biotechnol. Adv., 33, 1141-1161.
38. Ouellet, E., Foley, J.H., Conway, E.M., Haynes, C. (2015) Hi-Fi SELEX: a high-fidelity digital-PCR based therapeutic aptamer discovery platform. Biotechnol. Bioeng., 112, 1506-1522.
39. Luo, Z., Zhou, H., Jiang, H., Ou, H., Li, X., Zhang, L. (2015) Development of a fraction collection approach in capillary electrophoresis SELEX for aptamer selection. Analyst, 140, 2664-2670.
40. Roulet, E., Busso, S., Camargo, A.A., Simpson, A.J., Mermod, N., Bucher, P. (2002) High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites. Nat. Biotechnol., 20, 831-835.
41. Cho, M., Xiao, Y., Nie, J., Stewart, R., Csordas, A.T., Oh, S.S., Thomson, J.A., Soh, H.T. (2010) Quantitative selection of DNA aptamers through microfluidic selection and high-throughput sequencing. Proc. Natl. Acad. Sci. U.S.A., 107, 15373-15378.
42. Schutze, T., Wilhelm, B., Greiner, N., Braun, H., Peter, F., Morl, M., Erdmann, V.A., Lehrach, H., Konthur, Z., Menger, M. et al. (2011) Probing the SELEX process with next-generation sequencing. PLoS One, 6, e29604.
43. Eaton, R.M., Shallcross, J.A., Mael, L.E., Mears, K.S., Minkoff, L., Scoville, D.J., Whelan, R.J. (2015) Selection of DNA aptamers for ovarian cancer biomarker HE4 using CE-SELEX and high-throughput sequencing. Anal Bioanal. Chem., 407, 6965-6973.
44. Jing, M., Bowser, M.T. (2013) Tracking the emergence of high affinity aptamers for rhVEGF165 during capillary electrophoresis-systematic evolution of ligands by exponential enrichment using high throughput sequencing. Anal Chem., 85, 10761-10770.
45. Riley, K.R., Gagliano, J., Xiao, J., Libby, K., Saito, S., Yu, G., Cubicciotti, R., Macosko, J., Colyer, C.L., Guthold, M. et al. (2015) Combining capillary electrophoresis and next-generation sequencing for aptamer selection. Anal Bioanal. Chem., 407, 1527-1532.
46. Spiga, F.M., Maietta, P., Guiducci, C. (2015) More DNA-aptamers for small drugs: a capture-SELEX coupled with surface plasmon resonance and high-throughput sequencing. ACS Comb. Sci., 17, 326-333.
47. Dupont, D.M., Larsen, N., Jensen, J.K.,reasen, P.A., Kjems, J. (2015) Characterisation of aptamer-target interactions by branched selection and high-throughput sequencing of SELEX pools. Nucleic Acids Res., 43, e139.
48. McKeague, M., DeRosa, M.C. (2014) Aptamers and SELEX: tools for the development of transformative molecular recognition technology. Aptamers Synth. Antibodies, 1, 12-16.
49. Alam, K.K., Chang, J.L., Burke, D.H. (2015) FASTAptamer: a bioinformatic toolkit for high-throughput sequence analysis of combinatorial selections. Mol. Ther. Nucleic Acids, 4, e230.
50. Hoinka, J., Berezhnoy, A., Dao, P., Sauna, Z.E., Gilboa, E., Przytycka, T.M. (2015) Large scale analysis of the mutational landscape in HT-SELEX improves aptamer discovery. Nucleic Acids Res., 43, 5699-5707.
51. Chushak, Y., Stone, M.O. (2009) In silico selection of RNA aptamers. Nucleic Acids Res., 37, e87.
52. Shcherbinin, D.S., Gnedenko, O.V., Khmeleva, S.A., Usanov, S.A., Gilep, A.A., Yantsevich, A.V., Shkel, T.V., Yushkevich, I.V., Radko, S.P., Ivanov, A.S. et al. (2015) Computer-aided design of aptamers for cytochrome p450. J. Struct. Biol., 191, 112-119.
53. Luo, X., McKeague, M., Pitre, S., Dumontier, M., Green, J., Golshani, A., Derosa, M.C., Dehne, F. (2010) Computational approaches toward the design of pools for the in vitro selection of complex aptamers. RNA, 16, 2252-2262.
54. Tseng, C.Y., Ashrafuzzaman, M., Mane, J.Y., Kapty, J., Mercer, J.R., Tuszynski, J.A. (2011) Entropic fragment-based approach to aptamer design. Chem. Biol. Drug Des., 78, 1-13.
55. Ashrafuzzaman, M., Tseng, C.Y., Kapty, J., Mercer, J.R., Tuszynski, J.A. (2013) A computationally designed DNA aptamer template with specific binding to phosphatidylserine. Nucleic Acid Ther., 23, 418-426.
56. Robertson, M.P., Ellington, A.D. (1999) In vitro selection of an allosteric ribozyme that transduces analytes to amplicons. Nat. Biotechnol., 17, 62-66.
57. Wachsmuth, M., Findeiss, S., Weissheimer, N., Stadler, P.F., Morl, M. (2013) De novo design of a synthetic riboswitch that regulates transcription termination. Nucleic Acids Res., 41, 2541-2551.
58. Groher, F., Suess, B. (2014) Synthetic riboswitches-a tool comes of age. Biochimic. Biophys. Acta, 1839, 964-973.
59. Lai, D., Proctor, J.R., Meyer, I.M. (2013) On the importance of cotranscriptional RNA structure formation. RNA, 19, 1461-1473.
60. Thimmaiah, T., Voje, W.E. Jr and Carothers, J.M. (2015) Computational design of RNA parts, devices, and transcripts with kinetic folding algorithms implemented on multiprocessor clusters. Methods Mol. Biol., 1244, 45-61.
61. Carothers, J.M., Goler, J.A., Juminaga, D., Keasling, J.D. (2011) Model-driven engineering of RNA devices to quantitatively program gene expression. Science, 334, 1716-1719.
62. Endoh, T., Sugimoto, N. (2015) Rational design and tuning of functional RNA switch to control an allosteric intermolecular interaction. Anal. Chem., 87, 7628-7635.
63. Geertz, M., Shore, D., Maerkl, S.J. (2012) Massively parallel measurements of molecular interaction kinetics on a microfluidic platform. Proc. Natl. Acad. Sci. U.S.A., 109, 16540-16545.
64. Townshend, B., Kennedy, A.B., Xiang, J.S., Smolke, C.D. (2015) High-throughput cellular RNA device engineering. Nat. Methods, 12, 989-994.
65. Espah Borujeni, A., Mishler, D.M., Wang, J., Huso, W., Salis, H.M. (2016) Automated physics-based design of synthetic riboswitches from diverse RNA aptamers. Nucleic Acids Res., 44, 1-13.
66. Gu, H., Furukawa, K., Breaker, R.R. (2012) Engineered allosteric ribozymes that sense the bacterial second messenger cyclic diguanosyl 5-monophosphate. Anal. Chem., 84, 4935-4941.
67. Wittmann, A., Suess, B. (2011) Selection of tetracycline inducible self-cleaving ribozymes as synthetic devices for gene regulation in yeast. Mol. Biosyst., 7, 2419-2427.
68. Wittmann, A., Suess, B. (2012) Engineered riboswitches: expanding researchers' toolbox with synthetic RNA regulators. FEBS Lett., 586, 2076-2083.
69. Lynch, S.A., Desai, S.K., Sajja, H.K., Gallivan, J.P. (2007) A high-throughput screen for synthetic riboswitches reveals mechanistic insights into their function. Chem. Biol., 14, 173-184.
70. Muranaka, N., Sharma, V., Nomura, Y., Yokobayashi, Y. (2009) An efficient platform for genetic selection and screening of gene switches in Escherichia coli. Nucleic Acids Res., 37, e39.
71. Topp, S., Gallivan, J.P. (2008) Riboswitches in unexpected places-a synthetic riboswitch in a protein coding region. RNA, 14, 2498-2503.
72. Topp, S., Gallivan, J.P. (2008) Random walks to synthetic riboswitches-a high-throughput selection based on cell motility. Chem Bio Chem, 9, 210-213.
73. Wieland, M., Auslander, D., Fussenegger, M. (2012) Engineering of ribozyme-based riboswitches for mammalian cells. Methods, 56, 351-357.
74. Lynch, S.A., Gallivan, J.P. (2009) A flow cytometry-based screen for synthetic riboswitches. Nucleic Acids Res., 37, 184-192.
75. Hsu, H.T., Lin, Y.H., Chang, K.Y. (2014) Synergetic regulation of translational reading-frame switch by ligand-responsive RNAs in mammalian cells. Nucleic Acids Res., 42, 14070-14082.
76. Qi, L., Lucks, J.B., Liu, C.C., Mutalik, V.K., Arkin, A.P. (2012) Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals. Nucleic Acids Res., 40, 5775-5786.
77. Beisel, C.L., Chen, Y.Y., Culler, S.J., Hoff, K.G., Smolke, C.D. (2011) Design of small molecule-responsive microRNAs based on structural requirements for Drosha processing. Nucleic Acids Res., 39, 2981-2994.
78. Bloom, R.J., Winkler, S.M., Smolke, C.D. (2014) A quantitative framework for the forward design of synthetic miRNA circuits. Nat. Methods, 11, 1147-1153.
79. Fritz, J.J., White, D.A., Lewin, A.S., Hauswirth, W.W. (2002) Designing and characterizing hammerhead ribozymes for use in AAV vector-mediated retinal gene therapies. Methods Enzymol., 346, 358-377.
80. Regulski, E.E., Breaker, R.R. (2008) In-line probing analysis of riboswitches. Methods Mol. Biol., 419, 53-67.
81. Edwards, A.L., Garst, A.D., Batey, R.T. (2009) Determining structures of RNA aptamers and riboswitches by X-ray crystallography. Methods Mol. Biol., 535, 135-163.
82. Merino, E.J., Wilkinson, K.A., Coughlan, J.L., Weeks, K.M. (2005) RNA structure analysis at single nucleotide resolution by selective 2-hydroxyl acylation and primer extension (SHAPE). J. Am. Chem. Soc., 127, 4223-4231.
83. Souliere, M.F., Altman, R.B., Schwarz, V., Haller, A., Blanchard, S.C., Micura, R. (2013) Tuning a riboswitch response through structural extension of a pseudoknot. Proc. Natl. Acad. Sci. U.S.A., 110, E3256-E3264.
84. Heppell, B., Mulhbacher, J., Penedo, J.C., Lafontaine, D.A. (2009) Application of fluorescent measurements for characterization of riboswitch-ligand interactions. Methods Mol. Biol., 540, 25-37.
85. Blouin, S., Chinnappan, R., Lafontaine, D.A. (2011) Folding of the lysine riboswitch: importance of peripheral elements for transcriptional regulation. Nucleic Acids Res., 39, 3373-3387.
86. Steen, K.A., Siegfried, N.A., Weeks, K.M. (2011) Selective 2-hydroxyl acylation analyzed by protection from exoribonuclease (RNase-detected SHAPE) for direct analysis of covalent adducts and of nucleotide flexibility in RNA. Nat. Protoc., 6, 1683-1694.
87. Mortimer, S.A., Trapnell, C., Aviran, S., Pachter, L., Lucks, J.B. (2012) SHAPE-Seq: high-throughput RNA structure analysis. Curr. Protoc. Chem. Biol., 4, 275-297.
88. Watters, K.E., Abbott, T.R., Lucks, J.B. (2015) Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq. Nucleic Acids Res., 44, e12.
89. Chen, B., Zuo, X., Wang, Y.X., Dayie, T.K. (2012) Multiple conformations of SAM-II riboswitch detected with SAXS and NMR spectroscopy. Nucleic Acids Res., 40, 3117-3130.
90. Burke, D.H., Ozerova, N.D., Nilsen-Hamilton, M. (2002) Allosteric hammerhead ribozyme TRAPs. Biochemistry, 41, 6588-6594.
91. Burnouf, D., Ennifar, E., Guedich, S., Puffer, B., Hoffmann, G., Bec, G., Disdier, F., Baltzinger, M., Dumas, P. (2012) kinITC: a new method for obtaining joint thermodynamic and kinetic data by isothermal titration calorimetry. J. Am. Chem. Soc., 134, 559-565.
92. Karns, K., Vogan, J.M., Qin, Q., Hickey, S.F., Wilson, S.C., Hammond, M.C., Herr, A.E. (2013) Microfluidic screening of electrophoretic mobility shifts elucidates riboswitch binding function. J. Am. Chem. Soc., 135, 3136-3143.
93. Kennedy, A.B., Liang, J.C., Smolke, C.D. (2013) A versatile cis-blocking and trans-activation strategy for ribozyme characterization. Nucleic Acids Res., 41, e41.
94. Win, M.N., Liang, J.C., Smolke, C.D. (2009) Frameworks for programming biological function through RNA parts and devices. Chem. Biol., 16, 298-310.
95. Seeliger, J.C., Topp, S., Sogi, K.M., Previti, M.L., Gallivan, J.P., Bertozzi, C.R. (2012) A riboswitch-based inducible gene expression system for mycobacteria. PLoS One, 7, e29266.
96. Mishler, D.M., Gallivan, J.P. (2014) A family of synthetic riboswitches adopts a kinetic trapping mechanism. Nucleic Acids Res., 42, 6753-6761.
97. Soboleski, M.R., Oaks, J., Halford, W.P. (2005) Green fluorescent protein is a quantitative reporter of gene expression in individual eukaryotic cells. FASEB J., 19, 440-442.
98. Nienhaus, K., Nienhaus, G.U. (2014) Fluorescent proteins for live-cell imaging with super-resolution. Chem. Soc. Rev., 43, 1088-1106.
99. Weigand, J.E., Sanchez, M., Gunnesch, E.B., Zeiher, S., Schroeder, R., Suess, B. (2008) Screening for engineered neomycin riboswitches that control translation initiation. RNA, 14, 89-97.
100. Sharma, V., Nomura, Y., Yokobayashi, Y. (2008) Engineering complex riboswitch regulation by dual genetic selection. J. Am. Chem. Soc., 130, 16310-16315.
101. Noderer, W.L., Flockhart, R.J., Bhaduri, A., Diaz de Arce, A.J., Zhang, J., Khavari, P.A., Wang, C.L. (2014) Quantitative analysis of mammalian translation initiation sites by FACS-seq. Mol. Syst. Biol., 10, 748.
102. Kelly, J.R., Rubin, A.J., Davis, J.H., Ajo-Franklin, C.M., Cumbers, J., Czar, M.J., de Mora, K., Glieberman, A.L., Monie, D.D., Endy, D. (2009) Measuring the activity of BioBrick promoters using an in vivo reference standard. J. Biol. Eng., 3, 4.
103. Liang, J.C., Chang, A.L., Kennedy, A.B., Smolke, C.D. (2012) A high-throughput, quantitative cell-based screen for efficient tailoring of RNA device activity. Nucleic Acids Res., 40, e154.
104. Ma, A.T., Schmidt, C.M., Golden, J.W. (2014) Regulation of gene expression in diverse cyanobacterial species by using theophylline-responsive riboswitches. Appl. Environ. Microbiol., 80, 6704-6713.
105. Verhounig, A., Karcher, D., Bock, R. (2010) Inducible gene expression from the plastid genome by a synthetic riboswitch. Proc. Natl. Acad. Sci. U.S.A., 107, 6204-6209.
106. McKeague, M., De Girolamo, A., Valenzano, S., Pascale, M., Ruscito, A., Velu, R., Frost, N.R., Hill, K., Smith, M., McConnell, E.M. et al. (2015) Comprehensive analytical comparison of strategies used for small molecule aptamer evaluation. Anal. Chem., 87, 8608-8612.
107. Canton, B., Labno, A., Endy, D. (2008) Refinement and standardization of synthetic biological parts and devices. Nat. Biotechnol., 26, 787-793.
108. Bennett, B.D., Kimball, E.H., Gao, M., Osterhout, R., Van Dien, S.J., Rabinowitz, J.D. (2009) Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat. Chem. Biol., 5, 593-599.
109. Kellenberger, C.A., Sales-Lee, J., Pan, Y., Gassaway, M.M., Herr, A.E., Hammond, M.C. (2015) A minimalist biosensor: quantitation of cyclic Di-GMP using the conformational change of a riboswitch aptamer. RNA Biol., 1189-1197.
110. Kellenberger, C.A., Chen, C., Whiteley, A.T., Portnoy, D.A., 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.
111. Paige, J.S., Wu, K.Y., Jaffrey, S.R. (2011) RNA mimics of green fluorescent protein. Science, 333, 642-646.
112. You, M., Litke, J.L., Jaffrey, S.R. (2015) Imaging metabolite dynamics in living cells using a Spinach-based riboswitch. Proc. Natl. Acad. Sci. U.S.A., 112, E2756-E2765.
113. Song, W., Strack, R.L., Svensen, N., Jaffrey, S.R. (2014) Plug-and-play fluorophores extend the spectral properties of Spinach. J. Am. Chem. Soc., 136, 1198-1201.
114. Filonov, G.S., Moon, J.D., Svensen, N., 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.
115. Dolgosheina, E.V., Jeng, S.C., Panchapakesan, S.S., Cojocaru, R., Chen, P.S., Wilson, P.D., Hawkins, N., Wiggins, P.A., Unrau, P.J. (2014) RNA mango aptamer-fluorophore: a bright, high-affinity complex for RNA labeling and tracking. ACS Chem. Biol., 9, 2412-2420.
116. Michener, J.K., Smolke, C.D. (2012) High-throughput enzyme evolution in Saccharomyces cerevisiae using a synthetic RNA switch. Metab. Eng., 14, 306-316.
117. Meyer, A., Pellaux, R., Potot, S., Becker, K., Hohmann, H.P., Panke, S., Held, M. (2015) Optimization of a whole-cell biocatalyst by employing genetically encoded product sensors inside nanolitre reactors. Nat. Chem., 7, 673-678.
118. Yang, J., Seo, S.W., Jang, S., Shin, S.I., Lim, C.H., Roh, T.Y., Jung, G.Y. (2013) Synthetic RNA devices to expedite the evolution of metabolite-producing microbes. Nat. Commun., 4, 1413.
119. Lee, S.W., Oh, M.K. (2015) A synthetic suicide riboswitch for the high-throughput screening of metabolite production in Saccharomyces cerevisiae. Metab. Eng., 28, 143-150.
120. Zhou, L.B., Zeng, A.P. (2015) Exploring Lysine Riboswitch for Metabolic Flux Control and Improvement of l-Lysine Synthesis in Corynebacterium glutamicum. ACS Synth. Biol., 4, 729-734.
121. Galloway, K.E., Franco, E., Smolke, C.D. (2013) Dynamically reshaping signaling networks to program cell fate via genetic controllers. Science, 341, 1235005.
122. Chen, Y.Y., Jensen, M.C., 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.
123. Auslander, S., Ketzer, P., Hartig, J.S. (2010) A ligand-dependent hammerhead ribozyme switch for controlling mammalian gene expression. Mol. Biosyst., 6, 807-814.
124. Ketzer, P., Haas, S.F., Engelhardt, S., Hartig, J.S., Nettelbeck, D.M. (2012) Synthetic riboswitches for external regulation of genes transferred by replication-deficient and oncolytic adenoviruses. Nucleic Acids Res., 40, e167.
125. Bell, C.L., Yu, D., Smolke, C.D., Geall, A.J., Beard, C.W., Mason, P.W. (2015) Control of alphavirus-based gene expression using engineered riboswitches. Virology, 483, 302-311.
126. Gallardo, V.E., Behra, M. (2013) Fluorescent activated cell sorting (FACS) combined with gene expression microarrays for transcription enrichment profiling of zebrafish lateral line cells. Methods, 62, 226-231.