References
- Winkler WC, Breaker RR. Regulation of bacterial gene expression by riboswitches. Annu Rev Microbiol. 2005;59:487–517.
- Lynch SA, Desai SK, Sajja HK, et al. A high-throughput screen for synthetic riboswitches reveals mechanistic insights into their function. Chem Biol. 2007;14:173–184.
- Suess B, Hanson S, Berens C, et al. Conditional gene expression by controlling translation with tetracycline-binding aptamers. Nucleic Acids Res. 2003;31:1853–1858.
- Davidson ME, Harbaugh SV, Chushak YG, et al. Development of a 2, 4-dinitrotoluene-responsive synthetic riboswitch in E. coli cells. ACS Chem Biol. 2013;8:234–241.
- Findeiß S, Etzel M, Will S, et al. Design of artificial riboswitches as biosensors. Sensors. 2017;17:1990.
- Harbaugh SV, Goodson MS, Dillon K, et al. Riboswitch-based reversible dual color sensor. ACS Synth Biol. 2017;6:766–781.
- Muranaka N, Sharma V, Nomura Y, et al. Efficient design strategy for whole-cell and cell-free biosensors based on engineered riboswitches. Anal Lett. 2009;42:108–122.
- Siegal-Gaskins D, Tuza ZA, Kim J, et al. Gene circuit performance characterization and resource usage in a cell-free “breadboard”. ACS Synth Biol. 2014;3:416–425.
- Mishler DM, Gallivan JP. A family of synthetic riboswitches adopts a kinetic trapping mechanism. Nucleic Acids Res. 2014;42:6753–6761.
- Cole SD, Beabout K, Turner KB, et al. Quantification of interlaboratory cell-free protein synthesis variability. ACS Synth Biol. 2019;8:2080–2091.
- Stögbauer T, Windhager L, Zimmer R, et al. Experiment and mathematical modeling of gene expression dynamics in a cell-free system. Integr Biol. 2012;4:494–501.
- Niederholtmeyer H, Xu L, Maerkl SJ. Real-time mRNA measurement during an in vitro transcription and translation reaction using binary probes. ACS Synth Biol. 2013;2:411–417.
- Doerr A, de Reus E, van Nies P 1, et al. Modelling cell-free RNA and protein synthesis with minimal systems. Phys Biol. 2019;16:025001.
- van Nies P, Nourian Z, Kok M, et al. Unbiased tracking of the progression of mRNA and protein synthesis in bulk and in liposome‐confined reactions. ChemBioChem. 2013;14:1963–1966.
- Pédelacq JD, Cabantous S, Tran T, et al. Engineering and characterization of a superfolder green fluorescent protein. Nat Biotech. 2006;24:79.
- Davidson MW, Campbell RE. Engineered fluorescent proteins: innovations and applications. Nat Methods. 2009;6:713–717.
- Matsuura T, Tanimura N, Hosoda K, et al. Reaction dynamics analysis of a reconstituted Escherichia coli protein translation system by computational modeling. Proc Natl Acad Sci. 2017;114:E1336–E134.
- Grate D, Wilson C. Inducible regulation of the S. cerevisiae cell cycle mediated by an RNA aptamer–ligand complex. Bioorg Med Chem. 2001;9:2565–2570.
- Lynch SA, Gallivan JP. A flow cytometry-based screen for synthetic riboswitches. Nucleic Acids Res. 2009;37:184–192.
- Marshall R, Noireaux V. Quantitative modeling of transcription and translation of an all-E. coli cell-free system. Sci Rep. 2019;9:11980.
- Gyorgy A, Del Vecchio D 2014, Limitations and trade-offs in gene expression due to competition for shared cellular resources. In 2014 53rd IEEE Annual Conference on Decision and Control, CDC 2014 - Los Angeles, USA. 5431–5436.
- Kim DM, Swartz JR. Prolonging cell‐free protein synthesis with a novel ATP regeneration system. Biotechnol Bioeng. 1999;66:180–188.
- Hansen MM, Ventosa Rosquelles M, Yelleswarapu M, et al. Protein synthesis in coupled and uncoupled cell-free prokaryotic gene expression systems. ACS Synth Biol. 2016;5:1433–1440.
- Zimmermann GR, Jenison RD, Wick CL, et al. Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA. Nat Struct Mol Biol. 1997;4:644–649.
- Salis HM. The ribosome binding site calculator. In: Voigt C, editor. Methods in enzymology. Vol. 498. Academic Press: San Diego, CA; 2011. p. 19–42.
- Espah Borujeni A, Mishler DM, Wang J, et al. Automated physics-based design of synthetic riboswitches from diverse RNA aptamers. Nucleic Acids Res. 2015;44:1–13.
- Espah Borujeni A, Channarasappa AS, Salis HM. Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites. Nucleic Acids Res. 2014;42:2646–2659.
- Swartz JR, Jewett MC, Woodrow KA. Cell-free protein synthesis with prokaryotic combined transcription-translation. Methods Mol Biol. 2004;267:169–182.
- Kwon YC, Jewett MC. High-throughput preparation methods of crude extract for robust cell-free protein synthesis. Sci Rep. 2015;5:8663.
- Frazier JM, Chushak Y, Foy B. Stochastic simulation and analysis of biomolecular reaction networks. BMC Syst Biol. 2009;3:1–21.
- Garamella J, Marshall R, Rustad M, et al. The all E. coli TX-TL Toolbox 2.0: a platform for cell-free synthetic biology. ACS Synth Biol. 2016;5:344–355.