Steady-State Cell-Free Gene Expression with Microfluidic Chemostats.
Cell-free
Microfluidics
Steady-state gene expression
Synthetic biology
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2021
2021
Historique:
entrez:
6
1
2021
pubmed:
7
1
2021
medline:
30
3
2021
Statut:
ppublish
Résumé
Cell-free synthetic biology offers an approach to building and testing gene circuits in a simplified environment free from the complexity of a living cell. Recent advances in microfluidic devices allowed cell-free reactions to run under nonequilibrium, steady-state conditions enabling the implementation of dynamic gene regulatory circuits in vitro. In this chapter, we present a detailed protocol to fabricate a microfluidic chemostat device which enables such an operation, detailing essential steps in photolithography, soft lithography, and hardware setup.
Identifiants
pubmed: 33405223
doi: 10.1007/978-1-0716-1032-9_9
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
189-203Références
Purnick P, Weiss R (2009) The second wave of synthetic biology: from modules to systems. Nat Rev Mol Cell Biol 10:410–422
doi: 10.1038/nrm2698
Garenne D, Noireaux V (2019) Cell-free transcription-translation: engineering biology from the nanometer to the millimetre scale. Curr Opin Biotechnol 58:19–27
doi: 10.1016/j.copbio.2018.10.007
Takahashi MK et al (2015) Characterizing and prototyping genetic networks with cell-free transcription-translation reactions. Methods 86:60–72
doi: 10.1016/j.ymeth.2015.05.020
Perez JG et al (2016) Cell-free synthetic biology: engineering beyond the cell. Cold Spring Harb Perspect Biol 8:a023853
doi: 10.1101/cshperspect.a023853
de Maddalena LL et al (2016) GreA and GreB enhance expression of Escherichia coli RNA polymerase promoters in a reconstituted transcription-translation system. ACS Synth Biol 5:929–935
doi: 10.1021/acssynbio.6b00017
Niederholtmeyer H, Xu L, Maerkl SJ (2013) Real-time mRNA measurement during an in vitro transcription and translation using binary probes. ACS Synth Biol 2:411–417
doi: 10.1021/sb300104f
Wick S et al (2019) PERSIA for direct fluorescence measurements of transcription, translation, and enzyme activity in cell-free systems. ACS Synth Biol 8:1010–1025
doi: 10.1021/acssynbio.8b00450
Kwon Y-C, Jewett MC (2015) High-throughput preparation methods of crude extract for robust cell-free protein synthesis. Sci Rep 5:8663
doi: 10.1038/srep08663
Sun ZZ et al (2013) Protocols for implementing an Escherichia coli based TX-TL cell-free expression system for synthetic biology. J Vis Exp 79:1–15
Lavickova B, Maerkl SJ (2019) A simple, robust, and low-cost method to produce the PURE cell-free system. ACS Synth Biol 8:455–462
doi: 10.1021/acssynbio.8b00427
Dubuc E et al (2019) Cell-free microcompartmentalised transcription-translation for the prototyping of synthetic communication networks. Curr Opin Biotechnol 58:72–80
doi: 10.1016/j.copbio.2018.10.006
Niederholtmeyer H et al (2015) Rapid cell-free forward engineering of novel genetic ring oscillators. elife 4:1–18
doi: 10.7554/eLife.09771
Hori Y et al (2017) Cell-free extract based optimization of biomolecular circuits with droplet microfluidics. Lab Chip 17:3037–3042
doi: 10.1039/C7LC00552K
Chang J-C et al (2018) Microfluidic device for real-time formulation of reagents and their subsequent encapsulation into double emulsions. Sci Rep 8:8143
doi: 10.1038/s41598-018-26542-x
Spirin A et al (1988) A continuous cell-free translation system capable of producing polypeptides in high yield. Science 242:1162–1164
doi: 10.1126/science.3055301
Niederholtmeyer H et al (2013) Implementation of cell-free biological networks at steady state. Proc Natl Acad Sci 110:15985–15990
doi: 10.1073/pnas.1311166110
Karzbrun E et al (2014) Programmable on-chip DNA compartments as artificial cells. Science 6198:829–832
doi: 10.1126/science.1255550
Tayar A et al (2017) Synchrony and pattern formation of coupled genetic oscillators on a chip of artificial cells. Proc Natl Acad Sci 114:11609–11614
doi: 10.1073/pnas.1710620114
Rockel S, Geertz M, Maerkl SJ (2012) MITOMI: a microfluidic platform for in vitro characterization of transcription factor-DNA interaction. Methods Mol Biol 786:97–114
doi: 10.1007/978-1-61779-292-2_6
van der Linden A J et al (2019) A multilayer microfluidic platform for the conduction of prolonged cell-free gene expression. J Vis Exp 152:e59655
Ferry MS, Razinkov IA, Hasty J (2012) Microfluidics for synthetic biology: from design to execution. Methods Enzymol 497:295–372
doi: 10.1016/B978-0-12-385075-1.00014-7
Chau K et al (2011) Dependence of the quality of adhesion between poly(dimethylsiloxane) and glass surfaces on the composition of the oxidizing plasma. Microfluid Nanofluid 10:907–917
doi: 10.1007/s10404-010-0724-y
Swank Z, Laohakunakorn N, Maerkl SJ (2019) Cell-free gene-regulatory network engineering with synthetic transcription factors. Proc Natl Acad Sci U S A 116:5892–5901
doi: 10.1073/pnas.1816591116