title: Characterizing and prototyping genetic networks with cell-free transcription-translation reactions.
abstract: A central goal of synthetic biology is to engineer cellular behavior by engineering synthetic gene networks for a variety of biotechnology and medical applications. The process of engineering gene networks often involves an iterative 'design-build-test' cycle, whereby the parts and connections that make up the network are built, characterized and varied until the desired network function is reached. Many advances have been made in the design and build portions of this cycle. However, the slow process of in vivo characterization of network function often limits the timescale of the testing step. Cell-free transcription-translation (TX-TL) systems offer a simple and fast alternative to performing these characterizations in cells. Here we provide an overview of a cell-free TX-TL system that utilizes the native Escherichia coli TX-TL machinery, thereby allowing a large repertoire of parts and networks to be characterized. As a way to demonstrate the utility of cell-free TX-TL, we illustrate the characterization of two genetic networks: an RNA transcriptional cascade and a protein regulated incoherent feed-forward loop. We also provide guidelines for designing TX-TL experiments to characterize new genetic networks. We end with a discussion of current and emerging applications of cell free systems.
authors.affiliation: School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, NY 14850, United States.
authors.forename: Melissa K
authors.initials: MK
authors.lastname: Takahashi
authors.affiliation: Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States.
authors.forename: Clarmyra A
authors.initials: CA
authors.lastname: Hayes
authors.affiliation: School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, NY 14850, United States.
authors.forename: James
authors.initials: J
authors.lastname: Chappell
authors.affiliation: Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States.
authors.forename: Zachary Z
authors.initials: ZZ
authors.lastname: Sun
authors.affiliation: Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States.
authors.forename: Richard M
authors.initials: RM
authors.lastname: Murray
authors.affiliation: School of Physics and Astronomy, University of Minnesota, 115 Union Street SE, Minneapolis, MN 55455, United States. Electronic address: noireaux@umn.edu.
authors.forename: Vincent
authors.initials: V
authors.lastname: Noireaux
authors.affiliation: School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, NY 14850, United States. Electronic address: jblucks@cornell.edu.
authors.forename: Julius B
authors.initials: JB
authors.lastname: Lucks
mesh_terms: D001709:Biotechnology / Q000379:methods; D002474:Cell-Free System; D004926:Escherichia coli; D053263:Gene Regulatory Networks; D011401:Promoter Regions, Genetic; D014176:Protein Biosynthesis; D012313:RNA / Q000737:chemistry / Q000235:genetics; D014158:Transcription, Genetic
chemical_list: D012313:RNA
keywords: Cell-free systems; Genetic networks; Rapid prototyping; Synthetic biology; Transcription–translation (TX–TL)