title: Sealable femtoliter chamber arrays for cell-free biology.
abstract: Cell-free systems provide a flexible platform for probing specific networks of biological reactions isolated from the complex resource sharing (e.g., global gene expression, cell division) encountered within living cells. However, such systems, used in conventional macro-scale bulk reactors, often fail to exhibit the dynamic behaviors and efficiencies characteristic of their living micro-scale counterparts. Understanding the impact of internal cell structure and scale on reaction dynamics is crucial to understanding complex gene networks. Here we report a microfabricated device that confines cell-free reactions in cellular scale volumes while allowing flexible characterization of the enclosed molecular system. This multilayered poly(dimethylsiloxane) (PDMS) device contains femtoliter-scale reaction chambers on an elastomeric membrane which can be actuated (open and closed). When actuated, the chambers confine Cell-Free Protein Synthesis (CFPS) reactions expressing a fluorescent protein, allowing for the visualization of the reaction kinetics over time using time-lapse fluorescent microscopy. Here we demonstrate how this device may be used to measure the noise structure of CFPS reactions in a manner that is directly analogous to those used to characterize cellular systems, thereby enabling the use of noise biology techniques used in cellular systems to characterize CFPS gene circuits and their interactions with the cell-free environment.
authors: Bredesen Center, University of Tennessee, Knoxville; Center for Nanophase Materials Sciences, Oak Ridge National Laboratory.
authors: Sarah Elizabeth
authors: SE
authors: Norred
authors: Bredesen Center, University of Tennessee, Knoxville; Center for Nanophase Materials Sciences, Oak Ridge National Laboratory.
authors: Patrick M
authors: PM
authors: Caveney
authors: Bredesen Center, University of Tennessee, Knoxville; Center for Nanophase Materials Sciences, Oak Ridge National Laboratory.
authors: Scott T
authors: ST
authors: Retterer
authors: Bredesen Center, University of Tennessee, Knoxville; Center for Nanophase Materials Sciences, Oak Ridge National Laboratory.
authors: Jonathan B
authors: JB
authors: Boreyko
authors: Center for Nanophase Materials Sciences, Oak Ridge National Laboratory; Department of Materials Science and Engineering, University of Tennessee, Knoxville.
authors: Jason D
authors: JD
authors: Fowlkes
authors: Center for Nanophase Materials Sciences, Oak Ridge National Laboratory.
authors: Charles Patrick
authors: CP
authors: Collier
authors: Bredesen Center, University of Tennessee, Knoxville; Center for Nanophase Materials Sciences, Oak Ridge National Laboratory; Department of Materials Science and Engineering, University of Tennessee, Knoxville; simpsonML1@ornl.gov.
authors: Michael L
authors: ML
authors: Simpson
mesh_terms: D002474:Cell-Free System / Q000737:chemistry* / Q000378:metabolism*; D015870:Gene Expression; D053263:Gene Regulatory Networks; D008856:Microscopy, Fluorescence / Q000295:instrumentation / Q000379:methods; D055616:Microtechnology / Q000295:instrumentation / Q000379:methods; D040081:Protein Array Analysis / Q000295:instrumentation* / Q000379:methods*; D014176:Protein Biosynthesis