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Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator

Weitz, Maximilian and Kim, Jongmin and Kapsner, Korbinian and Winfree, Erik and Franco, Elisa and Simmel, Friedrich C. (2014) Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator. Nature Chemistry, 6 (4). pp. 295-302. ISSN 1755-4330. http://resolver.caltech.edu/CaltechAUTHORS:20140424-093502261

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Abstract

In vitro compartmentalization of biochemical reaction networks is a crucial step towards engineering artificial cell-scale devices and systems. At this scale the dynamics of molecular systems becomes stochastic, which introduces several engineering challenges and opportunities. Here we study a programmable transcriptional oscillator system that is compartmentalized into microemulsion droplets with volumes between 33 fl and 16 pl. Simultaneous measurement of large populations of droplets reveals major variations in the amplitude, frequency and damping of the oscillations. Variability increases for smaller droplets and depends on the operating point of the oscillator. Rather than reflecting the stochastic kinetics of the chemical reaction network itself, the variability can be attributed to the statistical variation of reactant concentrations created during their partitioning into droplets. We anticipate that robustness to partitioning variability will be a critical challenge for engineering cell-scale systems, and that highly parallel time-series acquisition from microemulsion droplets will become a key tool for characterization of stochastic circuit function


Item Type:Article
Related URLs:
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http://dx.doi.org/10.1038/NCHEM.1869DOIArticle
http://www.nature.com/nchem/journal/v6/n4/full/nchem.1869.htmlPublisherArticle
http://www.nature.com/nchem/journal/v6/n4/full/nchem.1869.html#supplementary-informationPublisherSupplementary information
http://dx.doi.org/10.1038/nchem.1923 PublisherAddendum
http://rdcu.be/cmCmPublisherFree ReadCube access
http://rdcu.be/cmCnPublisherFree ReadCube access -- addendum
ORCID:
AuthorORCID
Winfree, Erik0000-0002-5899-7523
Additional Information:© 2014 Macmillan Publishers Limited. Received 24 October 2012; Accepted 13 January 2014; Published online 16 February 2014; Corrected online 22 April 2014. The authors acknowledge financial support by the National Science Foundation grants CCF-0832824 (The Molecular Programming Project) and CMMI-1266402, by the Bourns College of Engineering at the University of California at Riverside (UC), the UC Regents Faculty Development Fellowship, the European Commission FP7 grant no. 248919 (Bacterial Computing with Engineered Populations), the German Research Foundation Cluster of Excellence Nanosystems Initiative Munich and the Elite Network of Bayern. Surfactant E2K0660 was supplied by RainDance Technologies. We acknowledge E. Friedrichs and R. Jungmann for initial experiments; U. Gerland, R. Murray and N. Karlsson for useful discussions, advice and support; and C. Martin, L. Ramìrez-Tapia, E. Stahl and H. Dietz for providing fluorescently labelled T7 RNAP. Author contributions: E.W., E.F. and F.C.S. designed the research; M.W., J.K. and E.F. performed the research; M.W., J.K., K.K. and E.F. analysed the data; E.W., E.F. and F.C.S wrote the paper.
Funders:
Funding AgencyGrant Number
NSFCCF-0832824
NSFCMMI-1266402
University of California Riverside Bourns College of Engineering UNSPECIFIED
UC Regents Faculty Development FellowshipUNSPECIFIED
European Commission FP7 grant248919
German Research Foundation Cluster of Excellence Nanosystems Initiative MunichUNSPECIFIED
Elite Network of BayernUNSPECIFIED
Bavaria California Technology Center (BaCaTe) UNSPECIFIED
Record Number:CaltechAUTHORS:20140424-093502261
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20140424-093502261
Official Citation:Weitz, M., Kim, J., Kapsner, K., Winfree, E., Franco, E., & Simmel, F. C. (2014). Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator. [Article]. Nat Chem, 6(4), 295-302. doi: 10.1038/nchem.1869
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:45185
Collection:CaltechAUTHORS
Deposited By: Jason Perez
Deposited On:24 Apr 2014 18:18
Last Modified:09 Nov 2017 00:44

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