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Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator

Nature Chemistry volume 6, pages 295–302 (2014)Cite this article

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An Addendum to this article was published on 22 April 2014

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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.

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Figure 1: An in vitro transcriptional oscillator.
Figure 2: Compartmentalized synthetic transcriptional oscillators.
Figure 3: Dynamical diversity in oscillatory behaviour caused by encapsulation of sustained and damped synthetic oscillator circuits.
Figure 4: Oscillations induced by compartmentalization.
Figure 5: Variation of oscillation periods and amplitudes with droplet radius for the sustained, damped and strongly damped oscillator tunings.
Figure 6: Numerical modelling of the compartmentalized oscillator.

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  • 22 April 2014

    The authors wish to add the following to the Acknowledgements section of this Article ‘E.F. and F.C.S. gratefully acknowledge funding from the Bavaria California Technology Center (BaCaTeC).’ The online versions of the Article have been amended accordingly.

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Acknowledgements

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.

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Authors and Affiliations

  1. Physik Department and WSI/ZNN, Systems Biophysics and Bionanotechnology, Technische Universität, München, 85748, Garching, Germany

    Maximilian Weitz, Korbinian Kapsner & Friedrich C. Simmel

  2. Bioengineering, California Institute of Technology, Pasadena, 91125, California, USA

    Jongmin Kim & Erik Winfree

  3. Computation and Neural Systems, California Institute of Technology, Pasadena, 91125, California, USA

    Erik Winfree

  4. Computer Science, California Institute of Technology, Pasadena, 91125, California, USA

    Erik Winfree

  5. Mechanical Engineering, University of California at Riverside, Riverside, 92521, California, USA

    Elisa Franco

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  1. Maximilian Weitz
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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.

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Correspondence to Elisa Franco or Friedrich C. Simmel.

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Weitz, M., Kim, J., Kapsner, K. et al. Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator. Nature Chem 6, 295–302 (2014). https://doi.org/10.1038/nchem.1869

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