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Principles of genetic circuit design

Abstract

Cells navigate environments, communicate and build complex patterns by initiating gene expression in response to specific signals. Engineers seek to harness this capability to program cells to perform tasks or create chemicals and materials that match the complexity seen in nature. This Review describes new tools that aid the construction of genetic circuits. Circuit dynamics can be influenced by the choice of regulators and changed with expression 'tuning knobs'. We collate the failure modes encountered when assembling circuits, quantify their impact on performance and review mitigation efforts. Finally, we discuss the constraints that arise from circuits having to operate within a living cell. Collectively, better tools, well-characterized parts and a comprehensive understanding of how to compose circuits are leading to a breakthrough in the ability to program living cells for advanced applications, from living therapeutics to the atomic manufacturing of functional materials.

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Figure 1: Potential uses of synthetic genetic circuits.
Figure 2: Logic gates built on the basis of different regulator types.
Figure 3: Methods of modifying circuit behavior.
Figure 4: Common failure modes and their impact on circuit dynamics.
Figure 5: Circuit performance within the context of a living cell.
Figure 6: Conceptual circuit for a therapeutic bacterium that colonizes a niche in the human microbiome and delivers a drug.

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Acknowledgements

C.A.V. and J.A.N.B. are supported by the US National Institute of General Medical Sciences (NIGMS grant P50 GMO98792 and R01 GM095765), Office of Naval Research (ONR) Multidisciplinary University Research Initiative (MURI grant 4500000552) and US National Science Foundation (NSF) Synthetic Biology Engineering Research Center (SynBERC EEC0540879) and by Life Technologies (A114510). J.A.N.B. is supported by an NSF Graduate Research Fellowship.

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Supplementary Note 1

Models used to generate figure 3 – the model is in SBML format and can be opened and run with SBML software. (XML 43 kb)

Supplementary Note 2

Models used to generate figures 3 and 4 – the model is in SBML format and can be opened and run with SBML software. (XML 107 kb)

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Brophy, J., Voigt, C. Principles of genetic circuit design. Nat Methods 11, 508–520 (2014). https://doi.org/10.1038/nmeth.2926

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