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Engineering genetic circuits that compute and remember

Nature Protocols volume 9, pages 1292–1300 (2014)Cite this article

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Abstract

Memory and logic are central to complex state-dependent computing, and state-dependent behaviors are a feature of natural biological systems. Recently, we created a platform for integrated logic and memory by using synthetic gene circuits, and we demonstrated the implementation of all two-input logic gates with memory in living cells. Here we provide a detailed protocol for the construction of two-input Boolean logic functions with concomitant DNA-based memory. This technology platform allows for straightforward assembly of integrated logic-and-memory circuits that implement desired behaviors within a couple of weeks. It should enable the encoding of advanced computational operations in living cells, including sequential-logic and biological-state machines, for a broad range of applications in biotechnology, basic science and biosensing.

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Figure 1: Our recombinase-based platform for building integrated logic-and-memory devices, such as the AND gate shown here, consists of converting computational functions into (promoter(s))-(terminator(s))-(output gene) designs.
Figure 2: Four states of the AND logic gate.
Figure 3: Long-term stable memory maintenance over multiple cell generations.

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Acknowledgements

We acknowledge G.F. Hatfull for the bxb1 gene and J.J. Collins for the riboregulator plasmids. We thank A.N. Billings and J. Rubens for help with the microscopy experiments and careful comments on the manuscript. This work was supported by the Defense Advanced Research Projects Agency (DARPA) and an Office of Naval Research Multidisciplinary University Research Initiative (MURI) grant. T.K.L. acknowledges support from the NIH New Innovator Award (1DP2OD008435).

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Author notes

  1. Piro Siuti and John Yazbek: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    Piro Siuti & Timothy K Lu

  2. Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    Piro Siuti, John Yazbek & Timothy K Lu

  3. Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    Piro Siuti, John Yazbek & Timothy K Lu

Authors
  1. Piro Siuti
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  2. John Yazbek
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Contributions

T.K.L. conceived of this study. All the experiments were implemented, constructed and performed by P.S. and J.Y. All authors analyzed the data, discussed the results and wrote the manuscript.

Corresponding author

Correspondence to Timothy K Lu.

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Competing interests

T.K.L. and P.S. have filed a provisional patent application (US patent application no. 14/105,994) on this work.

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Siuti, P., Yazbek, J. & Lu, T. Engineering genetic circuits that compute and remember. Nat Protoc 9, 1292–1300 (2014). https://doi.org/10.1038/nprot.2014.089

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