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Permanent genetic memory with >1-byte capacity

Nature Methods volume 11, pages 12611266 (2014) | Download Citation

Abstract

Genetic memory enables the recording of information in the DNA of living cells. Memory can record a transient environmental signal or cell state that is then recalled at a later time. Permanent memory is implemented using irreversible recombinases that invert the orientation of a unit of DNA, corresponding to the [0,1] state of a bit. To expand the memory capacity, we have applied bioinformatics to identify 34 phage integrases (and their cognate attB and attP recognition sites), from which we build 11 memory switches that are perfectly orthogonal to each other and the FimE and HbiF bacterial invertases. Using these switches, a memory array is constructed in Escherichia coli that can record 1.375 bytes of information. It is demonstrated that the recombinases can be layered and used to permanently record the transient state of a transcriptional logic gate.

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Acknowledgements

C.A.V., T.K.L. and L.Y. are supported by the US Defense Advanced Research Projects Agency (DARPA CLIO N66001-12-C-4016). C.A.V. and A.A.K.N. are supported by DARPA CLIO N66001-12-C-4018. C.A.V., M.T.L., A.A.K.N. and J.F.-R. are supported by the Office of Naval Research Multidisciplinary University Research Initiative (N00014-13-1-0074; Boston University MURI award 4500000552). C.A.V. is also supported by US National Institutes of Health (GM095765), the US National Institute of General Medical Sciences (P50 GMO98792) and the US National Science Foundation Synthetic Biology Engineering Research Center (SynBERC EEC0540879). A.A.K.N. receives government support FA9550-11-C-0028 and is supported by the National Defense Science and Engineering Graduate Fellowship 32 CFR 168a from the US Department of Defense Air Force Office of Scientific Research.

Author information

Affiliations

  1. Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

    • Lei Yang
    • , Alec A K Nielsen
    • , Jesus Fernandez-Rodriguez
    • , Timothy K Lu
    •  & Christopher A Voigt
  2. Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

    • Conor J McClune
    •  & Michael T Laub
  3. Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

    • Timothy K Lu

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Contributions

C.A.V. and L.Y. conceived of the study and designed the experiments. L.Y., A.A.K.N., C.J.M. and J.F.-R. performed the experiments and analyzed the data. C.A.V., L.Y., A.A.K.N. and C.J.M. wrote the manuscript. C.A.V., T.K.L. and M.T.L. managed the project.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Christopher A Voigt.

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DOI

https://doi.org/10.1038/nmeth.3147

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