SURF 2018: Integrase-based genetic circuits

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2018 SURF project description

  • Mentor: Richard Murray
  • Co-mentor: Andrey Shur

Integrases are bacteriophage proteins that catalyze recombination of phage DNA with the bacterial genome at specific DNA sequences known as attachment (att) sites. Serine integrases in particular can catalyze directional recombination between cognate att sites without additional cofactors and therefore are valuable tools in synthetic biology. Previous work has utilized serine integrases to construct genetic memory, logic gates, and event detectors.

We are interested in investigating new ways to use integrases for constructing circuits and building new circuits using integrases. Examples of work in this area include developing a method to "repress" att sites using dCas9, testing the limits of att site linear spacing, and constructing a "genetic tape recorder" that can make a chronological record of events in DNA.

References

  1. Bonnet, J., Subsoontorn, P. & Endy, D. Rewritable digital data storage in live cells via engineered control of recombination directionality. Proc. Natl. Acad. Sci. 109, 8884–8889 (2012).
  2. Roquet, N., Soleimany, A. P., Ferris, A. C., Aaronson, S. & Lu, T. K. Synthetic recombinase-based state machines in living cells. Science (80-. ). 353, aad8559-aad8559 (2016).
  3. Hsiao, V., Hori, Y., Rothemund, P. W. K. & Murray, R. M. A population-based temporal logic gate for timing and recording chemical events. Mol. Syst. Biol. 557, 1–17 (2016).
  4. Smith, M. C. A., Till, R. & Smith, M. C. M. Switching the polarity of a bacteriophage integration system. Mol. Microbiol. 51, 1719–1728 (2004).
  5. Shur, A. & Murray, R. M. Repressing Integrase attachment site operation with CRISPR-Cas9 in E. coli. bioRxiv (2017). doi:10.1101/110254
  6. Shur, A. & Murray, R. M. Proof of concept continuous event logging in living cells. bioRxiv (2017). doi:10.1101/225151