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Research Article

Rewritable digital data storage in live cells via engineered control of recombination directionality

Jerome Bonnet, Pakpoom Subsoontorn, and Drew Endy
  1. Department of Bioengineering, Room 269B, Y2E2 Building, 473 Via Ortega, Stanford University, Stanford, CA 94305

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PNAS first published May 21, 2012; https://doi.org/10.1073/pnas.1202344109
Jerome Bonnet
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Pakpoom Subsoontorn
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Drew Endy
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  • For correspondence: endy@stanford.edu
  1. Edited by David Baker, University of Washington, Seattle, WA, and approved April 6, 2012 (received for review February 8, 2012)

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Abstract

The use of synthetic biological systems in research, healthcare, and manufacturing often requires autonomous history-dependent behavior and therefore some form of engineered biological memory. For example, the study or reprogramming of aging, cancer, or development would benefit from genetically encoded counters capable of recording up to several hundred cell division or differentiation events. Although genetic material itself provides a natural data storage medium, tools that allow researchers to reliably and reversibly write information to DNA in vivo are lacking. Here, we demonstrate a rewriteable recombinase addressable data (RAD) module that reliably stores digital information within a chromosome. RAD modules use serine integrase and excisionase functions adapted from bacteriophage to invert and restore specific DNA sequences. Our core RAD memory element is capable of passive information storage in the absence of heterologous gene expression for over 100 cell divisions and can be switched repeatedly without performance degradation, as is required to support combinatorial data storage. We also demonstrate how programmed stochasticity in RAD system performance arising from bidirectional recombination can be achieved and tuned by varying the synthesis and degradation rates of recombinase proteins. The serine recombinase functions used here do not require cell-specific cofactors and should be useful in extending computing and control methods to the study and engineering of many biological systems.

  • DNA inversion
  • synthetic biology
  • genetic engineering
  • standard biological parts

Footnotes

  • ↵1To whom correspondence should be addressed. E-mail: endy{at}stanford.edu.
  • Author contributions: J.B., P.S., and D.E. designed research; J.B. and P.S. performed research; J.B., P.S., and D.E. analyzed data; and J.B., P.S., and D.E. wrote the paper.

  • The authors declare no conflict of interest.

  • This article is a PNAS Direct Submission.

  • This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1202344109/-/DCSupplemental.

Freely available online through the PNAS open access option.

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Rewritable biological bits
Jerome Bonnet, Pakpoom Subsoontorn, Drew Endy
Proceedings of the National Academy of Sciences May 2012, DOI: 10.1073/pnas.1202344109

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Rewritable biological bits
Jerome Bonnet, Pakpoom Subsoontorn, Drew Endy
Proceedings of the National Academy of Sciences May 2012, DOI: 10.1073/pnas.1202344109
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