Synthetic circuits integrating logic and memory in living cells

Nature Biotechnology

Volumn 31, Issue 5, 2013, Pages 448-452

  Siuti, Piro ^a,b   Yazbek, John ^b   Lu, Timothy K ^a,b  

^a USA   (United States)

^b Massachusetts Institute of Technology Cambridge   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOTECHNOLOGY APPLICATIONS; BOOLEAN LOGIC FUNCTIONS; DIGITAL-TO-ANALOG CONVERTERS; ESCHERICHIA COLI CELLS; FLUORESCENT REPORTER; GENETIC CIRCUITS; LONG-TERM MAINTENANCES; STATE-DEPENDENT;

ANALOG TO DIGITAL CONVERSION; BOOLEAN FUNCTIONS; ESCHERICHIA COLI; GENE EXPRESSION; POLYMERASE CHAIN REACTION;

LOGIC CIRCUITS;

ARTICLE; CELL COMMUNICATION; CELL LINE; ESCHERICHIA COLI; GENE EXPRESSION; HIGH THROUGHPUT SEQUENCING; INFORMATION SCIENCE; INTEGRATED CIRCUIT; LOGIC; MEMORY; MEMORY CONSOLIDATION; MOLECULAR RECOGNITION; PRIORITY JOURNAL; STABLE EXPRESSION; SYNTHETIC BIOLOGY;

ARTIFICIAL CELLS; COMPUTER STORAGE DEVICES; COMPUTERS, MOLECULAR; EQUIPMENT DESIGN; EQUIPMENT FAILURE ANALYSIS; ESCHERICHIA COLI; GENETIC ENGINEERING; SIGNAL PROCESSING, COMPUTER-ASSISTED; SYNTHETIC BIOLOGY; SYSTEMS INTEGRATION;

EID: 84875230351     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.2510     Document Type: Article

References (30)

1. Hasty, J., McMillen, D. & Collins, J.J. Engineered gene circuits. Nature 420, 224-230 (2002).
2. Regot, S. et al. Distributed biological computation with multicellular engineered networks. Nature 469, 207-211 (2011).
3. Auslander, S., Auslander, D., Muller, M., Wieland, M. & Fussenegger, M. Programmable single-cell mammalian biocomputers. Nature 487, 123-127 (2012).
4. Tamsir, A., Tabor, J.J. & Voigt, C.A. Robust multicellular computing using genetically encoded NOR gates and chemical 'wires'. Nature 469, 212-215 (2011).
5. Ajo-Franklin, C.M. et al. Rational design of memory in eukaryotic cells. Genes Dev. 21, 2271-2276 (2007).
6. Gardner, T.S., Cantor, C.R. & Collins, J.J. Construction of a genetic toggle switch in Escherichia coli. Nature 403, 339-342 (2000).
7. Friedland, A.E. et al. Synthetic gene networks that count. Science 324, 1199-1202 (2009).
8. Bonnet, J., Subsoontorn, P. & Endy, D. Rewritable digital data storage in live cells via engineered control of recombination directionality. Proc. Natl. Acad. Sci. USA 109, 8884-8889 (2012).
9. Benenson, Y. Biomolecular computing systems: principles, progress and potential. Nat. Rev. Genet. 13, 455-468 (2012).
10. Ham, T.S., Lee, S.K., Keasling, J.D. & Arkin, A.P. Design and construction of a double inversion recombination switch for heritable sequential genetic memory. PLoS ONE 3, e2815 (2008).
11. Ghosh, P., Pannunzio, N.R. & Hatfull, G.F. Synapsis in phage Bxb1 integration: selection mechanism for the correct pair of recombination sites. J. Mol. Biol. 349, 331-348 (2005).
12. Groth, A.C., Olivares, E.C., Thyagarajan, B. & Calos, M.P. A phage integrase directs effcient site-specifc integration in human cells. Proc. Natl. Acad. Sci. USA 97, 5995-6000 (2000).
13. Callura, J.M., Cantor, C.R. & Collins, J.J. Genetic switchboard for synthetic biology applications. Proc. Natl. Acad. Sci. USA 109, 5850-5855 (2012).
14. Tabor, J.J. et al. A synthetic genetic edge detection program. Cell 137, 1272-1281 (2009).
15. Rinaudo, K. et al. A universal RNAi-based logic evaluator that operates in mammalian cells. Nat. Biotechnol. 25, 795-801 (2007).
16. Gibson, D.G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343-345 (2009).
17. Ringrose, L., Chabanis, S., Angrand, P.O., Woodroofe, C. & Stewart, A.F. Quantitative comparison of DNA looping in vitro and in vivo: chromatin increases effective DNA fexibility at short distances. EMBO J. 18, 6630-6641 (1999).
18. Cheng, A.A. & Lu, T.K. Synthetic biology: an emerging engineering discipline. Annu. Rev. Biomed. Eng. 14, 155-178 (2012).
19. Lu, T.K., Khalil, A.S. & Collins, J.J. Next-generation synthetic gene networks. Nat. Biotechnol. 27, 1139-1150 (2009).
20. Davis, J.H., Rubin, A.J. & Sauer, R.T. Design, construction and characterization of a set of insulated bacterial promoters. Nucleic Acids Res. 39, 1131-1141 (2011).
21. Mijakovic, I., Petranovic, D. & Jensen, P.R. Tunable promoters in systems biology. Curr. Opin. Biotechnol. 16, 329-335 (2005).
22. Groth, A.C. & Calos, M.P. Phage integrases: biology and applications. J. Mol. Biol. 335, 667-678 (2004).
23. Gordley, R.M., Gersbach, C.A. & Barbas, C.F. III. Synthesis of programmable integrases. Proc. Natl. Acad. Sci. USA 106, 5053-5058 (2009).
24. Lux, M.W., Bramlett, B.W., Ball, D.A. & Peccoud, J. Genetic design automation: engineering fantasy or scientifc renewal? Trends Biotechnol. 30, 120-126 (2012).
25. Lu, T.K. & Collins, J.J. Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy. Proc. Natl. Acad. Sci. USA 106, 4629-4634 (2009).
26. Ortiz, M.E. & Endy, D. Engineered cell-cell communication via DNA messaging. J. Biol. Eng. 6, 16 (2012).
27. You, L., Cox, R.S., Weiss, R. & Arnold, F.H. Programmed population control by cell-cell communication and regulated killing. Nature 428, 868-871 (2004).
28. Bacchus, W. et al. Synthetic two-way communication between mammalian cells. Nat. Biotechnol. 30, 991-996 (2012).
29. McMillen, D., Kopell, N., Hasty, J. & Collins, J.J. Synchronizing genetic relaxation oscillators by intercell signaling. Proc. Natl. Acad. Sci. USA 99, 679-684 (2002).
30. Sambrook, J., Fritsch, E.F. & Maniatis, T. Molecular cloning: a laboratory manual. Cold Spring Laboratory Press 2 (1989).