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Iterative plug-and-play methodology for constructing and modifying synthetic gene networks

Abstract

We present a methodology for the design, construction and modification of synthetic gene networks. This method emphasizes post-assembly modification of constructs based on network behavior, thus facilitating iterative design strategies and rapid tuning and repurposing of gene networks. The ease of post-construction modification afforded by this approach and the ever-increasing repository of components within the framework will help accelerate the development of functional genetic circuits for synthetic biology.

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Figure 1: Plug-and-play methodology for synthetic gene networks.
Figure 2: Construction and tuning of a bistable genetic toggle switch.
Figure 3: Transformation of the genetic toggle switch into functional three- and four-node feed-forward loops.

References

  1. 1

    Gardner, T.S., Cantor, C.R. & Collins, J.J. Nature 403, 339–342 (2000).

    CAS  Article  Google Scholar 

  2. 2

    Elowitz, M.B. & Leibler, S. Nature 403, 335–338 (2000).

    CAS  Article  Google Scholar 

  3. 3

    Culler, S.J., Hoff, K.G. & Smolke, C.D. Science 330, 1251–1255 (2010).

    CAS  Article  Google Scholar 

  4. 4

    Danino, T., Mondragon-Palomino, O., Tsimring, L. & Hasty, J. Nature 463, 326–330 (2010).

    CAS  Article  Google Scholar 

  5. 5

    Khalil, A.S. & Collins, J.J. Nat. Rev. Genet. 11, 367–379 (2010).

    CAS  Article  Google Scholar 

  6. 6

    Khalil, A.S. et al. Cell 150, 647–658 (2012).

    CAS  Article  Google Scholar 

  7. 7

    Purnick, P.E. & Weiss, R. Nat. Rev. Mol. Cell Biol. 10, 410–422 (2009).

    CAS  Article  Google Scholar 

  8. 8

    Tamsir, A., Tabor, J.J. & Voigt, C.A. Nature 469, 212–215 (2011).

    CAS  Article  Google Scholar 

  9. 9

    Xie, Z., Wroblewska, L., Prochazka, L., Weiss, R. & Benenson, Y. Science 333, 1307–1311 (2011).

    CAS  Article  Google Scholar 

  10. 10

    Engler, C., Gruetzner, R., Kandzia, R. & Marillonnet, S. PLoS ONE 4, e5553 (2009).

    Article  Google Scholar 

  11. 11

    Gibson, D.G. et al. Nat. Methods 6, 343–345 (2009).

    CAS  Article  Google Scholar 

  12. 12

    Li, M.Z. & Elledge, S.J. Nat. Methods 4, 251–256 (2007).

    CAS  Article  Google Scholar 

  13. 13

    Mangan, S. & Alon, U. Proc. Natl. Acad. Sci. USA 100, 11980–11985 (2003).

    CAS  Article  Google Scholar 

  14. 14

    Cambray, G., Mutalik, V.K. & Arkin, A.P. Curr. Opin. Microbiol. 14, 624–630 (2011).

    CAS  Article  Google Scholar 

  15. 15

    Carothers, J.M., Goler, J.A., Juminaga, D. & Keasling, J.D. Science 334, 1716–1719 (2011).

    CAS  Article  Google Scholar 

  16. 16

    Ellis, T., Wang, X. & Collins, J.J. Nat. Biotechnol. 27, 465–471 (2009).

    CAS  Article  Google Scholar 

  17. 17

    Salis, H.M., Mirsky, E.A. & Voigt, C.A. Nat. Biotechnol. 27, 946–950 (2009).

    CAS  Article  Google Scholar 

  18. 18

    Beal, J. et al. ACS Synth. Biol. 1, 317–331 (2012).

    CAS  Article  Google Scholar 

  19. 19

    Lux, M.W., Bramlett, B.W., Ball, D.A. & Peccoud, J. Trends Biotechnol 30, 120–126 (2012).

    CAS  Article  Google Scholar 

  20. 20

    Chandran, D., Bergmann, F.T. & Sauro, H.M. J. Biol. Eng. 3, 19 (2009).

    Article  Google Scholar 

  21. 21

    Lutz, R. & Bujard, H. Nucleic Acids Res. 25, 1203–1210 (1997).

    CAS  Article  Google Scholar 

Download references

Acknowledgements

This work was supported by the Howard Hughes Medical Institute and the Office of Naval Research Multidisciplinary University Research Initiative.

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Contributions

K.D.L., R.B.A., A.S.K. and J.J.C. designed the study. K.D.L., R.B.A., R.J.K. and A.S.K. performed experiments. K.D.L., R.B.A., R.J.K., A.S.K. and J.J.C. wrote the manuscript. A.S.K. and J.J.C. supervised the project.

Corresponding authors

Correspondence to Ahmad S Khalil or James J Collins.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–4, Supplementary Tables 1–3 and Supplementary Note (PDF 475 kb)

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Litcofsky, K., Afeyan, R., Krom, R. et al. Iterative plug-and-play methodology for constructing and modifying synthetic gene networks. Nat Methods 9, 1077–1080 (2012). https://doi.org/10.1038/nmeth.2205

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