Rationally designed logic integration of regulatory signals in mammalian cells (original) (raw)

References

  1. Shapiro, E. & Benenson, Y. Bringing DNA computers to life. Sci. Am. 294, 44–51 (2006).
    Article CAS Google Scholar
  2. Jungmann, R., Renner, S. & Simmel, F. C. From DNA nanotechnology to synthetic biology. HFSP Journal 2, 99–109 (2008).
    Article CAS Google Scholar
  3. Shen-Orr, S. S., Milo, R., Mangan, S. & Alon, U. Network motifs in the transcriptional regulation network of Escherichia coli. Nature Genet. 31, 64–68 (2002).
    Article CAS Google Scholar
  4. Lee, T. I. et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799–804 (2002).
    Article CAS Google Scholar
  5. Weiss, R., Homsy, G. E. & Knight, T. F. in Evolution as Computation: DIMACS Workshop (eds Landweber, L. F. & Winfree, E.) 275–295 (Springer, 1999).
    Google Scholar
  6. Guet, C. C., Elowitz, M. B., Hsing, W. H. & Leibler, S. Combinatorial synthesis of genetic networks. Science 296, 1466–1470 (2002).
    Article CAS Google Scholar
  7. Basu, S., Gerchman, Y., Collins, C. H., Arnold, F. H. & Weiss, R. A synthetic multicellular system for programmed pattern formation. Nature 434, 1130–1134 (2005).
    Article CAS Google Scholar
  8. Anderson, J. C., Voigt, C. A. & Arkin, A. P. Environmental signal integration by a modular AND gate. Mol. Syst. Biol. 3, 133 (2007).
    Article Google Scholar
  9. Bronson, J. E., Mazur, W. W. & Cornish, V. W. Transcription factor logic using chemical complementation. Mol. Biosystems 4, 56–58 (2008).
    Article CAS Google Scholar
  10. Canton, B., Labno, A. & Endy, D. Refinement and standardization of synthetic biological parts and devices. Nature Biotechnol. 26, 787–793 (2008).
    Article CAS Google Scholar
  11. Sayut, D. J., Niu, Y. & Sun, L. H. Construction and enhancement of a minimal genetic AND logic gate. Appl. Environ. Microbiol. 75, 637–642 (2009).
    Article CAS Google Scholar
  12. Ellis, T., Wang, X. & Collins, J. J. Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nature Biotechnol. 27, 465–471 (2009).
    Article CAS Google Scholar
  13. Kramer, B. P., Fischer, C. & Fussenegger, M. BioLogic gates enable logical transcription control in mammalian cells. Biotechnol. Bioeng. 87, 478–484 (2004).
    Article CAS Google Scholar
  14. Mayo, A. E., Setty, Y., Shavit, S., Zaslaver, A. & Alon, U. Plasticity of the _cis_-regulatory input function of a gene. Plos Biol. 4, 555–561 (2006).
    Article CAS Google Scholar
  15. Cox, R. S., Surette, M. G. & Elowitz, M. B. Programming gene expression with combinatorial promoters. Mol. Syst. Biol. 3, 145 (2007).
    Google Scholar
  16. Rinaudo, K. et al. A universal RNAi-based logic evaluator that operates in mammalian cells. Nature Biotechnol. 25, 795–801 (2007).
    Article CAS Google Scholar
  17. Fukuda, Y., Kawasaki, H. & Taira, K. Construction of microRNA-containing vectors for expression in mammalian cells. Meth. Mol. Biol. 338, 167–173 (2006).
    CAS Google Scholar
  18. Buchler, N. E., Gerland, U. & Hwa, T. On schemes of combinatorial transcription logic. Proc. Natl Acad. Sci. USA 100, 5136–5141 (2003).
    Article CAS Google Scholar
  19. Schwake, G. et al. Predictive modeling of non-viral gene transfer. Biotech. Bioeng. 105, 805–813 (2010).
    CAS Google Scholar
  20. Marguet, P., Balagadde, F., Tan, C. M. & You, L. C. Biology by design: reduction and synthesis of cellular components and behaviour. J. Royal Soc. Interface 4, 607–623 (2007).
    Article CAS Google Scholar
  21. An, W. L. & Chin, J. W. Synthesis of orthogonal transcription–translation networks. Proc. Natl Acad. Sci. USA 106, 8477–8482 (2009).
    Article CAS Google Scholar
  22. Deans, T. L., Cantor, C. R. & Collins, J. J. A tunable genetic switch based on RNAi and repressor proteins for regulating gene expression in mammalian cells. Cell 130, 363–372 (2007).
    Article CAS Google Scholar
  23. Gardner, T. S., Cantor, C. R. & Collins, J. J. Construction of a genetic toggle switch in Escherichia coli. Nature 403, 339–342 (2000).
    Article CAS Google Scholar
  24. Lu, T. K., Khalil, A. S. & Collins, J. J. Next-generation synthetic gene networks. Nature Biotechnol. 27, 1139–1150 (2009).
    Article CAS Google Scholar
  25. Xie, Z., Liu, S. J., Bleris, L. & Benenson, Y. Logic integration of mRNA signals by an RNAi-based molecular computer. Nucleic Acids Res. 38, 2692–2701 (2010).
    Article CAS Google Scholar
  26. Valadi, H. et al. Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells. Nature Cell Biol. 9, 654–659 (2007).
    Article CAS Google Scholar
  27. Gullotti, E. & Yeo, Y. Extracellularly activated nanocarriers: a new paradigm of tumor targeted drug delivery. Mol. Pharmaceutics 6, 1041–1051 (2009).
    Article CAS Google Scholar
  28. Broz, P. et al. Toward intelligent nanosize bioreactors: a pH-switchable, channel-equipped, functional polymer nanocontainer. Nano Lett. 6, 2349–2353 (2006).
    Article CAS Google Scholar
  29. Lu, Q. Seamless cloning and gene fusion. Trends Biotechnol. 23, 199–207 (2005).
    Article CAS Google Scholar
  30. Stegmeier, F., Hu, G., Rickles, R. J., Hannon, G. J. & Elledge, S. J. A lentiviral microRNA-based system for single-copy polymerase II-regulated RNA interference in mammalian cells. Proc. Natl Acad. Sci. USA 102, 13212–13217 (2005).
    Article CAS Google Scholar

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