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Synthesis and materialization of a reaction–diffusion French flag pattern

Nature Chemistry volume 9, pages 990–996 (2017)Cite this article

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Abstract

During embryo development, patterns of protein concentration appear in response to morphogen gradients. These patterns provide spatial and chemical information that directs the fate of the underlying cells. Here, we emulate this process within non-living matter and demonstrate the autonomous structuration of a synthetic material. First, we use DNA-based reaction networks to synthesize a French flag, an archetypal pattern composed of three chemically distinct zones with sharp borders whose synthetic analogue has remained elusive. A bistable network within a shallow concentration gradient creates an immobile, sharp and long-lasting concentration front through a reaction–diffusion mechanism. The combination of two bistable circuits generates a French flag pattern whose ‘phenotype’ can be reprogrammed by network mutation. Second, these concentration patterns control the macroscopic organization of DNA-decorated particles, inducing a French flag pattern of colloidal aggregation. This experimental framework could be used to test reaction–diffusion models and fabricate soft materials following an autonomous developmental programme.

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Figure 1: In a shallow gradient of morphogen, a bistable DNA network produces a Polish flag; a sharp and immobile concentration profile.
Figure 2: A DNA-based network with two self-activating nodes that repress each other generates two immobile fronts that repel each other.
Figure 3: The combination of two orthogonal bistable networks produces a French flag pattern of DNA concentration that can be simply reprogrammed.
Figure 4: Materialization of Polish and French flag patterns with conditional bead aggregation.

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References

  1. Wolpert, L. & Tickle, C. Principles of Development (Oxford Univ. Press, 2011).

  2. Tompkins, N. et al. Testing Turing's theory of morphogenesis in chemical cells. Proc. Natl Acad. Sci. USA 111, 4397–4402 (2014).

    CAS  PubMed  Google Scholar 

  3. Yoshida, R., Takahashi, T., Yamaguchi, T. & Ichijo, H. Self-oscillating gel. J. Am. Chem. Soc. 118, 5134–5135 (1996).

    CAS  Google Scholar 

  4. Inostroza-Brito, K. E. et al. Co-assembly, spatiotemporal control and morphogenesis of a hybrid protein-peptide system. Nat. Chem. 7, 897–904 (2015).

    CAS  PubMed  Google Scholar 

  5. Turing, A. M. The chemical basis of morphogenesis. Phil. Trans. R. Soc. B. 237, 37–72 (1952).

    Google Scholar 

  6. Wolpert, L. Positional information and the spatial pattern of cellular differentiation. J. Theor. Biol. 25, 1–47 (1969).

    CAS  PubMed  Google Scholar 

  7. Green, J. B. & Sharpe, J. Positional information and reaction-diffusion: two big ideas in developmental biology combine. Development 142, 1203–1211 (2015).

    CAS  PubMed  Google Scholar 

  8. Rulands, S., Klünder, B. & Frey, E. Stability of localized wave fronts in bistable systems. Phys. Rev. Lett. 110, 038102 (2013).

    PubMed  Google Scholar 

  9. Quiñinao, C., Prochiantz, A. & Touboul, J. Local homeoprotein diffusion can stabilize boundaries generated by graded positional cues. Development 142, 1860–1868 (2015).

    PubMed  PubMed Central  Google Scholar 

  10. Sheth, R. et al. Hox genes regulate digit patterning by controlling the wavelength of a Turing-type mechanism. Science 338, 1476–1480 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Economou, A. D. et al. Periodic stripe formation by a Turing mechanism operating at growth zones in the mammalian palate. Nat. Genet. 44, 348–351 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Johnston, D. S. & Nüsslein-Volhard, C. The origin of pattern and polarity in the Drosophila embryo. Cell 68, 201–219 (1992).

    Google Scholar 

  13. Briscoe, J. & Small, S. Morphogen rules: design principles of gradient-mediated embryo patterning. Development 142, 3996–4009 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Castets, V., Dulos, E., Boissonade, J. & De Kepper, P. Experimental evidence of a sustained standing Turing-type nonequilibrium chemical pattern. Phys. Rev. Lett. 64, 2953 (1990).

    CAS  PubMed  Google Scholar 

  15. Isalan, M., Lemerle, C. & Serrano, L. Engineering gene networks to emulate Drosophila embryonic pattern formation. PLoS Biol. 3, 488–496 (2005).

    CAS  Google Scholar 

  16. Loose, M., Fischer-Friedrich, E., Ries, J., Kruse, K. & Schwille, P. Spatial regulators for bacterial cell division self-organize into surface waves in vitro. Science 320, 789–792 (2008).

    CAS  PubMed  Google Scholar 

  17. Padirac, A., Fujii, T., Estevez-Torres, A. & Rondelez, Y. Spatial waves in synthetic biochemical networks. J. Am. Chem. Soc. 135, 14586–14592 (2013).

    CAS  PubMed  Google Scholar 

  18. Chirieleison, S. M., Allen, P. B., Simpson, Z. B., Ellington, A. D. & Chen, X. Pattern transformation with DNA circuits. Nat. Chem. 5, 1000–1005 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Semenov, S. N., Markvoort, A. J., de Greef, T. F. A. & Huck, W. T. S. Threshold sensing through a synthetic enzymatic reaction-diffusion network. Angew. Chem. Int. Ed. 53, 8066–8069 (2014).

    CAS  Google Scholar 

  20. Tayar, A. M., Karzbrun, E., Noireaux, V. & Bar-Ziv, R. H. Propagating gene expression fronts in a one-dimensional coupled system of artificial cells. Nat. Phys. 11, 1037–1041 (2015).

    CAS  Google Scholar 

  21. Lewis, J., Slack, J. M. W. & Wolpert, L. Thresholds in development. J. Theor. Biol. 65, 579–590 (1977).

    CAS  PubMed  Google Scholar 

  22. François, P., Hakim, V. & Siggia, E. D. Deriving structure from evolution: metazoan segmentation. Mol. Syst. Biol. 3, 154 (2007).

    PubMed  PubMed Central  Google Scholar 

  23. Lopes, F. J., Vieira, F. M., Holloway, D. M., Bisch, P. M. & Spirov, A. V. Spatial bistability generates hunchback expression sharpness in the Drosophila embryo. PLoS Comput. Biol. 4, e1000184 (2008).

    PubMed  PubMed Central  Google Scholar 

  24. Scalise, D. & Schulman, R. Designing modular reaction-diffusion programs for complex pattern formation. Technology 2, 55–66 (2014).

    Google Scholar 

  25. Zadorin, A. S., Rondelez, Y., Galas, J.-C. & Estevez-Torres, A. Synthesis of programmable reaction-diffusion fronts using DNA catalyzers. Phys. Rev. Lett. 114, 068301 (2015).

    CAS  PubMed  Google Scholar 

  26. Montagne, K., Plasson, R., Sakai, Y., Fujii, T. & Rondelez, Y. Programming an in vitro DNA oscillator using a molecular networking strategy. Mol. Syst. Biol. 7, 466 (2011).

    PubMed  PubMed Central  Google Scholar 

  27. Fujii, T. & Rondelez, Y. Predator–prey molecular ecosystems. ACS Nano 7, 27–34 (2013).

    CAS  PubMed  Google Scholar 

  28. Padirac, A., Fujii, T. & Rondelez, Y. Bottom-up construction of in vitro switchable memories. Proc. Natl Acad. Sci. USA 109, E3212–E3220 (2012).

    CAS  PubMed  Google Scholar 

  29. Zambrano, A., Zadorin, A. S., Rondelez, Y., Estevez-Torres, A. & Galas, J. C. Pursuit-and-evasion reaction-diffusion waves in microreactors with tailored geometry. J. Phys. Chem. B 119, 5349–5355 (2015).

    CAS  PubMed  Google Scholar 

  30. Montagne, K., Gines, G., Fujii, T. & Rondelez, Y. Boosting functionality of synthetic DNA circuits with tailored deactivation. Nat. Commun. 7, 13474 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Manu et al. Canalization of gene expression and domain shifts in the Drosophila blastoderm by dynamical attractors. PLoS Comput. Biol. 5, e1000303 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Mirkin, C. A., Letsinger, R. L., Mucic, R. C. & Storhoff, J. J. A DNA-based method for rationally assembling nanoparticles into macroscopic materials. Nature 382, 607–609 (1996).

    CAS  PubMed  Google Scholar 

  33. Howard, J., Grill, S. W. & Bois, J. S. Turing's next steps: the mechanochemical basis of morphogenesis. Nat. Rev. Mol. Cell Biol. 12, 392–398 (2011).

    PubMed  Google Scholar 

  34. Vanag, V. K. & Epstein, I. R. Pattern formation mechanisms in reaction–diffusion systems. Int. J. Dev. Biol. 53, 673–681 (2009).

    PubMed  Google Scholar 

  35. van Roekel, H. W. H. et al. Programmable chemical reaction networks: emulating regulatory functions in living cells using a bottom-up approach. Chem. Soc. Rev. 44, 7465–7483 (2015).

    CAS  PubMed  Google Scholar 

  36. Rotermund, H. H., Jakubith, S., von Oertzen, A. & Ertl, G. Solitons in a surface reaction. Phys. Rev. Lett. 66, 3083–3086 (1991).

    CAS  PubMed  Google Scholar 

  37. Descalzi, O., Akhmediev, N. & Brand, H. R. Exploding dissipative solitons in reaction-diffusion systems. Phys. Rev. E 88, 042911 (2013).

    Google Scholar 

  38. Grzybowski, B. A., Bishop, K. J. M., Campbell, C. J., Fialkowski, M. & Smoukov, S. K. Micro- and nanotechnology via reaction-diffusion. Soft Matter 1, 114–128 (2005).

    CAS  Google Scholar 

  39. Nakouzi, E. & Steinbock, O. Self-organization in precipitation reactions far from the equilibrium. Sci. Adv. 2, e1601144 (2016).

    PubMed  PubMed Central  Google Scholar 

  40. Rothemund, P. W. K. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006).

    CAS  PubMed  Google Scholar 

  41. Franco, E. et al. Timing molecular motion and production with a synthetic transcriptional clock. Proc. Natl Acad. Sci. USA 108, E784–E793 (2011).

    CAS  PubMed  Google Scholar 

  42. Lee, J. B. et al. A mechanical metamaterial made from a DNA hydrogel. Nat. Nanotech. 7, 816–820 (2012).

    CAS  Google Scholar 

  43. Gartner, Z. J. & Liu, D. R. The generality of DNA-templated synthesis as a basis for evolving non-natural small molecules. J. Am. Chem. Soc. 123, 6961–6963 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Patwa, A., Gissot, A., Bestel, I. & Barthelemy, P. Hybrid lipid oligonucleotide conjugates: synthesis, self-assemblies and biomedical applications. Chem. Soc. Rev. 40, 5844–5854 (2011).

    CAS  PubMed  Google Scholar 

  45. Jin, R., Wu, G., Li, Z., Mirkin, C. A. & Schatz, G. C. What controls the melting properties of DNA-linked gold nanoparticle assemblies? J. Am. Chem. Soc. 125, 1643–1654 (2003).

    CAS  PubMed  Google Scholar 

  46. Wartlick, O., Kicheva, A. & González-Gaitán, M. Morphogen gradient formation. Cold Spring Harb. Persp. Biol. 1, a001255 (2009).

    Google Scholar 

  47. Gines, G. et al. Microscopic agents programmed by DNA circuits. Nat. Nanotech. 12, 351–359 (2017).

    CAS  Google Scholar 

  48. Giurumescu, C. A. & Asthagiri, A. R. in Systems Biomedicine (eds Liu, E. T. & Lauffenburger, D. A.) Ch. 14, 329–350 (Academic, 2010).

  49. Shvartsman, S. Y. & Baker, R. E. Mathematical models of morphogen gradients and their effects on gene expression. Wiley Interdiscip. Rev. Dev. Biol. 1, 715–730 (2012).

    CAS  PubMed  Google Scholar 

  50. Wakamatsu, T. et al. Structure of RecJ exonuclease defines its specificity for single-stranded DNA. J. Biol. Chem. 285, 9762–9769 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  51. Leunissen, M. E. et al. Towards self-replicating materials of DNA-functionalized colloids. Soft Matter 5, 2422 (2009).

    CAS  Google Scholar 

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Acknowledgements

We thank E. Frey for insightful discussions, A. Vlandas for help with gradient generation and B. Caller and D. Woods for comments on the text. Supported by European commission FET-Open (Ribonets, 323987), by ANR jeunes chercheurs programme (Dynano), by C'nano Ile-de-France (DNA2PROT) and by Ville de Paris Emergences programme (Morphoart).

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Authors and Affiliations

  1. Laboratoire Jean Perrin, Université Pierre et Marie Curie, 4 place Jussieu, Paris, 75005, France

    Anton S. Zadorin, Vadim Dilhas, Adrian Zambrano, Jean-Christophe Galas & André Estevez-Torres

  2. CNRS, UMR 8237, Paris, 75005, France

    Anton S. Zadorin, Vadim Dilhas, Adrian Zambrano, Jean-Christophe Galas & André Estevez-Torres

  3. LIMMS/CNRS-IIS, University of Tokyo, Komaba 4-6-2, Meguro-ku, Tokyo, Japan

    Yannick Rondelez & Guillaume Gines

  4. Ecole supérieure de physique et chimie industrielles, Laboratoire Gulliver, 10 rue Vauquelin, Paris, 75005, France

    Yannick Rondelez

  5. Ludwig-Maximilians-Universität München, Fakultät für Physik, Amalienstraße 54, Munich, 80799, Germany

    Georg Urtel

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  1. Anton S. Zadorin
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Contributions

A.S.Z., J.-C.G. and A.E.-T. performed most experiments and analysed the data. Y.R. and G.G. designed the network in Fig. 1 and J.-C.G. and A.E.-T. designed the networks in Figs 3 and  4. A.Z. and V.D. set up the bead experiments. G.U. performed critical control experiments. All the authors discussed the results. J.-C.G., A.S.Z., Y.R. and A.E.-T. designed research and J.-C.G. and A.E.-T. wrote the manuscript.

Corresponding authors

Correspondence to Jean-Christophe Galas or André Estevez-Torres.

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Zadorin, A., Rondelez, Y., Gines, G. et al. Synthesis and materialization of a reaction–diffusion French flag pattern. Nature Chem 9, 990–996 (2017). https://doi.org/10.1038/nchem.2770

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