Stable DNA-based reaction–diffusion patterns

Abstract

We demonstrate reaction–diffusion systems that generate stable patterns of DNA oligonucleotide concentrations within agarose gels, including linear and “hill” (i.e. increasing then decreasing) shapes in one and two dimensions. The reaction networks that produce these patterns are driven by enzyme-free DNA strand-displacement reactions, in which reactant DNA complexes continuously release and recapture target strands of DNA in the gel; a balance of these reactions produces stable patterns. The reactant complexes are maintained at high concentrations by liquid reservoirs along the gel boundary. We monitor our patterns using time-lapse fluorescence microscopy and show that the shape of our patterns can be easily tuned by manipulating the boundary reservoirs. Finally, we show that two overlapping, stable gradients can be generated by designing two sets of non-interacting release and recapture reactions with DNA strand-displacement systems. This paper represents a step toward the generation of scalable, complex reaction–diffusion patterns for programming the spatiotemporal behavior of synthetic materials.