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.

Kardar–Parisi–Zhang universality class for the critical dynamics of reaction–diffusion fronts

“…(1). For instance, recent advances in (bio)materials science are enabling material design and control at submicron and nano scales [66] through DNA circuits based on reaction-diffusion systems [67,68]. Working at such small scales, it is important to assess the potential quantitative and qualitative influence of external and internal noise in the relevant reaction-diffusion processes and systems.…”

Programmable patterns in a DNA-based reaction–diffusion system

“…To address this need, recent work has begun to explore the feasibility of DNA-only reaction-diffusion patterns. 29,[34][35][36][37] Toehold-mediated DNA strand displacement has proved to be a convenient framework for implementing complex reaction sequences using synthetic DNA in well-mixed test tubes. 38,39 Using the principles of strand displacement, researchers have created sophisticated reaction networks that perform computation like neural networks, 40,41 diagnostic classifiers, 42 dynamic 3D nanostructures 43,44 and even approximate the dynamics of formal, mathematically specified chemical reaction networks (CRNs).…”

DNA Reaction–Diffusion Attractor Patterns

“…Previously, Zenk et al. demonstrated the formation of stable 1‐dimensional DNA gradients in an agarose hydrogel medium by supplying reactants from liquid reservoirs at the edges of the gel [27] . Here, we construct attractor patterns using synthetic DNA strand displacement networks (Figure 1 a).…”

“…[12] Previously,Z enk et al demonstrated the formation of stable 1-dimensional DNAg radients in an agarose hydrogel medium by supplying reactants from liquid reservoirs at the edges of the gel. [27] Here,weconstruct attractor patterns using synthetic DNAs trand displacement networks ( Figure 1a). We show how such patterns form as designed and can recover their original shapes after perturbations.T oprecisely perturb patterns,w eu se UV light-triggered strand displacement reactions that degrade the patterned species (Figure 1b,c).…”