DNA Reaction–Diffusion Attractor Patterns

Abstract

Living systems can form and recover complex chemical patterns with precisely sized features in the ranges of tens or hundreds of microns.W eshow howdesigned reactiondiffusion processes can likewise produce precise patterns, termed attractor patterns,t hat reform their precise shape after being perturbed. We use oligonucleotide reaction networks, photolithography,a nd microfluidic delivery to form precisely controlled attractor patterns and study the responses of these patterns to different localized perturbations.Linear and "hill"shaped patterns formed and stabilized into shapes and at time scales consistent with reaction-diffusion models.W hen patterns were perturbed in particular locations with UV light, they reliably reformed their steady-state profiles.R ecovery also occurred after repeated perturbations.B yd esigning the farfrom-equilibrium dynamics of ac hemical system, this study shows howitispossible to design spatial patterns of molecules that are sustained and regenerated by continually evolving towards aspecific steady state configuration.

A model of spatio-temporal regulation within biomaterials using DNA reaction–diffusion waveguides

“…In this study, we use computational analyses and measure the kinetics of reactions in well-mixed solution to support the idea that super-diffusive propagation of chemical waves using DNA strand displacement amplification should be feasible over length scales of hundreds of micrometres using concentration ranges of oligonucleotides commonly used in strand displacement processes [55–57]. The use of thresholding reactions provides a way of mitigating deleterious fuel–carrier side reactions that might otherwise trigger spurious amplification.…”

Cascaded pattern formation in hydrogel medium using the polymerisation approach

“…As the polymerisation approach is driven by DNA hybridisation reactions, this method is compatible with other DNA-based systems such as enzymatic reactions 42,43 and DNA hydrogel. 41,[44][45][46][47][48] For example, if sufficient DNA can be supplied, gel-sol transition of DNA material may be possible. 55 As potential applications of this cascaded pattern formation, we can anticipate building artificial systems that autonomously construct their own structures, mimicking the pattern formation process seen in the development of living organisms.…”

“…Example patterns formed in the hydrogel medium by DNA include fixed lines, metaboric lines, rings, and detected edges. [25][26][27][28]41 Moreover, because the polymer network of the hydrogel medium can completely suppress the diffusion of larger molecules, the formed pattern can be maintained over time after the reaction reaches equilibrium. 25 Another advantage of the hydrogel is that it can be moulded into any shape, and specific DNA species can be immobilised at designated positions in the gel.…”

Multi-domain Automated Patterning of DNA-Functionalized Hydrogels

“…Molecular programs can also be localized, i.e., specific molecules can be anchored in place, and interact with diffusing molecules to produce spatiotemporal molecular programs. Spatiotemporal molecular programs can sequentially release DNA at prescribed times and locations, or generate stable chemical gradients within a microfluidic chamber (4)(5)(6). The DNA molecules that specify a spatiotemporal program can be conjugated to substrates such as hydrogels, surfaces, colloids, cell surfaces, or proteinosomes (3,(7)(8)(9)(10)(11).…”