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

In multi-cellular organisms, cells and tissues coordinate biochemical signal propagation across length scales spanning micrometres to metres. Designing synthetic materials with similar capacities for coordinated signal propagation could allow these systems to adaptively regulate themselves across space and over time. Here, we combine ideas from cell signalling and electronic circuitry to propose a biochemical waveguide that transmits information in the form of a concentration of a DNA species on a directed path. The waveguide could be seamlessly integrated into a soft material because there is virtually no difference between the chemical or physical properties of the waveguide and the material it is embedded within. We propose the design of DNA strand displacement reactions to construct the system and, using reaction-diffusion models, identify kinetic and diffusive parameters that enable super-diffusive transport of DNA species via autocatalysis. Finally, to support experimental waveguide implementation, we propose a sink reaction and spatially inhomogeneous DNA concentrations that could mitigate the spurious amplification of an autocatalyst within the waveguide, allowing for controlled waveguide triggering. Chemical waveguides could facilitate the design of synthetic biomaterials with distributed sensing machinery integrated throughout their structure and enable coordinated self-regulating programmes triggered by changing environmental conditions.

DNA Reaction-Diffusion Attractor Patterns.

Living systems can form and recover complex chemical patterns with precisely sized features in the ranges of tens or hundreds of microns. We show how designed reaction-diffusion processes can likewise produce precise patterns, termed attractor patterns, that reform their precise shape after being perturbed. We use oligonucleotide reaction networks, photolithography, and 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. When patterns were perturbed in particular locations with UV light, they reliably reformed their steady-state profiles. Recovery also occurred after repeated perturbations. By designing the far-from-equilibrium dynamics of a chemical system, this study shows how it is possible to design spatial patterns of molecules that are sustained and regenerated by continually evolving towards a specific steady state configuration.

Feedback regulation of crystal growth by buffering monomer concentration.

Crystallization is a ubiquitous means of self-assembly that can organize matter over length scales orders of magnitude larger than those of the monomer units. Yet crystallization is notoriously difficult to control because it is exquisitely sensitive to monomer concentration, which changes as monomers are depleted during growth. Living cells control crystallization using chemical reaction networks that offset depletion by synthesizing or activating monomers to regulate monomer concentration, stabilizing growth conditions even as depletion rates change, and thus reliably yielding desired products. Using DNA nanotubes as a model system, here we show that coupling a generic reversible bimolecular monomer buffering reaction to a crystallization process leads to reliable growth of large, uniformly sized crystals even when crystal growth rates change over time. Buffering could be applied broadly as a simple means to regulate and sustain batch crystallization and could facilitate the self-assembly of complex, hierarchical synthetic structures.

Programming the Sequential Release of DNA.

This study presents a mechanism for releasing a series of different short DNA sequences from sequestered complexes, one after another, using coupled biochemical reactions. The process uses stages of coupled DNA strand-displacement reactions that first release an output molecule and then trigger the initiation of the next release stage. We demonstrate the sequential release of 25 nM of four different sequences of DNA over a day, both with and without a centralized "clock" mechanism to regulate release timing. We then demonstrate how the presence of a target input molecule can determine which of several different release pathways are activated, analogous to branching conditional statements in computer programming. This sequential release circuit offers a means to schedule downstream chemical events, such as steps in the assembly of a nanostructure, or stages in a material's response to a stimulus.

Controlling Matter at the Molecular Scale with DNA Circuits.

In recent years, a diverse set of mechanisms have been developed that allow DNA strands with specific sequences to sense information in their environment and to control material assembly, disassembly, and reconfiguration. These sequences could serve as the inputs and outputs for DNA computing circuits, enabling DNA circuits to act as chemical information processors to program complex behavior in chemical and material systems. This review describes processes that can be sensed and controlled within such a paradigm. Specifically, there are interfaces that can release strands of DNA in response to chemical signals, wavelengths of light, pH, or electrical signals, as well as DNA strands that can direct the self-assembly and dynamic reconfiguration of DNA nanostructures, regulate particle assemblies, control encapsulation, and manipulate materials including DNA crystals, hydrogels, and vesicles. These interfaces have the potential to enable chemical circuits to exert algorithmic control over responsive materials, which may ultimately lead to the development of materials that grow, heal, and interact dynamically with their environments.

DNA Strand Buffers.

A buffer reaction actively resists changes to the concentration of a chemical species. Typically, buffering reactions have only been able to regulate the concentration of hydronium (i.e., pH) and other ions. Here, we develop a new class of buffers that regulate the concentrations of short sequences of DNA (i.e., oligonucleotides). A buffer's behavior is determined by its set point concentration, capacity to resist disturbances, and response time after a disturbance. We provide simple mathematical formulas for selecting rate constants to tune each of these properties and show how to design DNA sequences and concentrations to implement the desired rate constants. We demonstrate several oligonucleotide buffers that maintain oligonucleotide set point concentrations between 10 and 80 nM in the presence of disturbances of 50 to 500 nM, with response times of less than 10 min to 1.5 h. Multiple buffers can regulate different sequences of DNA in parallel without crosstalk. Oligonucleotide buffers could stabilize and restore reactant concentrations in DNA circuits or in self-assembly processes, allowing such systems to operate reliably for extended durations. These buffers might also be coupled to other reactions to buffer molecules other than DNA. In general, an oligonucleotide buffer can be viewed as a chemical "battery" that maintains the total chemical potential of a buffered species in a closed system.

DNA Strand-Displacement Timer Circuits.

Chemical circuits can coordinate elaborate sequences of events in cells and tissues, from the self-assembly of biological complexes to the sequence of embryonic development. However, autonomously directing the timing of events in synthetic systems using chemical signals remains challenging. Here we demonstrate that a simple synthetic DNA strand-displacement circuit can release target sequences of DNA into solution at a constant rate after a tunable delay that can range from hours to days. The rates of DNA release can be tuned to the order of 1-100 nM per day. Multiple timer circuits can release different DNA strands at different rates and times in the same solution. This circuit can thus facilitate precise coordination of chemical events in vitro without external stimulation.

Chemical reaction networks: Colour by number.

Using chemical reactions and diffusion to control pattern formation requires the careful design of reaction networks and a balance of kinetics that is difficult to achieve. Now, it has been shown that DNA-based reaction networks provide a robust method for transforming patterns.