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DNA polymerization gels are a new class of soft programmable materials capable of reversible 100-fold volumetric size changes induced by DNA-specific strand displacement reactions. By incorporating DNA circuits and spatial patterns, these gels could orchestrate complex, self-regulating processes of relevance to biosensing, robotics, and medicine. However, the ultrasoft nature of the gels and slow response times can limit applicability. We developed GO-DNA composite polymerization gels (CPGs) by blending DNA gels with graphene oxide (GO). Photopatterned ultra-thin GO-DNA CPG films, as thin as 8 μm, were achieved. Notably, GO-DNA CPGs exhibited similar rates of swelling but 60 times faster shrinking, suggesting that the introduction of inorganic nanoparticles could provide a means to tune the mechanical properties and swelling characteristics of DNA polymerization gels. 

Chemical systems have the potential to direct the next generation of dynamic materials if they can be integrated with a material while acting as the material’s own regulatory network. Chemical networks that use DNA and RNA strand displacement coupled with RNA synthesis and degradation, such as genelets, are promising chemical systems for this role. Genelets can produce a range of dynamic behaviors that respond to unique sets of environmental inputs. While a number of networks that generate specific types of outputs which vary in both time and amplitude have been developed, there are fewer examples of networks that recognize specific types of inputs in time and amplitude. Advanced chemical circuits in biology are capable of reading a given substrate concentration with relatively high accuracy to direct downstream function, demonstrating that such a chemical circuit is possible. Taking inspiration from this, we designed a genelet circuit which responds to a range of inputs by delivering a binary output based on the input concentration, and tested the network’s performance using an in silico model of circuit behavior. By modifying the concentrations of two circuit elements, we demonstrated that such a network topography could yield various target input concentration profiles to which a given circuit is sensitive. The number of unique elements in the final network topography as well as the individual circuit element concentrations are commensurate with properties of circuits that have been demonstrated experimentally. These factors suggest that such a network could be built and characterized in the laboratory.

 

Characterizing the relative onset time, strength, and duration of molecular signals is critical for understanding the operation of signal transduction and genetic regulatory networks. However, detecting multiple such molecules as they are produced and then quickly consumed is challenging. A MER can encode information about transient molecular events as stable DNA sequences and are amenable to downstream sequencing or other analysis. Here, we report the development of a de novo molecular event recorder that processes information using a strand displacement reaction network and encodes the information using the primer exchange reaction, which can be decoded and quantified by DNA sequencing. The event recorder was able to classify the order at which different molecular signals appeared in time with 88% accuracy, the concentrations with 100% accuracy, and the duration with 75% accuracy. This simultaneous and highly programmable multiparameter recording could enable the large-scale deciphering of molecular events such as within dynamic reaction environments, living cells, or tissues.

 

DNA-coated colloids can crystallize into a multitude of lattices, ranging from face-centered cubic to diamond, opening avenues to producing structures with useful photonic properties. The potential design space of DNA-coated colloids is large, but its exploration is hampered by a reliance on chemically modified DNA that is slow and expensive to commercially synthesize. Here we introduce a method to controllably tailor the sequences of DNA-coated particles by covalently appending new sequence domains onto the DNA grafted to colloidal particles. The tailored particles crystallize as readily and at the same temperature as those produced via direct chemical synthesis, making them suitable for self-assembly. Moreover, we show that particles coated with a single sequence can be converted into a variety of building blocks with differing specificities by appending different DNA sequences to them. This method will make it practical to identify optimal and complex particle sequence designs and paves the way to programming the assembly kinetics of DNA-coated colloids. 

The development of biomolecular stimuli-responsive hydrogels is important for biomimetic structures, soft robots, tissue engineering, and drug delivery. DNA polymerization gels are a new class of soft materials composed of polymer gel backbones with DNA duplex crosslinks that can be swollen by sequential strand displacement using hairpin-shaped DNA strands. The extensive swelling can be tuned using physical parameters such as salt concentration and biomolecule design. Previously, DNA polymerization gels have been used to create shape-changing gel automata with a large design space and high programmability. Here we systematically investigate how the swelling response of DNA polymerization gels can be tuned by adjusting the design and concentration of DNA crosslinks in the hydrogels or DNA hairpin triggers, and the ionic strength of the solution in which swelling takes place. We also explore the effect hydrogel size and shape have on the swelling response. Tuning these variables can alter the swelling rate and extent across a broad range and provide a quantitative connection between biochemical reactions and macroscopic material behaviour.

 

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.