Feedback regulation of crystal growth by buffering monomer concentration

Abstract

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.

Biochemical control of DNA condensation

“…In addition to designed thermodynamic interactions, DNA nanotechnology also offers methods to control kinetic responses with precision, by taking advantage of strand displacement and branch migration reactions 13 . This coherent design and implementation platform has also enabled the demonstration of systems in which reactions implementing logic or dynamic circuits and self-assembling structures coexist and exchange information for sustained periods of time, with approaches that can be readily extended to couple DNA-based reactions with DNA-based condensates [14][15][16][17][18] .…”

Fueling DNA Self-Assembly via Gel-Released Regulators

“…Later on, joining events yield fewer and longer nanotubes . The nanotube density in the 10% and 20% mini-gels peaks about 30 min after the solution control peaks, while the density in the 30% mini-gel peaks at about 2 h. Taken together, mean length and density for the 30% mini-gel show that slower AI diffusion limits the rate of nanotube nucleation but supports elongation of nucleated nanotubes and sustains their growth …”

“…After UV irradiation, the solution was transferred to a microplate reader. To reduce adsorption of released fluorescent DNA onto the tube walls, the buffer was supplemented with a 20 nt PolyT strand (5× the maximal level of fluorescent DNA). , Plate reader data was background subtracted, normalized, and averaged with in-house scripts. For more details, see SI Section 3.2.…”

DNAzyme- and light-induced dissipative and gated DNA networks

“…26 Not surprisingly, the information encoded in DNA was applied to develop out-of-equilibrium transcriptional circuits acting as transcriptional oscillators 27 or transcriptional switches, and bistable regulatory networks. 28 Also, enzyme-based DNA machineries relying on polymerization/endonuclease/nickase were used to generate out-of-equilibrium circuits revealing oscillatory behaviors 29 or applied to drive the dissipative reconfiguration of a constitutional dynamic networks. 30 In addition, fuel-responsive DNA-based aptamers revealing enzyme-guided transient release and uptake of loads 31 and light-controlled ATP-fueled out-of-equilibrium DNA ligation cycles 32 were demonstrated.…”