Supramolecular chemistry is moving into a direction in which the composition of a chemical equilibrium is no longer determined by thermodynamics but by the efficiency with which kinetic states can be populated by energy consuming processes. Herein, we show that DNA is ideally suited for programming chemically fueled dissipative self-assembly processes. Advantages of the DNA-based systems presented in this study include a perfect control over the activation site for the chemical fuel in terms of selectivity and affinity, highly selective fuel consumption that occurs exclusively in the activated complex, and a high tolerance for the presence of waste products. Finally, it is shown that chemical fuels can be used to selectively activate different functions in a system of higher complexity embedded with multiple response pathways.

We show herein that allostery offers ak ey strategy for the design of out-of-equilibrium systems by engineering allosteric DNA-based nanodevices for the transient loading and release of small organic molecules.T od emonstrate the generality of our approach, we used two model DNA-based aptamers that bind ATPand cocaine through atarget-induced conformational change.W er e-engineered these aptamers so that their affinity towards their specific target is controlled by aDNA sequence acting as an allosteric inhibitor.The use of an enzyme that specifically cleaves the inhibitor only when it is bound to the aptamer generates at ransient allosteric control that leads to the release of ATPorcocaine from the aptamers. Our approach confirms that the programmability and predictability of nucleic acids make synthetic DNA/RNAt he perfect candidate material to re-engineer synthetic receptors that can undergo chemical fuel-triggered release of small-molecule cargoes and to rationally design non-equilibrium systems.

Synthetic DNA has emerged as a powerful self‐assembled material for the engineering of nanoscale supramolecular devices and materials. Recently dissipative self‐assembly of DNA‐based supramolecular structures has emerged as a novel approach providing access to a new class of kinetically controlled DNA materials with unprecedented life‐like properties. So far, dissipative control has been achieved using DNA‐recognizing enzymes as energy dissipating units. Although highly efficient, enzymes pose limits in terms of long‐term stability and inhibition of enzyme activity by waste products. Herein, we provide the first example of kinetically controlled DNA nanostructures in which energy dissipation is achieved through a non‐enzymatic chemical reaction. More specifically, inspired by redox signalling, we employ redox cycles of disulfide‐bond formation/breakage to kinetically control the assembly and disassembly of tubular DNA nanostructures in a highly controllable and reversible fashion.

DNA nanotechnology has emerged as a powerful tool to precisely design and control molecular circuits, machines, and nanostructures. A major goal in this field is to build devices with life-like properties such as directional motion, transport, communication and adaptation. In this Review, we provide an overview of the nascent field of dissipative DNA nanotechnology, which aims at developing life-like systems by combining programmable nucleic acid reactions with energy dissipating processes. We first delineate the notions, terminology and characteristic features of dissipative DNA-based systems and then we survey DNA-based circuits, devices and materials whose functions are controlled by chemical fuels. We emphasize how energy consumption enables these systems to perform work and cyclical tasks, in contrast with DNA devices that operate without dissipative processes. The ability to take advantage of chemical fuel molecules brings dissipative DNA systems closer to active molecular devices in nature, and points to the transformative potential of dissipative DNA nanotechnology toward the synthesis of living matter.

We demonstrate a strategy that allows for the spontaneous reconfiguration of self-assembled DNA polymers exploiting RNA as chemical fuel. To do this, we have rationally designed orthogonally addressable DNA building blocks that can be transiently deactivated by RNA fuels and subtracted temporarily from participation in the self-assembly process. Through a fine modulation of the rate at which the building blocks are reactivated we can carefully control the final composition of the polymer and convert a disordered polymer in a higher order polymer, which is disfavored from a thermodynamic point of view. We measure the dynamic reconfiguration via fluorescent signals and confocal microscopy, and we derive a kinetic model that captures the experimental results. Our approach suggests a novel route toward the development of biomolecular materials in which engineered chemical reactions support the autonomous spatial reorganization of multiple components.

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Functional molecular nanodevices and nanomachines have attracted a growing interest for their potential use in life science and nanomedicine. In particular, due to their versatility and modularity DNA-based nanodevices appear extremely promising. However, a limitation of such devices is represented by the limited number of molecular stimuli and cues that can be used to control and regulate their function. Here we demonstrate the possibility to rationally control and regulate DNA-based nanodevices using biocatalytic reactions catalyzed by different enzymes. To demonstrate the versatility of our approach, we have employed three model DNA-based systems and three different enzymes (belonging to several classes, i.e., transferases and hydrolases). The possibility to use enzymes and enzymatic substrates as possible cues to operate DNA-based molecular nanodevices will expand the available toolbox of molecular stimuli to be used in the field of DNA nanotechnology and could open the door to many applications including enzyme-induced drug delivery and enzyme-triggered nanostructures assembly.

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