Abstract
Concatenation and communication between chemically distinct chemical reaction networks (CRNs) is an essential principle in biology for controlling dynamics of hierarchical structures. Here, to provide a model system for such biological systems, we demonstrate autonomous lifecycles of DNA nanotubes (DNTs) by two concatenated CRNs using different thermodynamic principles: (1) ATP-powered ligation/restriction of DNA components and (2) input strand-mediated DNA strand displacement (DSD) using energy gains provided in DNA toeholds. This allows to achieve hierarchical non-equilibrium systems by concurrent ATP-powered ligation-induced DSD for activating DNT self-assembly and restriction-induced backward DSD reactions for triggering DNT degradation. We introduce indirect and direct activation of DNT self-assemblies, and orthogonal molecular recognition allows ATP-fueled self-sorting of transient multicomponent DNTs. Coupling ATP dissipation to DNA nanostructures via programmable DSD is a generic concept which should be widely applicable to organize other DNA nanostructures, and enable the design of automatons and life-like systems of higher structural complexity.
Highlights
Concatenation and communication between chemically distinct chemical reaction networks (CRNs) is an essential principle in biology for controlling dynamics of hierarchical structures
Building on our previous design[42], we first concatenate an ATP-fueled enzymatic reaction network (ERN) of an ATP-powered ligation/ restriction system of DNA components with transient DNA strand displacement (DSD) cascades using energy gains provided in DNA toeholds to regulate DNA nanostructure formation as shown for DNA nanotubes (DNTs) (Fig. 1a)
The DNT self-assembly is coupled upstream to the ATPdriven dynamic steady state (DySS) with a transient lifecycle, giving rise to a synthetic hierarchical non-equilibrium DNT selfassembly system powered by ATP
Summary
Concatenation and communication between chemically distinct chemical reaction networks (CRNs) is an essential principle in biology for controlling dynamics of hierarchical structures. To provide a model system for such biological systems, we demonstrate autonomous lifecycles of DNA nanotubes (DNTs) by two concatenated CRNs using different thermodynamic principles: (1) ATP-powered ligation/restriction of DNA components and (2) input strand-mediated DNA strand displacement (DSD) using energy gains provided in DNA toeholds This allows to achieve hierarchical non-equilibrium systems by concurrent ATPpowered ligation-induced DSD for activating DNT self-assembly and restriction-induced backward DSD reactions for triggering DNT degradation. By programming orthogonal molecular recognition into parallel systems, we further achieve ATP-fueled and transiently selfsorting DNTs. We envision that our strategies to control ATPfueled, non-equilibrium DNA nanostructure self-assembly will inspire to develop life-like materials with reconfigurable responses as well as hierarchical control mechanism on a structural and network level
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