Coupling DNA Origami Filament Growth to an Autocatalytic Production of Fuel

Abstract

In this study, the hierarchical assembly of DNA origami filaments (DOF) initiated by an autocatalytic DNA reaction network (DRN) is investigated. The so‐formed filaments are subsequently disassembled by toehold‐mediated strand displacement mechanisms. Using fluorescence resonance energy transfer, the kinetics of DOF growth after direct addition of fuel and compared it to the polymerization process triggered by the release of fuel from the DRN is monitored. Optimization of design and experimental conditions enabled to fine‐tune the kinetics of the two processes, ensuring that the release of fuel from the DRN outpaced the consumption of fuel by the downstream polymerization reaction. This resulted in a sustained and controlled DOF growth leading to micrometer‐long filament structures. Finally, although the presence of a toehold in the fuel strand reduced the efficiency of monomer association in the polymerization process, a 10‐fold excess of the anti‐fuel strand is efficient in dissociating the filament structures, permitting a potential reset for new reactions. The study shows that the kinetics of DNA origami filaments growth can be finely manipulated by a cascade of upstream reactions, suggesting alternative approaches for the creation of programmable DNA‐based nanomaterials that can sense and respond to more complex and distant events.