Rapid Reconfiguration and Tunable Control of DNA-based Mechanisms

Precise robotic motion is ever-present within our cells with proteins like ATP synthase and kinesin, functioning much like macroscopic machines using multiple components and defined motion paths. Structural DNA nanotechnology enables researchers to construct mechanisms with similar functionality exhibiting nanoscale spatial and dynamic control by employing its vast physical design space and directed self-assembly methods. Our early work contributed to a library of DNA devices with controllable motion, primarily using strand invasion to bind or displace reconfigurable components with timescales of minutes or longer. Here, we present a strategy for tunable actuation in near real time. We demonstrate an approach using a simple modification to existing devices that adds weak binding sites on complementary components. A network of short DNA handles is activated by increasing cation concentration, raising the avidity of the network to join components. Likewise, reconfiguration is quickly reversible in decreased salt conditions. Actuation kinetics are measured via single molecule FRET using buffer exchange through a simple microfluidic system. This level of temporal control over DNA devices serves as a foundation for real-time manipulation of molecular systems.