A nanoscale reciprocating rotary mechanism with coordinated mobility control

Abstract

Biological molecular motors transform chemical energy into mechanical work by coupling cyclic catalytic reactions to large-scale structural transitions. Mechanical deformation can be surprisingly efficient in realizing such coupling, as demonstrated by the F1FO ATP synthase. Here, we describe a synthetic molecular mechanism that transforms a rotary motion of an asymmetric camshaft into reciprocating large-scale transitions in a surrounding stator orchestrated by mechanical deformation. We design the mechanism using DNA origami, characterize its structure via cryo-electron microscopy, and examine its dynamic behavior using single-particle fluorescence microscopy and molecular dynamics simulations. While the camshaft can rotate inside the stator by diffusion, the stator’s mechanics makes the camshaft pause at preferred orientations. By changing the stator’s mechanical stiffness, we accelerate or suppress the Brownian rotation, demonstrating an allosteric coupling between the camshaft and the stator. Our mechanism provides a framework for manufacturing artificial nanomachines that function because of coordinated movements of their components.

Steric Communication between Dynamic Components on DNA Nanodevices

“…These interactions enable fluctuating components to regulate the dynamic properties of distal ones, such as amplitudes of motion or thermodynamics of binding interactions. Steric interactions have recently been demonstrated to constrain rotational motions of tight-fitting components in DNA origami rotary mechanisms, 38 including facilitating processive rotation in nanoscale motors. 39 Here we establish the ability to convey steric interactions between two distal thermally fluctuating components.…”

DNA Droplets: Intelligent, Dynamic Fluid

“…To date, these advantages have been exploited for the precise fabrication of well-defined higher-order structures, including DNA origami, [31,[38][39][40] DNA tiles, [32,41,42,43] DNA 2D arrays, [44] DNA supramolecular polyhedra, [45] and DNA nanostructures with dynamic mechanical motion. [46][47][48] Beyond nanometer scales, the sequence specificity of DNA has been applied to biomolecular polymerization for the fabrication of DNA hydrogels, space-spanning 3D networked structures with elasticity and water retention. Since the pioneering work, [30] DNA hydrogels have attracted significant attention as smart biomaterial with stimuli-responsiveness, [49][50][51][52][53][54][55] biocompatibility, [56][57][58][59] controllable physical [60][61][62][63] and chemical [64,65] properties, and ease of functionalization.…”

Regulating DNA-Hybridization Using a Chemically Fueled Reaction Cycle

“…If structural DNA nanotechnology enables virtually building of any architecture on the nanometer scale, the combination with actuation mechanisms could fulfill the dream of a fully synthetic biomolecular machine. ,, Several strategies to control the actuation of DNA nanodevices have been employed. Toehold-mediated strand displacement reaction − is a popular approach that relies on user-designed DNA sequences with partial complementarity, making it easy to implement.…”