Dynamic DNA Origami Device for Measuring Compressive Depletion Forces.

The ability to self-assemble nanodevices with programmed structural dynamics that can sense and respond to the local environment could enable transformative applications in fields including molecular robotics, nanomanufacturing, and nanomedicine. The responsive function of biomolecules is often driven by alterations in conformational distributions mediated by highly sensitive interactions with the local environment. Here, we mimic this approach by engineering inherent nanoscale structural dynamics (nanodynamics) into a DNA device that exhibits a distribution of conformations including two stable states separated by a transition state where the energy barrier height is on the scale of the thermal energy, kBT = 4.1 pN·nm, enabling spontaneous transitions between states. We further establish design principles to regulate the equilibrium and kinetic behavior by substituting a few DNA strand components. We use single-molecule Förster resonance energy transfer measurements to show these nanodynamic properties are sensitive to sub-piconewton depletion forces in the presence of molecular crowding agents, and the device can measure depletion forces with a resolution of ∼100 fN. We anticipate that this approach of engineering nanodynamic DNA devices will enable molecular-scale systems that sense and respond to their local environment with extremely high sensitivity.

Automated Quantification of the Impact of Defects on the Mechanical Behavior of Deoxyribonucleic acid Origami Nanoplates.

Deoxyribonucleic acid (DNA) origami is a method for the bottom-up self-assembly of complex nanostructures for applications, such as biosensing, drug delivery, nanopore technologies, and nanomechanical devices. Effective design of such nanostructures requires a good understanding of their mechanical behavior. While a number of studies have focused on the mechanical properties of DNA origami structures, considering defects arising from molecular self-assembly is largely unexplored. In this paper, we present an automated computational framework to analyze the impact of such defects on the structural integrity of a model DNA origami nanoplate. The proposed computational approach relies on a noniterative conforming to interface-structured adaptive mesh refinement (CISAMR) algorithm, which enables the automated transformation of a binary image of the nanoplate into a high fidelity finite element model. We implement this technique to quantify the impact of defects on the mechanical behavior of the nanoplate by performing multiple simulations taking into account varying numbers and spatial arrangements of missing DNA strands. The analyses are carried out for two types of loading: uniform tensile displacement applied on all the DNA strands and asymmetric tensile displacement applied to strands at diagonal corners of the nanoplate.