Coarse-Grained and Statistical Mechanical Modeling of Dynamic, Mechanically Compliant DNA Hinges

Structural DNA nanotechnology takes advantage of base-pairing interactions to assemble DNA strands into rigid 2D and 3D nanostructures of exquisite geometries and complexity. Recently, this approach has been used to design dynamic, mechanically-compliant DNA nanostructures by exploiting differences in the mechanical properties of single- and double-stranded DNA. Here, we use coarse-grained molecular dynamics simulations to provide some of the first insights into the conformational dynamics of a mechanically-compliant nanostructure, a DNA origami hinge recently designed and studied experimentally. We show that the simulations can accurately reproduce the experimentally measured equilibrium angles between hinge arms for a range of hinge designs. The simulations also reveal important insights into the structural and mechanical properties of the hinges that are challenging to obtain experimentally. We also introduce a novel approach for rapidly predicting equilibrium hinge conformations based on the force-deformation characteristics of its components. Lastly, we present a statistical-mechanical model for describing salt-triggered actuation that is currently being used to guide ongoing experimental efforts towards designing DNA hinge-based actuators.