Structural DNA nanotechnology takes advantage of the strong specificity of base-pairing interactions to self-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-stranded DNA (ssDNA), double-stranded DNA (dsDNA), and interconnected bundles of dsDNA helices. Such structures can be readily tuned to exhibit specific equilibrium conformations and conformational distributions, and also actuated to exhibit large-scale conformational transitions. Here, we use coarse-grained molecular dynamics simulations to provide some of the first insights into the conformational dynamics of a mechanically-compliant nanostructure, namely, the set of DNA origami hinges recently designed and studied experimentally. We demonstrate 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 various properties of the hinges that are challenging to obtain experimentally, such as the local stability of their hybridized portions, conformations of their single- and double-stranded components, their global or principal motions, and differences in their bending mechanisms with respect to design parameters. We also introduce a novel approach for rapidly predicting the equilibrium angles of the hinges based on individual force-deformation characteristics of their components. Lastly, we present a simple statistical-mechanical model for describing salt-triggered actuation of such hinges from an “open” to “closed” states that is being used to guide ongoing experimental efforts towards designing DNA hinge-based actuators.

Coarse-grained and statistical mechanics modeling of dynamic, mechanically compliant DNA hinges

254th National Meeting (2017)

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.