Characterizing the free-energy landscapes of DNA origamis

TL;DR

This paper demonstrates a method combining coarse-grained modeling and umbrella sampling to compute free-energy landscapes of large DNA nanostructures, revealing insights into their mechanical behavior and bistability.

Contribution

It introduces a novel application of umbrella sampling with distance-based order parameters to analyze the free-energy landscapes of complex DNA origami structures.

Findings

Homogeneous bending of DNA nanotubes follows the worm-like chain model.

Extreme bending causes nanotubes to buckle with localized kinks.

Twisted DNA origami sheets exhibit bistability with two nearly-degenerate minima.

Abstract

We show how coarse-grained modelling combined with umbrella sampling using distance-based order parameters can be applied to compute the free-energy landscapes associated with mechanical deformations of large DNA nanostructures. We illustrate this approach for the strong bending of DNA nanotubes and the potentially bistable landscape of twisted DNA origami sheets. The homogeneous bending of the DNA nanotubes is well described by the worm-like chain model; for more extreme bending the nanotubes reversibly buckle with the bending deformations localized at one or two "kinks". For a twisted one-layer DNA origami, the twist is coupled to the bending of the sheet giving rise to a free-energy landscape that has two nearly-degenerate minima that have opposite curvatures. By contrast, for a two-layer origami, the increased stiffness with respect to bending leads to a landscape with a single free-energy minimum that has a saddle-like geometry. The ability to compute such landscapes is likely to be particularly useful for DNA mechanotechnology and for understanding stress accumulation during the self-assembly of origamis into higher-order structures.