The free-energy landscape of a mechanically bistable DNA origami

TL;DR

This study uses coarse-grained simulations to analyze the free-energy landscape of a bistable DNA origami, revealing a discrepancy between predicted and experimental stability of the second state.

Contribution

The paper demonstrates that defect-free DNA origami may have a single free-energy minimum, challenging previous experimental inferences of bistability.

Findings

Simulations predict a single stable state for the DNA origami.

The second state is not energetically favored in the model.

Discrepancies suggest assembly defects may influence experimental observations.

Abstract

Molecular simulations using coarse-grained models allow the structure, dynamics and mechanics of DNA origamis to be comprehensively characterized. Here, we focus on the free-energy landscape of a jointed DNA origami that has been designed to exhibit two mechanically stable states and for which a bistable landscape has been inferred from ensembles of structures visualized by electron microscopy. Surprisingly, simulations using the oxDNA model predict that the defect-free origami has a single free-energy minimum. The expected second state is not stable because the hinge joints do not simply allow free angular motion but instead lead to increasing free-energetic penalties as the joint angles relevant to the second state are approached. This raises interesting questions about the cause of this difference between simulations and experiment, such as how assembly defects might affect the ensemble of structures observed experimentally.