Force-Induced Unravelling of DNA Origami

Abstract

The mechanical properties of DNA nanostructures are of widespread interest as applications that exploit their stability under constant or intermittent external forces become increasingly common. We explore the force response of DNA origami in comprehensive detail by combining AFM single molecule force spectroscopy experiments with simulations using oxDNA, a coarse-grained model of DNA at the nucleotide level, to study the unravelling of an iconic origami system: the Rothemund tile. We contrast the force-induced melting of the tile with simulations of an origami 10-helix bundle. Finally, we simulate a recently proposed origami biosensor, whose function takes advantage of origami behavior under tension. We observe characteristic stick-slip unfolding dynamics in our force-extension curves for both the Rothemund tile and the helix bundle and reasonable agreement with experimentally observed rupture forces for these systems. Our results highlight the effect of design on force response: we observe regular, modular unfolding for the Rothemund tile that contrasts with strain-softening of the 10-helix bundle which leads to catastropic failure under monotonically increasing force. Further, unravelling occurs straightforwardly from the scaffold ends inward for the Rothemund tile, while the helix bundle unfolds more nonlinearly. The detailed visualization of the yielding events provided by simulation allows preferred pathways through the complex unfolding free-energy landscape to be mapped, as a key factor in determining relative barrier heights is the extensional release per base pair broken. We shed light on two important questions: how stable DNA nanostructures are under external forces and what design principles can be applied to enhance stability.

Design, optimization, and analysis of large DNA and RNA nanostructures through interactive visualization, editing, and molecular simulation

“…At which point, the external forces and backbone force limitations were released and a production simulation run was performed using the same force field for 10 9 steps with a stepsize of 15.15 fs (0.005 oxDNA time units). This corresponds to a total run time in the microsecond range; however, previous work with the oxDNA model 37,50 suggests, in part, due to the increased diffusion coefficient, this direct conversion is an underestimate of the corresponding experimental time. However, as is the problem with all coarse-grained models, it is impossible to establish a direct correspondence between the simulation and experimental time because different processes in a coarse-grained simulation can scale to the experiment with different ratios.…”

“…To remedy this, several coarsegrained models have been developed [28][29][30][31][32][33][34][35][36] , each of which with a unique focus on a specific part of the DNA nanostructural design and characterization pipeline. In particular, the oxDNA/oxRNA models have grown in popularity in recent years and have been used for studying DNA/RNA nanostructures and devices 23,32,[37][38][39] as well as RNA/DNA biophysics 30,40,41 . The models represent each nucleotide as a single rigid body, where the interactions between nucleotides are empirically parameterized to reproduce basic structural, mechanical and thermodynamic properties of DNA and RNA FIG.…”

TacoxDNA: A user‐friendly web server for simulations of complex DNA structures, from single strands to origami

“…DNA origami are all‐DNA mesoscopic objects that possess well‐defined structures and can be assembled with high fidelity and good yield, finding applications in materials science, DNA nanotechnology, biomedicine, and more . Mesoscale simulations can be used to investigate their assembly kinetics and mechanics, as well as to aid the design of origami with tailored properties . More detailed ( e.g .…”

“…The tools revolve around, but are not limited to, the oxDNA model. This model, which some of us helped develop, offers a good balance between a realistic description of nucleotides and their effective interactions and is amenable to extensive MD simulations of filaments with thousands of base pairs …”

Twist-bend coupling and the statistical mechanics of DNA: perturbation theory and beyond

“…oxDNA is a coarse-grained model describing DNA as two intertwined strings of rigid nucleotides [29]. It has been used for the study of a variety of DNA properties, ranging from single molecules to large-scale complexes [15,16,29,[31][32][33]. To date, two versions of oxDNA exist: one with symmetric grooves (oxDNA1) [29] and one with asymmetric grooves (oxDNA2) [32].…”