Predicting the pathways of DNA origami folding with a new mesoscopic model

DNA origami exploits the specific base pairing of DNA to fabricate intricate and dynamic nanostructures. In this method, single-stranded oligonucleotides (staples) are designed to collectively hybridize with a single long strand (scaffold), folding it into a target shape. Despite its centrality to DNA origami, the folding process remains poorly understood. Previously, we introduced a mesoscopic model that captures the entire folding process, from freely floating strands to the eventual product. The model coarse grains DNA to 8 base pairs per bead, integrates motion with Brownian dynamics, and uses switchable force fields to enact changes in DNA mechanical properties upon hybridization and dehybridization. Here, we present a significantly more efficient implementation of the model that enables longer timescales, larger origamis, and more realistic concentrations. Furthermore, it supports new conditions such as multiple staple copies, sequence-dependent binding, and temperature annealing. Using these capabilities, we simulated several large and complex DNA origami, observing the pathways through which each design tends to misfold. Moreover, we analyzed assembly kinetics, product crystallinity, and staple hybridization times to uncover relationships between origami design, product quality, and yield. These findings demonstrate the model's ability to reveal key features of DNA origami self-assembly and predict folding quality for specific designs.