Modelling the Dynamic Self Assembly of DNA Nanostructures Using a Switchable Forcefield Coarse Grained Model

DNA nanotechnology leverages DNA's canonical binding rules and geometry to use it as a building material for nanoscale devices and sensors. While fundamentally simple, the self-assembly process of DNA nanostructures is still poorly understood. Many experimental and computational efforts have sought to better understand DNA origami folding, but the small length scale of individual events and long timescale over which folding occurs have acted as barriers. We have developed a new coarse grained model which uses a switchable forcefield to reasonably capture the mechanical behavior of single stranded DNA, double stranded DNA, motifs like crossovers, and transition events like hybridization, at a coarseness level of 8 nucleotides per particle; this enables simulation of DNA at timescales sufficient to capture the self-assembly of full-sized 15 kilobase DNA origami. We simulated the self-assembly of some common DNA Origami structures and studied the kinetics of self assembly. Our current results indicate the existence of a previously undocumented folding mechanism whereby origami exhibit early compaction followed by a significant reduction in the rate constant of staple binding until the completion of folding.