Mechanical Energy Needed for Cyclizing a DNA Origami Rectangle

DNA nanotechnology has emerged as a versatile bottom-up approach to construct complex nanoscale architectures from programmable DNA self-assembly. For example, a DNA origami structure is composed of double-stranded DNA helices and crossovers that connect neighboring folded scaffold segments. To ensure the structural integrity and programmed functions, it is important to understand the mechanical aspects of the self-assembled structures. In this work, we used a DNA origami rectangle as a model system to study the structural deformability and related mechanics. We performed molecular dynamics (MD) simulations based on a coarse-grained model on oxDNA, an open-source software. We computed mechanical energy needed to cyclize the origami rectangle, and compared the results with experiment and theory. We found that the initial curvature is overcome gradually from initial to the last stage of cyclization and that the energy associated with cyclization matches with the experimental and theoretical results. This work offers detailed insights into DNA mechanics and deformability, which could be useful for studying energy driven process on self-assembled nanostructures.