Rapid Computational Analysis Of Dna Origami Assemblies At Near-Atomic Resolution

Structural DNA nanotechnology plays an ever-increasing role in advanced biomolecular applications. Here, we present a computational method to analyze structured DNA assemblies rapidlyat near-atomic resolution. Both high computational efficiency andmolecular-level accuracy are achieved by developing a multiscale analysis framework. The sequence-dependent relative geometry and mechanical properties of DNA motifs are characterized by the all-atommolecular dynamics simulation and incorporated into the structural finite element model successfully without significant loss of atomic information. The proposed method can predict the three-dimensional shape, equilibrium dynamic properties, and mechanical rigidities of monomeric to hierarchically assembled DNA structures at near-atomic resolution without adjusting any model parameters.The calculation takes less than only 15 min for most origami-scale DNA nanostructures consisting of 7000-8000 base-pairs.Hence, it is expected to be highly utilized in an iterative design-analysis-revision process for structured DNA assemblies.