This work seeks to remedy two deficiencies in the current nucleic acid nanotechnology software environment: the lack of both a fast and user-friendly visualization tool and a standard for structural analyses of simulated systems. We introduce here oxView, a web browser-based visualizer that can load structures with over 1 million nucleotides, create videos from simulation trajectories, and allow users to perform basic edits to DNA and RNA designs. We additionally introduce open-source software tools for extracting common structural parameters to characterize large DNA/RNA nanostructures simulated using the coarse-grained modeling tool, oxDNA, which has grown in popularity in recent years and is frequently used to prototype new nucleic acid nanostructural designs, model biophysics of DNA/RNA processes, and rationalize experimental results. The newly introduced software tools facilitate the computational characterization of DNA/RNA designs by providing multiple analysis scripts, including mean structures and structure flexibility characterization, hydrogen bond fraying, and interduplex angles. The output of these tools can be loaded into oxView, allowing users to interact with the simulated structure in a 3D graphical environment and modify the structures to achieve the required properties. We demonstrate these newly developed tools by applying them to design and analysis of a range of DNA/RNA nanostructures.

The fields of DNA and RNA nanotechnology have progressed from pioneering, proof-of-principle experiments to fully-fledged applications in material science, biology and medicine. These applications exploit the intrinsic programmability of nucleic acids to generate nano-and even micro-scale structures with tailored properties. However, the design of the DNA/RNA sequences that self-assemble into a desired structure is not straightforward and often relies on expensive trial-and-error experimental protocols. A complementary approach is provided by computer simulations, which can model biomacromolecules at different levels of detail, ranging from atomistic to continuous, and can be leveraged to investigate the whole range of timeand length-scales relevant for applications. Here we present oxDNA, a software package that has been designed to efficiently run coarse-grained simulations of DNA and RNA and also features an analysis suite aimed at post-processing the analysis of oxDNA/oxRNA trajectories.