Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation.

ABSTRACT: 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/RN

SUBMITTER: Poppleton E 

PROVIDER: S-EPMC7337935 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature