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

Abstract

<jats:title>Abstract</jats:title> <jats:p>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.</jats:p>

Clustering of death receptor for apoptosis using nanoscale patterns of peptides

“…Because of the different structural design methods for W and L, they are expected to possess differences in local rigidity and propensity for thermal fluctuation. The mean structures, which were computed from oxDNA molecular dynamics simulation 40,41 in 500 mM Na + (simulation parameter), showed that the L-type structure tended to stay flatter than the W types( Fig.1e). Root mean square fluctuation (RMSF) values of the Ws are estimated to be around 5-time higher than those of the Ls (Fig.1e), further validating its higher local structural flexibility.…”

The Art of Designing DNA Nanostructures with CAD Software

“…This model can also be used to predict the involved forces when unraveling a DNA origami by force-induced melting, and it has been experimentally verified via Atomic Force Microscope (AFM), making it an interesting example for the flexibility of this software [ 98 ]. A recently-developed web browser-based visualization tool, oxView, provides a fast and user-friendly interface to the underlying code, and it includes additional modules for characterizing aspects, such as structural [ 99 ], and a tool, TacoxDNA, is also available for converting common CAD output files (e.g., from Cadnano or Tiamat) into representations that are suitable for simulation via OxDNA [ 100 ].…”

“…(v) [ 28 ], Copyright The American Association for the Advancement of Science, 2016. (bottom left to right): (i) Holiday junction was created using oxView [ 99 ]. (v) [ 28 ], Copyright The American Association for the Advancement of Science, 2016.…”

Generating DNA Origami Nanostructures through Shape Annealing

“…The oxDNA topology and configuration files are then imported to oxDNA to evaluate structural validation. The results from oxDNA are analyzed using the RMSF scripts and visualized in oxView, which are both developed by Poppleton et al [39]. The last frame of the oxDNA simulation is then converted to PDB using TacoxDNA.…”