Molecular simulation has become an integral part of the DNA/RNA nanotechnology research pipeline. In particular, understanding the dynamics of structures and single-molecule events has improved the precision of nanoscaffolds and diagnostic tools. Here we present oxView, a design tool for visualization, design, editing and analysis of simulations of DNA, RNA and nucleic acid–protein nanostructures. oxView provides an accessible software platform for designing novel structures, tweaking existing designs, preparing them for simulation in the oxDNA/RNA molecular simulation engine and creating visualizations of simulation results. In several examples, we present procedures for using the tool, including its advanced features that couple the design capabilities with a coarse-grained simulation engine and scripting interface that can programmatically edit structures and facilitate design of complex structures from multiple substructures. These procedures provide a practical basis from which researchers, including experimentalists with limited computational experience, can integrate simulation and 3D visualization into their existing research programs.
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The input files for examples in this protocols are available in the examples directory (github.com/sulcgroup/oxdna-viewer/tree/master/examples) and in Supplementary Data.
All source code presented in this protocol are freely available under a GNU Public License at github.com/sulcgroup/oxdna-viewer. The Python analysis scripts used for analysis are available under GNU Public License at github.com/sulcgroup/oxdna_analysis_tools. The oxDNA simulation code and documentation are available from dna.physics.ox.ac.uk. The DNA/RNA–protein version of the model is in a separate branch available at https://github.com/sulcgroup/anm-oxdna. A bleeding-edge version of oxDNA that will replace the main branch at some point in the future can be found at github.com/lorenzo-rovigatti/oxDNA.
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We acknowledge support from NSF grant 1931487 and ONR grant N000142012094. This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 765703 (to J.B.). We thank users of the tool for their helpful feedback and bug reports, and members of Yan and Šulc labs at ASU and Doye, Louis and Turberfield labs in Oxford for testing the tool.
The authors declare no competing interests.
Peer review information
Nature Protocols thanks David Doty, Manish K. Gupta and Christopher Maffeo for their contribution to the peer review of this work.
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Key references using this protocol
Poppleton, E. et al. Nucleic Acids Res. 48, e72 (2020): https://doi.org/10.1093/nar/gkaa417
Yao, G. et al. Nat. Chem. 12, 1067–1075 (2020): https://doi.org/10.1038/s41557-020-0539-8
Procyk, J. et al. Soft Matter 17, 3586–3593 (2021): https://doi.org/10.1039/D0SM01639J
OxView and oxDNA file format description, scripting examples, ANM-oxDNA simulation setup, trajectory analysis and Listings S1-S17.
Importing and simulating nanostructures in oxView
Building hybrid DNA-protein system in oxView
Source codes of files for respective protocols, along with examples of expected outcomes
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Cite this article
Bohlin, J., Matthies, M., Poppleton, E. et al. Design and simulation of DNA, RNA and hybrid protein–nucleic acid nanostructures with oxView. Nat Protoc 17, 1762–1788 (2022). https://doi.org/10.1038/s41596-022-00688-5
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