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Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and
Erik Poppleton1, Joakim Bohlin2, Michael Matthies1
1School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA.
Nucleic Acids Research
|May 26, 2020
Summary
New software tools, oxView and oxDNA analysis scripts, enhance nucleic acid nanotechnology by providing fast visualization and standard structural analysis for DNA and RNA designs.
Area of Science:
- Biophysics
- Computational Biology
- Nanotechnology
Background:
- Current software for nucleic acid nanotechnology lacks efficient visualization and standardized structural analysis tools.
- The oxDNA coarse-grained modeling tool is increasingly used for DNA/RNA nanostructure design and biophysical simulations.
Purpose of the Study:
- To introduce oxView, a web-based visualizer for large nucleic acid structures and simulation trajectories.
- To develop open-source software tools for comprehensive structural characterization of simulated DNA/RNA nanostructures.
- To integrate visualization and analysis for improved design and understanding of nucleic acid nanostructures.
Main Methods:
- Development of oxView, a browser-based visualization tool capable of handling over 1 million nucleotides and simulation data.
- Creation of analysis scripts for extracting parameters like mean structure, flexibility, hydrogen bond fraying, and interduplex angles.
- Application of the software suite to design and analyze various DNA and RNA nanostructures.
Main Results:
- oxView enables efficient visualization and basic editing of complex DNA/RNA designs.
- The analysis tools provide standardized characterization of simulated nanostructures.
- Integration of oxView and analysis tools facilitates iterative design and property optimization.
Conclusions:
- The developed software addresses key limitations in nucleic acid nanotechnology research.
- oxView and associated analysis tools enhance the computational design and characterization of DNA/RNA nanostructures.
- These tools support both simulation-based research and experimental validation in the field.
