Design and simulation of DNA, RNA and hybrid protein–nucleic acid nanostructures with oxView

Joakim Bohlin, Michael Matthies, Erik Poppleton, Jonah Procyk, Aatmik Mallya, Hao Yan, Petr Šulc

Published: 2022-06-05 DOI: 10.1038/s41596-022-00688-5

molecular dynamics

nanostructures

oxView

simulation

DNA/RNA design

AI 解读

Fabrication of angstrom-scale two-dimensional channels for mass transport

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The eINTACT method for studying nuclear changes in host plant cells targeted by bacterial effectors in native infection contexts

Rapid reaction optimization by robust and economical quantitative benchtop19F NMR spectroscopy

Profiling native pulmonary basement membrane stiffness using atomic force microscopy

Photoimmunotechnology as a powerful biological tool for molecular-based elimination of target cells and microbes, including bacteria, fungi and viruses

Measuring key human carbohydrate digestive enzyme activities using high-performance anion-exchange chromatography with pulsed amperometric detection

Neural cell isolation from adult macaques for high-throughput analyses and neurosphere cultures

Preparation, validation and use of a vasoactive tryptophan-derived hydroperoxide and relevant control compounds

Neuronal subtype-specific growth cone and soma purification from mammalian CNS via fractionation and fluorescent sorting for subcellular analyses and spatial mapping of local transcriptomes and proteomes

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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
Introduction
Materials
- Equipment
- Data format
Procedure 1: importing designs from other software into oxView
Procedure 2: free-form nanostructure design and editing
Procedure 3: interactive design and simulation
Procedure 4: external simulation and analysis of results
- Create a video of the simulation
- Analyze the simulation
Procedure 5: scripting in the browser console
Procedure 6: protein–nobreaknucleic acid hybrid structure visualization and design
Procedure 7: design of protein–nobreakDNA hybrid cage
Procedure 8: export for 3D printing or advanced rendering
Procedure 9: VR visualization
Troubleshooting
Timing
Anticipated results
- References
- References
References
ACKNOWLEDGMENTS
ACKNOWLEDGMENTS

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Design and simulation of DNA, RNA and hybrid protein–nucleic acid nanostructures with oxView

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