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

Supplementary information

Supplementary Information

OxView and oxDNA file format description, scripting examples, ANM-oxDNA simulation setup, trajectory analysis and Listings S1-S17.

Supplementary Video 1

Importing and simulating nanostructures in oxView

Supplementary Video 2

Building hybrid DNA-protein system in oxView

Supplementary Data

Source codes of files for respective protocols, along with examples of expected outcomes

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

Efficient and strand-specific profiling of replicating chromatin with enrichment and sequencing of protein-associated nascent DNA in mammalian cells

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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References

Supplementary information

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

Supplementary information

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