License: Creative Commons Attribution 4.0 International license (CC BY 4.0)
When quoting this document, please refer to the following
DOI: 10.4230/LIPIcs.DNA.27.5
URN: urn:nbn:de:0030-drops-146722
URL: https://drops.dagstuhl.de/opus/volltexte/2021/14672/
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Levy, Nicolas ; Schabanel, Nicolas

ENSnano: A 3D Modeling Software for DNA Nanostructures

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LIPIcs-DNA-27-5.pdf (14 MB)


Abstract

Since the 1990s, increasingly complex nanostructures have been reliably obtained out of self-assembled DNA strands: from "simple" 2D shapes to 3D gears and articulated nano-objects, and even computing structures. The success of the assembly of these structures relies on a fine tuning of their structure to match the peculiar geometry of DNA helices. Various softwares have been developed to help the designer. These softwares provide essentially four kind of tools: an abstract representation of DNA helices (e.g. cadnano, scadnano, DNApen, 3DNA, Hex-tiles); a 3D view of the design (e.g., vHelix, Adenita, oxDNAviewer); fully automated design (e.g., BScOR, Daedalus, Perdix, Talos, Athena), generally dedicated to a specific kind of design, such as wireframe origami; and coarse grain or thermodynamical physics simulations (e.g., oxDNA, MrDNA, SNUPI, Nupack, ViennaRNA,...). MagicDNA combines some of these approaches to ease the design of configurable DNA origamis.
We present our first step in the direction of conciliating all these different approaches and purposes into one single reliable GUI solution: the first fully usable version (design from scratch to export) of our general purpose 3D DNA nanostructure design software ENSnano. We believe that its intuitive, swift and yet powerful graphical interface, combining 2D and 3D editable views, allows fast and precise editing of DNA nanostructures. It also handles editing of large 2D/3D structures smoothly, and imports from the most common solutions. Our software extends the concept of grids introduced in cadnano. Grids allow to abstract and articulated the different parts of a design. ENSnano also provides new design tools which speeds up considerably the design of complex large 3D structures, most notably: a 2D split view, which allows to edit intricate 3D structures which cannot easily be mapped in a 2D view, and a copy, paste & repeat functionality, which takes advantage of the grids to design swiftly large repetitive chunks of a structure. ENSnano has been validated experimentally, as proven by the AFM images of a DNA origami entirely designed in ENSnano.
ENSnano is a light-weight ready-to-run independent single-file app, running seamlessly in most of the operating systems (Windows 10, MacOS 10.13+ and Linux). Precompiled versions for Windows and MacOS are ready to download on ENSnano website. As of writing this paper, our software is being actively developed to extend its capacities in various directions discussed in this article. Still, its 3D and 2D editing interface is already meeting our usability goals. Because of its stability and ease of use, we believe that ENSnano could already be integrated in anyone’s design chain, when precise editing of a larger nanostructure is needed.

BibTeX - Entry

@InProceedings{levy_et_al:LIPIcs.DNA.27.5,
  author =	{Levy, Nicolas and Schabanel, Nicolas},
  title =	{{ENSnano: A 3D Modeling Software for DNA Nanostructures}},
  booktitle =	{27th International Conference on DNA Computing and Molecular Programming (DNA 27)},
  pages =	{5:1--5:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-205-1},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{205},
  editor =	{Lakin, Matthew R. and \v{S}ulc, Petr},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/opus/volltexte/2021/14672},
  URN =		{urn:nbn:de:0030-drops-146722},
  doi =		{10.4230/LIPIcs.DNA.27.5},
  annote =	{Keywords: Software, DNA nanostructure, Molecular design, molecular self-assembly}
}

Keywords: Software, DNA nanostructure, Molecular design, molecular self-assembly
Collection: 27th International Conference on DNA Computing and Molecular Programming (DNA 27)
Issue Date: 2021
Date of publication: 08.09.2021
Supplementary Material: Software (Source Code): https://github.com/thenlevy/ensnano archived at: https://archive.softwareheritage.org/swh:1:dir:0569f133306e7972335c4600d2be5794f467c0ba


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