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ENSnano: A 3D Modeling Software for DNA Nanostructures

Authors Nicolas Levy, Nicolas Schabanel

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Author Details

Nicolas Levy
  • École Normale Supérieure de Lyon, LIP (UMR 5668, Équipe MC2), France
Nicolas Schabanel
  • CNRS, École Normale Supérieure de Lyon, LIP (UMR 5668, Équipe MC2) and IXXI, France

Funding

  • Schabanel, Nicolas: this work was supported in part by ENSL emergence "Algorithmes en ADN", CNRS MITI "NoPrExProgMol", "AMARP" and "Scalable DNA algorithms", and CNRS INS2I "Algadène" grants.

Acknowledgements

We want to thank Damien Woods, Pierre-Étienne Meunier, Pierre Marcus, Octave Hazard, Constantine Evans, Trent Rogers, and Dave Doty for fruitful discussions about this project. We would also like to thanks the students who followed the lecture CR11 on DNA computing at the ÉNS de Lyon in 2020 for their contribution to the rocket design in ENSnano.

Cite AsGet BibTex

Nicolas Levy and Nicolas Schabanel. ENSnano: A 3D Modeling Software for DNA Nanostructures. In 27th International Conference on DNA Computing and Molecular Programming (DNA 27). Leibniz International Proceedings in Informatics (LIPIcs), Volume 205, pp. 5:1-5:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
https://doi.org/10.4230/LIPIcs.DNA.27.5

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.

Subject Classification

ACM Subject Classification
  • Computer systems organization → Molecular computing
  • Computing methodologies → Molecular simulation
  • Applied computing → Molecular structural biology
Keywords
  • Software
  • DNA nanostructure
  • Molecular design
  • molecular self-assembly

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Supplementary Materials

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