ENSnano: A 3D Modeling Software for DNA Nanostructures

Abstract

7 Since the 1990s, increasingly complex nanostructures have been reliably obtained out of self-assembled 8 DNA strands: from “simple” 2D shapes to 3D gears and articulated nano-objects, and even computing 9 structures. The success of the assembly of these structures relies on a fine tuning of their structure 10 to match the peculiar geometry of DNA helices. Various softwares have been developed to help 11 the designer. These softwares provide essentially four kind of tools: an abstract representation of 12 DNA helices (e.g. cadnano, scadnano, DNApen, 3DNA, Hex-tiles); a 3D view of the design (e.g., 13 vHelix, Adenita, oxDNAviewer); fully automated design (e.g., BScOR, Daedalus, Perdix, Talos, 14 Athena), generally dedicated to a specific kind of design, such as wireframe origami; and coarse grain 15 or thermodynamical physics simulations (e.g., oxDNA, MrDNA, SNUPI, Nupack, ViennaRNA,...). 16 MagicDNA combines some of these approaches to ease the design of configurable DNA origamis. 17 We present our first step in the direction of conciliating all these different approaches and 18 purposes into one single reliable GUI solution: the first fully usable version (design from scratch to 19 export) of our general purpose 3D DNA nanostructure design software ENSnano . We believe that 20 its intuitive, swift and yet powerful graphical interface, combining 2D and 3D editable views, allows 21 fast and precise editing of DNA nanostructures. It also handles editing of large 2D/3D structures 22 smoothly, and imports from the most common solutions. Our software extends the concept of 23 grids introduced in cadnano . Grids allow to abstract and articulated the different parts of a design. 24 ENSnano also provides new design tools which speeds up considerably the design of complex large 3D 25 structures, most notably: a 2D split view , which allows to edit intricate 3D structures which cannot 26 easily be mapped in a 2D view, and a copy, paste & repeat functionality, which takes advantage 27 of the grids to design swiftly large repetitive chunks of a structure. ENSnano has been validated 28 experimentally, as proven by the AFM images of a DNA origami entirely designed in ENSnano . 29 ENSnano is a light-weight ready-to-run independent single-file app, running seamlessly in most of 30 the operating systems (Windows 10, MacOS 10.13+ and Linux). Precompiled versions for Windows 31 and MacOS are ready to download on ENSnano website. As of writing this paper, our software is 32 being actively developed to extend its capacities in various directions discussed in this article. Still, 33 its 3D and 2D editing interface is already meeting our usability goals. Because of its stability and 34 ease of use, we believe that ENSnano could already be integrated in anyone’s design chain, when 35 precise editing of a larger nanostructure is needed.