ENSnano: A 3D Modeling Software for DNA Nanostructures

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 chunk