Adenita: interactive 3D modelling and visualization of DNA nanostructures

Abstract

DNA nanotechnology is a rapidly advancing field, which increasingly attracts interest in many different disciplines, such as medicine, biotechnology, physics and biocomputing. The increasing complexity of novel applications requires significant computational support for the design, modelling and analysis of DNA nanostructures. However, current in silico design tools have not been developed in view of these new applications and their requirements. Here, we present Adenita, a novel software tool for the modelling of DNA nanostructures in a user-friendly environment. A data model supporting different DNA nanostructure concepts (multilayer DNA origami, wireframe DNA origami, DNA tiles etc.) has been developed allowing the creation of new and the import of existing DNA nanostructures. In addition, the nanostructures can be modified and analysed on-the-fly using an intuitive toolset. The possibility to combine and re-use existing nanostructures as building blocks for the creation of new superstructures, the integration of alternative molecules (e.g. proteins, aptamers) during the design process, and the export option for oxDNA simulations are outstanding features of Adenita, which spearheads a new generation of DNA nanostructure modelling software. We showcase Adenita by re-using a large nanorod to create a new nanostructure through user interactions that employ different editors to modify the original nanorod.

DNA origami

“…ATHENA 51 integrates features of other existing 2G software, specifically that of DAEDALUS, PERDIX, TALOS and METIS. Adenita 52 is an open source platform that combines almost all of the 1G and 2G design software capabilities. It can design lattice-based wireframes, multilayered structures, free-form tiles and single-stranded tiles.…”

Coarse-grained nucleic acid–protein model for hybrid nanotechnology

“…12 At the same time, computational tools for the study and design of DNA and RNA nanostructures have become increasingly relevant as size and complexity of nanostructures grow. Design tools such as Adenita 13 MagicDNA, 14 CaDNAno, 15 and Tiamat 16 are essential for the structural design of DNA origamis. New coarsegrained models have been introduced to study DNA nanostructures, as the sizes (thousands or more) as well as rare events (formation or breaking of large sections of base pairs) involved in the study of these systems make atomistic-resolution modeling impractical.…”

The Art of Designing DNA Nanostructures with CAD Software

“…This, of course, would require close coordination between development teams, and it might also lead to the side-effect increased server load and according wait times, since integrated submission for analysis within the program would almost certainly lead to increased use. ADENITA is one very recent approach to merge most features into one software, which is a plugin for the free to use molecular design platform SAMSON [ 103 ]. ADENITA enables the integration of all widely used preexisting file formats, the use of non-DNA molecules (like proteins and aptamers), and it is compatible with oxDNA for detailed structural evaluation.…”