Adenita: interactive 3D modelling and visualization of DNA nanostructures.
Authorsde Llano, Elisa
Wilson, Amanda J
KAUST DepartmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Computer Science Program
Visual Computing Center (VCC)
Permanent link to this recordhttp://hdl.handle.net/10754/664373
MetadataShow full item record
AbstractDNA 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.
CitationDe Llano, E., Miao, H., Ahmadi, Y., Wilson, A. J., Beeby, M., Viola, I., & Barisic, I. (2020). Adenita: interactive 3D modelling and visualization of DNA nanostructures. Nucleic Acids Research. doi:10.1093/nar/gkaa593
SponsorsEuropean Union's Horizon 2020 Research and Innovation programme ; WWTF under the ILLVISATION [VRG11-010]; King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) [OSR-2019-CPF-410]. Funding for open access charge: H2020 Project MARA .
PublisherOxford University Press (OUP)
JournalNucleic acids research
Except where otherwise noted, this item's license is described as This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial Licens which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.
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