Adenita: interactive 3D modelling and visualization of DNA nanostructures.
Type
ArticleAuthors
de Llano, Elisa
Miao, Haichao
Ahmadi, Yasaman

Wilson, Amanda J
Beeby, Morgan

Viola, Ivan

Barisic, Ivan

KAUST Department
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) DivisionComputer Science Program
Visual Computing Center (VCC)
Date
2020-07-21Online Publication Date
2020-07-21Print Publication Date
2020-09-04Submitted Date
2020-02-18Permanent link to this record
http://hdl.handle.net/10754/664373
Metadata
Show full item recordAbstract
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.Citation
De 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/gkaa593Sponsors
European Union's Horizon 2020 Research and Innovation programme [686647]; 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 [686647].Publisher
Oxford University Press (OUP)Journal
Nucleic acids researchPubMed ID
32692355ae974a485f413a2113503eed53cd6c53
10.1093/nar/gkaa593
Scopus Count
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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