Adenita: interactive 3D modelling and visualization of DNA nanostructures

Nucleic Acids Research
Elisa De LlanoIvan Barisic

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 mode...Continue Reading

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Citations

Jan 6, 2021·Soft Matter·Jonah ProcykPetr Šulc
Dec 23, 2020·Nature Protocols·Conor LanphereStefan Howorka
May 1, 2021·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Martin GlaserDavid M Smith
May 20, 2021·Nucleic Acids Research·Erik PoppletonPetr Šulc
Sep 12, 2021·Nucleic Acids Research·Hyungmin JunMark Bathe
Nov 9, 2021·Nucleic Acids Research·Erik PoppletonPetr Šulc

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Methods Mentioned

BETA
biosensing
biosensor

Software Mentioned

TIAMAT
Adenita
Primer3
Adenita SAMSON Edition Linux
Daedalus
Cadnano
Maya
ntthal
vHelix
Adenita SAMSON Edition Win

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