Unified Nanotechnology Format: One Way to Store Them All

Journal Article · 23 December 2021 · Molecules

DOI: https://doi.org/10.3390/molecules27010063 · OSTI ID:1845652

Kuťák, David ^[1]; Poppleton, Erik  ^[2]; Miao, Haichao ^[3]; Šulc, Petr ^[2]; Barišić, Ivan  ^[4]

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1. Austrian Inst. of Technology (AIT), Vienna (Austria); Masaryk Univ., Brno (Czech Republic). Visitlab
2. Arizona State Univ., Tempe, AZ (United States). Center for Molecular Design and Biomimetics
3. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Center for Applied Scientific Computing
4. Austrian Inst. of Technology (AIT), Vienna (Austria)

The domains of DNA and RNA nanotechnology are steadily gaining in popularity while proving their value with various successful results, including biosensing robots and drug delivery cages. Nowadays, the nanotechnology design pipeline usually relies on computer-based design (CAD) approaches to design and simulate the desired structure before the wet lab assembly. To aid with these tasks, various software tools exist and are often used in conjunction. However, their interoperability is hindered by a lack of a common file format that is fully descriptive of the many design paradigms. Therefore, in this paper, we propose a Unified Nanotechnology Format (UNF) designed specifically for the biomimetic nanotechnology field. UNF allows storage of both design and simulation data in a single file, including free-form and lattice-based DNA structures. By defining a logical and versatile format, we hope it will become a widely accepted and used file format for the nucleic acid nanotechnology community, facilitating the future work of researchers and software developers. Together with the format description and publicly available documentation, we provide a set of converters from existing file formats to simplify the transition. Finally, we present several use cases visualizing example structures stored in UNF, showcasing the various types of data UNF can handle.

• Research Organization: Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
• Sponsoring Organization: European Research Council (ERC); National Science Foundation (NSF); USDOE National Nuclear Security Administration (NNSA)
• Grant/Contract Number: AC52-07NA27344
• OSTI ID: 1845652
• Report Number(s): LLNL-JRNL-829736; 1045811
• Journal Information: Molecules, Journal Name: Molecules Journal Issue: 1 Vol. 27; ISSN 1420-3049
• Publisher: MDPICopyright Statement
• Country of Publication: United States
• Language: English