Business Unit Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria.
Visualization Laboratory, Faculty of Informatics, Masaryk University, 60200 Brno, Czech Republic.
Molecules. 2021 Dec 23;27(1):63. doi: 10.3390/molecules27010063.
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.
DNA 和 RNA 纳米技术领域的关注度稳步上升，并且通过各种成功的结果证明了其价值，包括生物传感机器人和药物输送笼。如今，纳米技术设计流程通常依赖于基于计算机的设计 (CAD) 方法，在湿实验室组装之前设计和模拟所需的结构。为了辅助这些任务，存在各种软件工具，并且经常结合使用。但是，由于缺乏完全描述许多设计范例的通用文件格式，它们的互操作性受到阻碍。因此，在本文中，我们提出了专门为仿生纳米技术领域设计的统一纳米技术格式 (UNF)。UNF 允许在单个文件中存储设计和模拟数据，包括自由形式和基于晶格的 DNA 结构。通过定义逻辑和通用的格式，我们希望它将成为核酸纳米技术社区广泛接受和使用的文件格式，为研究人员和软件开发人员的未来工作提供便利。我们提供了一组从现有文件格式转换的转换器，以简化过渡。最后，我们展示了几个使用 UNF 存储的示例结构的用例，展示了 UNF 可以处理的各种类型的数据。
