Unified Nanotechnology Format: OneWay to Store Them All

David Kuták, Erik Poppleton, Haichao Miao, Petr Šulc, Ivan Barišic

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish (US)
Article number63
JournalMolecules
Volume27
Issue number1
DOIs
StatePublished - Jan 1 2022

Keywords

  • Coarse-grained simulations
  • Computer-aided design
  • DNA nanotechnology
  • DNA origami
  • DNA-protein engineering
  • File format
  • Molecular file formats
  • RNA nanotechnology

ASJC Scopus subject areas

  • Analytical Chemistry
  • Chemistry (miscellaneous)
  • Molecular Medicine
  • Pharmaceutical Science
  • Drug Discovery
  • Physical and Theoretical Chemistry
  • Organic Chemistry

Fingerprint

Dive into the research topics of 'Unified Nanotechnology Format: OneWay to Store Them All'. Together they form a unique fingerprint.

Cite this