Unified Nanotechnology Format: One Way to Store Them All
Abstract
:1. Introduction
2. State of the Art
3. Format Description
3.1. Overall Goal
- Due to the popularity of the multilayer DNA origami technique, the format should be able to explicitly store designs of such lattice-constrained nanostructures. However, at the same time, it must also support the storing of the free-form DNA nanostructures, allowing for the description of arbitrarily shaped designs and simulation outcomes.
- The format should be viable for DNA-protein and RNA-protein nanotechnology engineering by storing coarse-grained representations of protein structures.
- For conversion from fully atomistic models to coarse-grained ones and vice versa, the format should have some way of referencing the original source data from crystallography, NMR, cryoEM, and all-atom simulation experiments.
- Related to the previous point, the format should support references to other types of molecules to allow the creation of more complex molecular scenes, possibly including all-atom structures together with coarse-grained ones.
- To facilitate the implementation of the format in various tools, it must be well defined, with a clear and properly explained terminology. Furthermore, the documentation of its structure should be easily available.
- The UNF file itself should be human-readable to allow for quick changes using a simple text editor in case of need. At the same time, it must be easy to process from the perspective of software developers.
- Ideally, the format should reuse well-defined concepts and terms from the existing DNA nanotechnology file formats and software applications to make the transition from other ways of data storage easier.
- Finally, due to the nature of the goal summarized at the beginning of this chapter, it is expected that the format will gradually evolve to meet the needs of its potential end-users. Therefore, it should be open for extension, making it possible to shape it in the future without a need for a complete rewrite.
3.2. UNF File Structure
3.3. Data Hierarchy
3.3.1. General File Information
3.3.2. Design Data
3.3.3. Structural Data
3.3.4. Other Data
4. Converters from Existing Formats
4.1. Cadnano ⇄ UNF Converter
4.2. PDB → UNF Converter
4.3. oxDNA/oxView ⇄ UNF
5. Use Cases
5.1. Multi-Component Designs
5.2. Multilayer DNA Origami Structures and All-Atom Molecules
5.3. Coarse-Grained DNA-Protein Hybrids
5.4. Coarse-Grained RNA Structures
6. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Sample Availability
Appendix A
- The official UNF repository is accessible via the following link: https://github.com/barisicgroup/unf (accessed on 15 November 2021).
- The repository of the oxView application is available using this link: https://github.com/sulcgroup/oxdna-viewer (accessed on 15 November 2021).
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Kuťák, D.; Poppleton, E.; Miao, H.; Šulc, P.; Barišić, I. Unified Nanotechnology Format: One Way to Store Them All. Molecules 2022, 27, 63. https://doi.org/10.3390/molecules27010063
Kuťák D, Poppleton E, Miao H, Šulc P, Barišić I. Unified Nanotechnology Format: One Way to Store Them All. Molecules. 2022; 27(1):63. https://doi.org/10.3390/molecules27010063
Chicago/Turabian StyleKuťák, David, Erik Poppleton, Haichao Miao, Petr Šulc, and Ivan Barišić. 2022. "Unified Nanotechnology Format: One Way to Store Them All" Molecules 27, no. 1: 63. https://doi.org/10.3390/molecules27010063