From scattered DNA origami files to a usable design workflow

Finding a DNA origami structure is only the first step. The file may come from a paper, a repository, or a colleague—and it may not be in the format your modeling or simulation workflow expects. Before you can inspect or adapt it, you need to know what the file contains, whether Adenita can load it, and what checks to make before reusing it.

A practical approach is to treat structure reuse as a short workflow: locate a candidate, identify its format and provenance, open it in Adenita, then validate its suitability for your next step.

Start with the format, not just the download

Adenita can load caDNAno designs in .json format, as well as Adenita component files in .adnpart and .adn formats. It can also load a .ply mesh using the Daedalus algorithm. These formats are not interchangeable: a file that is useful as a visual reference may not contain the design information you need for editing or simulation.

Before downloading, check the repository entry or accompanying paper for the actual files provided. If you want to edit a caDNAno design, look for its design file rather than assuming that an image or a rendered structure will be enough. If your goal is simulation, check whether the source provides oxDNA files, or whether you will need to export the design from Adenita.

Where to look for examples

  • Nanobase is a public repository for DNA, RNA, and hybrid nanostructures. Entries may include design files, images, publication details, and—when available—oxDNA files.
  • oxDNA.org example files provides a small set of topology and configuration files that can help you explore oxDNA workflows.
  • The Oxford Research Archive example includes caDNAno .json files and oxDNA inputs accompanying a DNA-origami simulation tutorial.
  • The caDNAno Repository collects caDNAno v2 designs recreated from published research. Because these are recreated files, compare them with the corresponding papers and validate them before relying on them in a research workflow.

You can also browse SAMSON Connect shared documents for reusable components. For example, Tom Moore’s SAMSON Connect page includes shared DNA crossover motifs and mechanical components.

DNA origami components shared by Tom Moore on SAMSON Connect

Examples of reusable DNA origami components shared on SAMSON Connect.

A simple import-and-review sequence

  1. Record the source. Keep the repository or paper link, author information, and any license or citation details alongside the file. This makes it easier to give credit and to understand how the structure was produced.
  2. Check the file type. Match the extension to the task: caDNAno .json or Adenita .adnpart/.adn for supported design inputs; oxDNA files for oxDNA workflows. Confirm the source’s notes if the format is unclear.
  3. Open it in Adenita. Install Adenita from the SAMSON Connect Marketplace, restart SAMSON, and open Adenita from Home > Apps or Find everything…. Use its load function to bring a supported design or component into the workspace.
  4. Inspect before combining or exporting. Adenita lets you edit and combine DNA nanostructures, save components as .adnpart, and export designs as sequence data or in oxDNA format. Check that the imported structure is the one you intended and that its source information is available before moving downstream.
  5. Validate for the next workflow. A file being loadable does not by itself establish that it is appropriate for a particular experiment or simulation. Check the associated publication and repository notes; for simulation, make sure the structure is supported by your tools and relax or validate it when necessary before production runs.

If you plan to combine components, keep the scale of the project in mind: the documentation notes that the number of components you can load depends on your graphics card and CPU. Adenita is also in alpha, so interface details and behavior may change. When adapting a design for a specific purpose, treat the imported model as a starting point rather than a substitute for checking its provenance and suitability.

For more detail on Adenita’s editors, importing, saving, and oxDNA export, see the original Adenita documentation page.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.

Comments are closed.