Starting a DNA nanostructure project from a blank canvas can be a surprisingly slow way to begin. You may need a familiar motif, a published example, or simply a test structure to check that your tools are working. The challenge is not just finding a design: it is figuring out whether the file can be opened, what you can do with it once it is loaded, and how to prepare it for the next stage of your workflow.
Adenita, an extension for the SAMSON molecular design platform, can help with that handoff. It can load caDNAno designs, Adenita component files, and certain mesh files; lets you inspect and edit DNA structures; and can export sequences or structures in oxDNA format. Here is a practical way to use those capabilities without treating every imported design as ready for production work.
1. Start with a structure that matches your goal
If you want to study a published design or test an import workflow, look for an existing structure before building one yourself. The documentation points to sources such as Nanobase, the oxDNA example files, and the Oxford Research Archive example files. SAMSON Connect’s shared documents can also provide reusable components, including DNA crossover motifs and mechanical components.
Before downloading, decide what you need the file for. A design file you can edit is different from a structure intended mainly for a simulation workflow. Check the associated publication, citation, and license. In particular, community-recreated caDNAno designs should be checked against their source papers and validated before use in research.
Reusable examples can be a helpful starting point, but they still need to be checked for provenance and suitability.
2. Match the file type to the loading route
Adenita supports caDNAno 2.5 designs in .json format, Adenita component files in .adnpart format, Adenita files in .adn format, and meshes in .ply format. A .ply mesh is loaded using the Daedalus algorithm. In Adenita’s main interface, use the load function and choose the relevant file.
There is an important distinction between loading a component into your current workspace and loading a SAMSON-format file: the documentation notes that loading using SAMSON files creates a new document. If you are combining existing components, keep this behavior in mind so you know where your design has opened. Adenita components can be combined, subject to the resources available on your computer.
To install the extension, add Adenita from the SAMSON Connect Marketplace and restart SAMSON. You can then open it from Home > Apps or by using Find everything….
3. Inspect before you edit or export
Once the structure is open, use Adenita’s interface and editors to understand what is in the workspace. The available tools include editors for breaking or connecting strands, deleting nucleotides or base pairs, changing bases, and creating single or double strands. You can also create lattices, nanotubes, and wireframe structures. These tools make it possible to adjust a design, but they also make it worth taking a moment to confirm that you have selected the intended component or strand before editing.
Think of import, inspection, and modification as separate steps. First confirm that the expected design is present. Then identify which components or strands you intend to change. Only after that should you make edits or combine components. This simple pause helps keep an imported example distinct from your modified working version.
4. Save in a way that fits the next step
If you want to preserve a reusable component, Adenita can save the selection as an .adnpart file. To save the DNA nanostructures handled by Adenita in the current workspace, use its save-all function to create an .adn file. The documentation notes that systems not handled through Adenita will not be saved by that function. You can also save the entire workspace as a SAMSON document.
For downstream use, Adenita offers sequence export as CSV and export in a format appropriate for oxDNA coarse-grained simulations. Choose the output according to the next tool in your workflow rather than assuming that one export represents every aspect of the design. After export, check that the file is in the format your downstream tools expect; validate or relax the structure when appropriate before production simulations.
A compact handoff checklist
- Identify the source, publication, and license for the design.
- Confirm that the file type is supported: caDNAno
.json, Adenita.adnpartor.adn, or a Daedalus-compatible.plymesh. - Check whether loading the file adds a component to the current workspace or opens a new document.
- Inspect the structure before editing, combining, or exporting it.
- Save reusable components separately when useful, and select CSV or oxDNA export to match the next task.
- Validate the structure and its suitability before relying on it in a research or simulation workflow.
Adenita is still in alpha, and some of its video tutorials show an older SAMSON interface, so the current documentation is a useful reference when a control looks different. For more details on installation, editors, file handling, and tutorials, visit the Adenita documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.