Reusing a published DNA origami design sounds simple: find a structure, open it, and move on to the next step. In practice, modelers often encounter a more basic problem first: the files may come from different tools, use different formats, or include only some of the information needed for the next stage. A little planning before you import can save time and make the handoff to simulation more predictable.
Adenita, an extension for SAMSON, can help you bring several DNA nanostructure formats into one workspace, inspect and edit them, and export sequences or oxDNA files. Here is a practical way to think through that workflow.
1. Start with the file you actually have
Before downloading a design, check the repository entry and its accompanying paper. Look for the original design file, publication details, and any stated license. For example, Nanobase hosts DNA, RNA, and hybrid nanostructure entries that may include design files and publication information. The caDNAno Repository collects recreated caDNAno v2 designs, so compare a downloaded model with its associated publication and validate it before relying on it in a research workflow.
The file extension gives you a useful first clue about the import route:
.json: Adenita can load caDNAno designs, including caDNAno 2.5 designs through its load function..adnpart: an Adenita component that can be loaded into a workspace and reused..adn: an Adenita file containing DNA nanostructures..ply: a mesh that Adenita can load using the Daedalus algorithm.
These formats are not interchangeable. Identify what you have before planning the rest of the workflow. Some example oxDNA resources instead provide topology and configuration files; those are useful for oxDNA workflows, but are not the same thing as a caDNAno design file.
2. Import into a workspace, then inspect before editing
Install SAMSON, add Adenita from the marketplace, and restart SAMSON so the extension can install. Open Adenita from Home > Apps or use Find everything…. In Adenita’s main interface, use the load control to bring in a supported design or component. A component can be loaded into the current workspace; loading through SAMSON files creates a new document.
Once loaded, take a moment to inspect the structure at the available visualization scales before making changes. Adenita’s editors cover tasks such as breaking or connecting strands, changing bases, deleting nucleotides or base pairs, and creating strands, lattices, nanotubes, or wireframes. Choose an editor for the specific task rather than making several changes at once: it is easier to spot an unintended edit when you can compare the structure before and after.
Adenita’s main interface provides access to loading, saving, exporting, and design tools.
3. Keep reusable parts separate from the whole design
If you plan to reuse only part of a design, save the selected component in Adenita’s .adnpart format. To preserve the DNA nanostructures handled by Adenita in the current design, use its save-all option to create an .adn file. Note the distinction: the Adenita save-all option does not save systems that are not handled through Adenita. To preserve the broader SAMSON workspace, save the workspace as a SAMSON document.
This small choice can prevent a common handoff surprise: assuming that one save operation has captured every object in the document. When sharing a project, specify whether you are providing a reusable DNA component, an Adenita design file, or the complete SAMSON document.
4. Choose an export for the next task
Adenita can export a sequence list as a CSV file or export in a format appropriate for oxDNA coarse-grained simulations. The right choice depends on what comes next: a sequence-oriented workflow needs the sequence export, while an oxDNA workflow needs the simulation-oriented export. Confirm that the exported files are the ones your downstream tools expect, and validate or relax a structure when appropriate before production simulations.
For ready-to-use examples, the oxDNA example files provide topology and configuration files. The Oxford Research Archive also provides example caDNAno designs and oxDNA inputs alongside a DNA-origami simulation tutorial. Check citations and licenses when reusing any repository files.
Reusable DNA origami components shared on SAMSON Connect can be a useful starting point. Check each item’s accompanying information before reuse.
The key is to treat import, editing, saving, and export as separate decisions. That makes it easier to preserve the right version of a design and communicate clearly what a handoff contains. For interface details and video walkthroughs, learn more in the Adenita documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.