From a published DNA origami design to a usable model

Finding a DNA origami structure is only the first step. Molecular modelers often need to answer a more practical set of questions: Can this design be opened in my software? Can I inspect or adapt it? What should I save, and what format will my next workflow need?

Adenita, an extension for the SAMSON molecular design platform, can help bridge those steps. It supports loading caDNAno designs in .json format, Adenita components in .adnpart format, and Adenita files in .adn format. Once a structure is loaded, you can inspect and edit it, combine components, save your work, or export it as sequences or in oxDNA format for a coarse-grained simulation workflow.

Start with a structure you can trace

Before rebuilding a published design from scratch, look for an existing file. Repositories can save time and provide useful examples—but a structure is more than a shape on screen. Its associated design file, publication, and reuse terms matter too.

• Nanobase hosts DNA, RNA, and hybrid nanostructures. Entries may include original design files, publication details, images, and, where available, oxDNA files.
• oxDNA.org example files offers sample topology and configuration files for testing oxDNA workflows.
• The Oxford Research Archive provides caDNAno and oxDNA input files associated with an oxDNA DNA-origami 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 using them in a research workflow.

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

A practical import-to-export route

1. Check the source. Record the repository entry, paper, and any license or reuse information. Confirm which file is the design and which files are intended for visualization or simulation.
2. Install and open Adenita. Install SAMSON, add Adenita from the SAMSON Connect Marketplace, then restart SAMSON. Open the extension from Home > Apps or use Find everything….
3. Load the design. Use Adenita’s load function for a supported caDNAno .json file or an Adenita .adnpart or .adn file. The interface also lists .ply meshes, which are loaded using the Daedalus algorithm. Check the file type before choosing a route.
4. Inspect before changing anything. Use the available editors to examine strands and components, and make edits only when needed. Adenita includes tools for creating strands, lattices, nanotubes, and wireframes, as well as tools for connecting, merging, tagging, or modifying structures.
5. Save deliberately. Save a reusable component as .adnpart, or save Adenita-managed DNA nanostructures together in an .adn file. The documentation notes that systems not handled through Adenita are not saved in that .adn file; save the full workspace as a SAMSON document when you need to preserve the broader scene.
6. Export for the next task. Adenita can export a CSV sequence file or a format appropriate for oxDNA. Choose based on the downstream workflow, then check that the exported files are supported by the tools you plan to use.

Keep the handoff honest

Importing a design is not the same as validating it for a particular experiment or simulation. Preserve the source and citation, review the structure, and check the output format and assumptions required by the next tool. If a file was reconstructed from a paper, compare it with the publication. If the goal is production simulation, validate or relax the structure when necessary before proceeding.

Adenita is currently in alpha, and some of its tutorial videos were recorded with an older SAMSON interface. Treat the videos as demonstrations of workflows rather than guaranteed descriptions of every current control.

For the complete interface guide, editor descriptions, videos, and references, see the Adenita documentation.

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