Start with a published DNA origami design—not a blank canvas

Rebuilding a DNA origami structure from scratch is often the least useful part of a modeling task. You may only need to inspect a published design, adapt a component, combine structures, or prepare a model for a simulation workflow. The challenge is finding a usable starting point—and knowing what each file can and cannot do.

Adenita in SAMSON can load caDNAno designs, Adenita component files, and certain other structure files. With a little preparation, you can turn a repository download into a more organized modeling workflow instead of a frustrating file-format guessing game.

Choose a source that fits the task

For caDNAno designs, Adenita accepts .json files in the caDNAno 2.5 format. Adenita components can be stored as .adnpart, while .adn files can contain Adenita DNA nanostructures. The interface also supports .ply meshes, which are used with the Daedalus algorithm to generate wireframe DNA structures.

There are several places to look for examples. Nanobase provides a public collection of DNA, RNA, and hybrid nanostructures; entries may include original design files and publication details. The caDNAno Repository collects recreated caDNAno v2 designs based on published research. For oxDNA workflows, oxDNA.org offers example files, and the Oxford Research Archive includes example caDNAno and oxDNA files associated with a tutorial.

Reusable components are also shared through SAMSON Connect Shared documents. For example, Tom Moore’s page includes published components and example structures.

A practical import-to-export workflow

1. Check the source before downloading. Note the associated paper, citation, and license. If a design was recreated from a publication, compare it with the paper and treat the file as something to verify—not as an automatically validated model.
2. Identify the format. A caDNAno design should be a compatible .json file. If you have an Adenita component, look for .adnpart; for a saved Adenita design, look for .adn. For a wireframe workflow, Adenita can load a .ply mesh using Daedalus.
3. Load it into Adenita. Open Adenita from Home > Apps or use Find everything…. Use its load function to bring a design or component into the workspace. Loading a SAMSON file creates a new document.
4. Inspect before editing. Look over the structure and its components, then make only the changes required for your task. Adenita includes editors for operations such as connecting strands, deleting nucleotides or base pairs, modifying tags or bases, and creating strands, lattices, nanotubes, or wireframes.
5. Save with the right scope. Save a reusable component as .adnpart, or save the current Adenita DNA nanostructures as .adn. The latter does not save systems that are not handled through Adenita. To preserve the entire workspace, save it as a SAMSON document.
6. Export for the next tool. Adenita can export sequences as CSV or export in a format appropriate for oxDNA. Check that the chosen output matches your downstream workflow. For simulation, validate or relax a structure when needed before using it in production.

Keep the provenance attached

A useful model is more than a file that opens. Keep the original source, publication details, and license information alongside your working copy, and record any changes you make. This makes it easier to revisit the design, cite it correctly, and distinguish a published or recreated structure from your own modifications.

Adenita is in alpha, and some interface details may change. For installation steps, editor descriptions, and video walkthroughs, see the Adenita documentation page.

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