From scattered files to a usable DNA origami model

Starting a DNA nanostructure project often means solving two problems before the modeling begins: finding a design worth reusing and figuring out whether its file format fits the next step in your workflow. Rebuilding a published structure from scratch can take time, while a file that opens in one tool may not be suitable for editing or simulation in another.

Adenita, an extension for SAMSON, can help bring several parts of that workflow together. It supports importing caDNAno designs and Adenita component files, inspecting and editing DNA nanostructures, combining components, and exporting sequences or structures for oxDNA workflows. The key is to choose a source file based on what you want to do with it—not just on whether it contains a DNA design.

Choose a starting point that matches your task

If you want an editable design, Adenita can load caDNAno designs in .json format, as well as Adenita .adnpart components and .adn files. The documentation also describes loading .ply meshes through the Daedalus algorithm. These options serve different purposes, so check the file type before planning your next step.

  • Nanobase is a public repository for DNA, RNA, and hybrid nanostructures. Entries may include design files, images, publication details, and sometimes oxDNA files.
  • The caDNAno Repository collects caDNAno v2 JSON designs recreated from research articles. Because they are recreated files, compare them with the associated papers and validate a design before relying on it.
  • SAMSON Connect shared documents can provide reusable components. For example, Tom Moore’s page includes shared DNA origami components and example structures.
  • oxDNA.org example files and the Oxford Research Archive examples are useful references for oxDNA workflows. Their presence in an oxDNA format does not, by itself, mean they are caDNAno files for editing in Adenita.

Reusable DNA origami components shared on SAMSON Connect

Examples of components shared by Tom Moore on SAMSON Connect. Check each item’s publication, citation, and license information before reuse.

A practical import-to-export path

  1. Install the tools. Install SAMSON from SAMSON Connect, add Adenita from the extension page, and restart SAMSON. Open Adenita from Home > Apps or use Find everything….
  2. Load a suitable design. Use Adenita’s load function for a caDNAno 2.5 .json file or an Adenita .adnpart or .adn file. A SAMSON document can also be opened as a new document. Keep track of the original source and any associated paper.
  3. Inspect before editing. Use the interface and editors to examine the structure at the available visualization scales. Adenita includes tools for tagging or modifying bases, connecting strands, breaking bonds, and working with components. Treat imported designs as models to inspect and validate, not as automatically verified experimental or simulation-ready structures.
  4. Save for the right kind of reuse. Save a selected component in .adnpart when you want to reuse that component later. Save Adenita-managed DNA nanostructures in .adn when saving the current Adenita design. The documentation notes that systems not handled through Adenita are not included in this .adn save. A SAMSON document is the option for saving the workspace.
  5. Export for the next workflow. Adenita provides sequence export as CSV and export in a format appropriate for oxDNA. Before starting a simulation, confirm the output suits the simulation tools and workflow you intend to use; validate or relax the structure where needed.

Adenita main interface in SAMSON

This format-aware approach helps avoid a common handoff problem: confusing a file that is useful for visualization or simulation examples with one intended for editing as a caDNAno design. It also makes it easier to preserve provenance—keep the source, citation, and license alongside the model, and record any changes you make.

Adenita is noted as being in alpha, and some older video tutorials show an earlier SAMSON interface. For current setup details and the complete list of capabilities, see the Adenita documentation page.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.

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