A DNA origami project can begin in one tool, continue in another, and end in a simulation workflow. The frustrating part is often not designing the shape—it is keeping track of what each file contains, what can be edited, and what needs to be exported for the next step. Adenita, an extension for the SAMSON molecular design platform, brings several of these tasks into one workspace: importing, inspecting, editing, combining, saving, and exporting DNA nanostructures.
This walkthrough focuses on a practical handoff: start with an existing design, make or organize changes, preserve a reusable copy, and prepare an export for downstream work. It is an orientation rather than a guarantee that every imported structure is ready for production simulation.
Start with the right input
First identify the format you have and what you want to do with it. Adenita can load caDNAno 2.5 designs in .json format, Adenita files such as .adnpart and .adn, and .ply meshes, which are processed using the Daedalus algorithm. These are not interchangeable file types: a caDNAno design is an input design, a mesh can be used to generate a wireframe design, and Adenita’s formats are useful for saving its components or DNA nanostructures.
If you are looking for a starting structure, repositories can save time. Nanobase includes DNA, RNA, and hybrid nanostructure entries; the caDNAno Repository collects recreated designs from published work; and SAMSON Connect has shared documents with reusable components. Before building on someone else’s model, check its publication, citation, and license information. Recreated designs should also be checked against the corresponding paper.
Inspect before you edit
After loading a design, use the viewport and Adenita’s editors to examine its strands and components at the level that suits the task. The available tools include editors for breaking or connecting strands, deleting nucleotides or base pairs, merging components, tagging nucleotides, and modifying double-strand twist. Creation tools can add single or double strands, lattices, nanotubes, and wireframe structures. For wireframes generated from shapes, Adenita uses the Daedalus algorithm.
A useful habit is to separate structural changes from file management. Before changing a shared or imported design, consider saving a working copy. Adenita can save a selected component as .adnpart, which is convenient when you want to reuse that part later. Its save-all function writes Adenita-handled DNA nanostructures to .adn; systems not handled through Adenita are not included. Saving the whole SAMSON workspace as a SAMSON document is a different option when you need to preserve the broader workspace.
Make the handoff explicit
When the structure is ready for another step, choose the export based on what that step needs. Adenita can export a sequence list as CSV or export in a format appropriate for oxDNA coarse-grained simulations. These outputs serve different purposes: a sequence file records sequence information, while an oxDNA export is intended for a simulation workflow.
If you need to assign a scaffold sequence, Adenita provides a set-scaffold function. The selected scaffolds receive the sequence specified through the Options menu, and paired scaffold nucleotides receive complementary bases. The interface also includes a calculation function for melting temperatures and Gibbs free energies of binding regions, provided a path to ntthal has been specified in Options.
Before using an export in a research workflow, confirm that the output format is supported by the downstream tools and inspect or validate the structure as needed. For simulation, the documentation recommends relaxing or validating a structure when necessary before production runs. This check matters because a file being exportable does not by itself establish that it is suitable for every simulation setup.
A compact workflow to remember
- Identify the input format and select an appropriate starting design.
- Load it into Adenita, then inspect the structure before editing.
- Save a reusable component or a working copy when appropriate.
- Choose a sequence or oxDNA export according to the next task.
- Check the export, citations, and any required validation before relying on it.
Adenita is currently in alpha, and some interface details may change. The documentation also includes video tutorials for common tasks, though the videos were recorded with an older SAMSON version. Read the original Adenita documentation for installation steps, interface details, and the full set of tutorial videos.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.