Starting a DNA nanostructure project often means more than finding a shape you like. A design may come as a caDNAno file, an Adenita component, or simulation files—and those formats serve different purposes. It can be easy to lose time trying to open the wrong file, or to treat a downloaded structure as ready for simulation before checking what it contains.
A practical approach is to decide what you need to do first: inspect an existing design, edit or combine structures, or prepare a model for a downstream simulation. Adenita, an extension for SAMSON, can help with these steps while keeping DNA nanostructures available for inspection at multiple levels of detail.
Start with a source that fits your task
If you want to learn from published examples or avoid building a design from scratch, look for a repository that provides the original design files and publication details. Nanobase is a public repository for DNA, RNA, and hybrid nanostructures; entries may include design files, images, publication information, and oxDNA files. The caDNAno Repository collects caDNAno v2 JSON designs recreated from research articles. Because these are recreated files, check the associated paper and validate the design before relying on it.
For oxDNA examples, oxDNA.org provides sample topology and configuration files. An Oxford Research Archive collection includes caDNAno JSON designs and oxDNA input files accompanying a DNA-origami simulation tutorial. These sources can be useful for testing workflows, but a simulation example is not automatically the right starting point for every design question.
Match the file to the next step
Adenita can load caDNAno designs in .json format, along with Adenita component files such as .adnpart and .adn. Its interface can also load a mesh in .ply, which is used with the Daedalus algorithm. In broad terms, choose the file according to what you have and what you want to do next:
- Inspect or edit a caDNAno design: begin with its
.jsonfile. - Reuse a saved Adenita component: load the
.adnpartfile. - Continue working with an Adenita design: use the relevant
.adnfile. - Prepare for coarse-grained simulation: use Adenita’s export options for oxDNA, then check that the resulting files are suitable for your simulation workflow.
Adenita can also export a design as a CSV sequence file. Its interface includes options to save a selected component as .adnpart or save Adenita-managed DNA nanostructures as .adn. Note that saving the entire Adenita design does not save systems that Adenita does not handle.
Inspect before you build on the file
Once the design is loaded, take time to understand its components and strands before making edits. Adenita’s editors support actions such as connecting strands, breaking bonds between consecutive nucleotides, changing bases, and deleting nucleotides or base pairs. Other tools create single- or double-stranded DNA, lattices, nanotubes, and wireframes. These capabilities make it possible to adapt or combine structures, but they also make it important to keep track of what you changed.
For reusable components and examples, SAMSON Connect’s Shared documents includes structures shared by community members. For example, Tom Moore’s SAMSON Connect page contains DNA crossover motifs and other components. Check the license, citation, and publication information for any structure you reuse.
Keep provenance and simulation checks in the workflow
A simple record can prevent confusion later: note where a design came from, which file you opened, what edits you made, and which format you exported. Keep the associated paper or repository entry alongside that record. If the destination is a simulation, confirm that your tools support the exported format and validate or relax the structure when needed before production runs. The documentation describes Adenita’s oxDNA export, but it does not imply that every imported design is simulation-ready without further checks.
For the installation steps, interface details, editor descriptions, and video tutorials, 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.