Don’t start from a blank helix: finding and reusing DNA origami designs

Starting a DNA nanostructure project from scratch can mean more than designing the shape: first you need a structure to work with, then a way to get it into your modeling environment, and finally a format that suits your next step. Reusing a published or shared design can make that first stage easier—but only if you know what file you have and what to check before relying on it.

Adenita, an extension for the SAMSON integrative molecular design platform, can load caDNAno designs in .json format and Adenita component files in .adnpart or .adn format. It can also export designs as sequence files or in oxDNA format. That makes it useful for a workflow that begins with an existing design and continues through inspection, editing, and export.

Find a structure that fits your starting point

Different repositories provide different kinds of material. Nanobase is a public repository for DNA, RNA, and hybrid nanostructures; entries may include original design files, publication details, and, where available, oxDNA files. The caDNAno Repository collects caDNAno v2 designs recreated from published research. Since those files are recreated, use the associated paper to check the intended design rather than treating the file as an unquestioned source of truth.

If you specifically need examples for an oxDNA workflow, oxDNA.org provides a small set of example topology and configuration files. The Oxford Research Archive also hosts input files accompanying a DNA-origami simulation tutorial, including caDNAno designs and oxDNA inputs.

For reusable building blocks, explore SAMSON Connect Shared documents. Tom Moore’s SAMSON Connect page includes shared components and example structures, such as crossover motifs and mechanical components.

A practical import-to-export workflow

1. Choose the file for the task. If you want to inspect or edit a caDNAno design in Adenita, look for a .json design. If you are reusing an Adenita component, look for .adnpart or .adn. An oxDNA topology or configuration file belongs to an oxDNA workflow; it is not the same thing as a caDNAno design file.
2. Install and open Adenita. Install SAMSON, add Adenita from the SAMSON Connect extension page, and restart SAMSON so the extension can install. Open it from Home > Apps or use Find everything….
3. Load the design and inspect it before editing. Adenita’s load function accepts caDNAno 2.5 .json files and Adenita .adnpart or .adn files. Use the available editors to examine strands and components, and make edits only after you understand what the imported structure represents. For example, Adenita includes tools to connect strands, break a bond between consecutive nucleotides, modify bases, and reorganize components.
4. Keep the source and check provenance. Record the repository entry, paper, and license alongside your working file. For recreated designs, compare the structure with the cited publication. Validate the design for your intended use; a file being importable does not by itself establish that it is appropriate for a particular experiment or simulation.
5. Save and export deliberately. Save a reusable selection as .adnpart, or save Adenita-managed DNA nanostructures as .adn. The documentation notes that saving all in .adn does not include systems that Adenita does not handle. When preparing for downstream work, choose the sequence export or oxDNA export that matches your workflow, then check the resulting files in the tools you plan to use.

One useful habit is to separate the original downloaded file from your edited working copy. That way, if an edit or conversion causes confusion, you can return to the source and compare. Also check the license and citation information before reusing a community design, and relax or validate a structure when necessary before production simulations.

Adenita is noted as being in alpha, so interface details may change. The documentation page includes an interface overview, a list of editors, and videos for common tasks; the videos were recorded with an older version of SAMSON, so some controls may look different. Read the Adenita documentation to learn more.

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