If you’ve designed DNA nanostructures in Cadnano, there’s a good chance you’ve hit a wall when trying to bring those designs to life in 3D with more flexibility and detail. Whether you’re preparing for a simulation, looking to merge multiple DNA structures, or simply want a better sense of spatial configuration, transferring your design into a 3D environment is often easier said than done.
Adenita, a SAMSON Extension, provides a bridge between Cadnano and rich 3D modeling. In this post, we’ll guide you through the process of importing Cadnano designs into Adenita so you can visualize, edit, and combine DNA nanostructures in a multiscale 3D workspace.
Why import into Adenita?
Cadnano is widely used for the design of scaffolded DNA origami structures at the abstract level, focusing on helices and staple routing. But if you want to:
- View your structures in 3D, from atomistic to coarse scales,
- Combine DNA structures with other molecular systems like proteins,
- Edit individual strands or geometries intuitively,
- Export to formats for simulations (like oxDNA),
…then Adenita offers the tools you need to go further.
How to import Cadnano files into Adenita
The process is straightforward once Adenita is installed:
- In SAMSON, open Adenita (found in Home > Apps or via Find everything…).
- Click the
button in Adenita’s main interface. - From the file dialog, select your Cadnano design file in
.jsonformat (Cadnano 2.5 is supported).
The structure will now appear in your active SAMSON workspace, displayed using Adenita’s multiscale visualization: from the full helix arrangement to individual base pairs.
What happens after importing?
Once your design is loaded, you’re free to:
- Edit the structure: Add, break, or connect strands using intuitive tools.
- Combine it with other components, such as protein models or imported DNA parts.
- Generate exports for sequence analysis or simulations (e.g., oxDNA format or .csv files).
- Visualize at different scales: Zoom into atomic details or zoom out to view higher-order architecture.
How reusable are the components?
Adenita allows you to save imported components for future projects using the .adnpart format. This means you can build modular libraries of structural motifs—whether it’s a DNA nanotube or a specific crossover motif—and drag them into your workflow as needed.
Also, you can load multiple Cadnano files and assemble them into larger structures. You’re only limited by your system’s memory and processing capability.
Can I undo design steps?
Yes. Adenita works within SAMSON’s undo/redo system. You can explore edits freely and refine your design without concern over losing earlier steps.
Summing up
Moving your Cadnano designs into Adenita opens new possibilities in DNA nanostructure modeling. You get the power of real 3D visualization and editing while maintaining compatibility with commonly used tools in the DNA nanotech community.
Ready to try it out? Start here to dive into the official Adenita documentation on importing DNA nanostructures.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.