Reusing Designs: How to Import Cadnano Structures into Adenita

Designing DNA nanostructures from scratch can be time-consuming. But if you’ve already built components in Cadnano, you don’t have to start over when moving into 3D modeling. Adenita, an extension for the SAMSON platform, allows you to directly import Cadnano-generated structures (.json) and continue working from there, integrating them into more complex DNA, protein, or hybrid nanostructures.

This approach solves a common challenge for molecular designers who want to go beyond the 2D capabilities of Cadnano and visualize or simulate their work in 3D. Here’s how importing works — and why it’s useful.

Why Import Cadnano Designs?

Many researchers and designers start building DNA structures in Cadnano thanks to its user-friendly editor. However, Cadnano’s abstractions are mostly 2D-based, and don’t allow integration with proteins or advanced simulations. Adenita enables 3D manipulation and connectivity across biomolecular structures, including DNA-protein assemblies, using CAD-like precision.

If you’re working on DNA origami, importing your design into Adenita lets you:

  • Combine your DNA structures with others (or with protein structures)
  • Visualize them across multiple abstraction levels (from all-atom to high-level models)
  • Export them in formats like oxDNA for simulation

How to Import Designs from Cadnano

Once you have Adenita installed in SAMSON, follow these steps to import your design:

  1. Open the Adenita interface under Home > Apps or by searching with Find everything....
  2. Select the Load button Load in the main UI.
  3. Choose your Cadnano .json file. Adenita will process your strands and render them in 3D.
  4. You can now edit, connect, tag, and export your structure as needed.

Adenita also supports import of other formats like .ply (for meshes using the Daedalus algorithm), .adn and .adnpart (Adenita’s native formats).

Tips for Better Imports

  • Make sure your Cadnano structure is well-formed. Overlapping strands or incomplete helices may need to be addressed.
  • Cadnano 2.5 format is supported. Other versions might require conversion.
  • After import, you can assign scaffolds, break or reconnect strands, merge components, or edit sequences directly in Adenita.

Visual Integration

Adenita renders imported structures in its multiscale viewer, allowing you to examine DNA’s geometry and base-pairing, and to modify properties like twist and sequence pairing. Below is an example of the Adenita main interface after importing structures:

Adenita's interface

From here, you can use editors on the left toolbar (click … if hidden) to further modify strands or change layout.

Export and Simulation

Once your imported structures are ready, export options in Adenita let you generate CSV sequence files or prepare your design for simulation with oxDNA. This creates new opportunities for kinetic analysis, stability studies, and visualization.

Conclusion

Whether you’re transitioning from 2D to 3D, or integrating DNA with other biomolecules, importing Cadnano designs into Adenita offers a seamless bridge between design and simulation. It’s a smoother workflow for researchers aiming to prototype DNA architectures with structural realism and analytical depth.

To learn more about Adenita and its capabilities, visit the official tutorial page: https://documentation.samson-connect.net/tutorials/adenita/adenita/.

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

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