When working on DNA nanostructures, it’s common to rely on tools like Cadnano or custom editors to design staple and scaffold strands. However, as research progresses and designs become more modular, the ability to reuse and import these components across different workflows becomes not just helpful—but essential. That’s where Adenita, the DNA nanostructure toolkit in SAMSON, offers a useful feature: design import and reuse.
In this blog post, we’ll explore how you can import DNA nanostructures into Adenita and reuse them to build more complex configurations. If you’ve ever needed to revisit an earlier component, combine structures, or work with designs from other tools, you’re in the right place.
Supported Formats for Import
Adenita supports the import of designs from multiple sources:
- Cadnano (
.json): Import designs created in Cadnano 2.5 directly into your workspace. - Ply Meshes (
.ply): These are interpreted using the Daedalus algorithm to convert 3D geometries into DNA wireframes. - Adenita formats (
.adnand.adnpart): Designed for internal use in Adenita to save and reuse entire assemblies or components.
How to Import
Once you’re inside the SAMSON environment with Adenita installed, importing is straightforward:
- Go to Home > Apps and launch Adenita (or use “Find everything…”).
- In Adenita’s main interface, click the
icon. - Choose the appropriate file type (
.json,.ply,.adn, or.adnpart) and select your file to import.
You can either load complete designs or modular components into your current workspace. Keep in mind that loading from SAMSON documents creates a new document, while using the Adenita import keeps it within the current one.
Why This Matters
DNA nanostructure design is iterative. You might test one approach using a square lattice, switch to a nanotube, or isolate a portion of a design for simulations. Without the ability to import and mix components, you’d waste time reconstructing models from scratch. With Adenita, any portion of your structure saved in .adnpart format can be reloaded, reconnected, and repurposed.
This is especially useful when collaborating across teams—if one researcher builds a DNA frame and another needs to embed a protein-binding region inside it, components can be easily shared and merged.
Tips for Modular Design
- Use Save Selection
to export only the relevant part of a structure as a .adnpartfile. - To merge components, use the Merge tool
to assign strands across objects. - Combine visual and sequence-based strategies: you can assign sequences and export them in formats compatible with oxDNA simulation environments.
Here’s a snapshot of the loading functionality directly in the interface:
Conclusion
Importing previous work or collaborating with structured design components in Adenita enables modularity and reuse, ultimately speeding up your research process. Whether you’re transitioning from Cadnano, building a library of reusable parts, or modeling hybrid DNA-protein assemblies, understanding how and when to import is a key part of your workflow.
Learn more about Adenita and its full capabilities in the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.