Designing and simulating DNA origami structures has become an increasingly important part of molecular modeling and nanotechnology research. Whether you’re designing nanorobots, cages for drug delivery, or programmable matter, one common frustration is the challenge of managing and visualizing complex DNA structures efficiently. For users working with cadnano or custom-designed DNA parts, the question is often: how can I read, manipulate, and visualize these files all in one place?
SAMSON, the integrative platform for molecular design, offers a built-in solution to handle these tasks through its dedicated Adenita extension. This blog post will walk you through the file formats supported for DNA origami within SAMSON, explain typical use cases, and help streamline your workflow—whether you’re a beginner or an experienced researcher.
What File Formats Are Supported for DNA Origami?
The Adenita extension in SAMSON supports several file formats specific to DNA origami modeling and design:
- ADN – Adenita’s native format. Use this to save and reopen complex DNA nanostructures created within the extension.
- ADNPART – A format used for storing reusable DNA parts, useful for modular design strategies.
- JSON – Load cadnano designs or older-format Adenita parts with this widely-used format in DNA origami.
- PLY – Load mesh files from cadnano to visualize and interact with structures in 3D.
This built-in format compatibility means you won’t need to juggle multiple tools anymore when you switch between design, simulation, and presentation.
Typical Workflow
Here’s a simple use scenario using SAMSON and the Adenita extension:
- Design your structure in cadnano and export it as a
.jsonor.plyfile. - Open SAMSON and activate the Adenita extension (available from the Extension Store).
- Load your structure into SAMSON. You’ll now be able to visualize, edit, or even combine multiple structures via Adenita’s interactive interface.
- Save your assembled or modified structure in
.adnor.adnpartformat to reuse or share it later.
This modular handling of DNA parts and mesh is especially useful for collaborative teams building large or reusable designs.
Why It Matters
DNA origami projects often involve multi-step workflows involving several file formats and tools. With DNA design software such as cadnano, the visual richness is excellent, but simulation and integration into broader molecular projects can be limited. SAMSON simplifies this complexity by allowing you to unify your entire process—visualization, modification, annotation, simulation, and export—inside one platform, with file format support tailored for your needs.
Integration with the rest of SAMSON means your DNA designs aren’t siloed from other components of your molecular system. You can simulate, visualize, and even animate DNA constructs together with proteins, drugs, or other nanostructures, enabling richer exploration and faster iterations.
To learn more about supported formats in SAMSON, please visit the full documentation here: https://documentation.samson-connect.net/users/latest/supported-formats/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net