One of the most common challenges DNA nanostructure designers face is transitioning from visual design to simulation. Creating a structure is just the beginning — taking it to analysis or dynamics studies in simulation tools like oxDNA or using sequence design pipelines requires the right file formats and outputs. If you’re using Adenita in SAMSON, this part of your workflow can be significantly streamlined.
In this post, we will explore how you can export your DNA nanostructures in Adenita into useful formats, such as CSV sequence files and oxDNA files, to bridge the gap between visualization and computation.
Why export matters in DNA nanotechnology
Exporting your design is an essential step for:
- Running coarse-grained simulations using oxDNA
- Analyzing binding regions or thermodynamic properties
- Integrating DNA assembly into custom pipelines
- Sharing modular structures with collaborators
How to export in Adenita
Once your DNA nanostructure is ready in Adenita, exporting it is straightforward and customizable.
Step 1: Save vs Export
It’s important to know the difference between:
- Save functions (which use
.adnand.adnpartformats for Adenita workspaces and components — useful for continuing your design later) - Export functions (which generate CSV and oxDNA files for simulation or sequence analysis)
To export, use the icon that looks like this: 
CSV sequence export
This option outputs your scaffold and staple sequences as a list, making it easy to use them for synthesis, sequence validation, or in specialized design tools.
The exported CSV file includes sequence information per strand, which can be cross-referenced to structure design, especially useful if you’ve tagged or named your strands during editing.
oxDNA export
If you’re working with simulations, exporting directly to oxDNA is a critical feature. Adenita can generate a set of oxDNA files that include:
topology fileconfiguration file
These output files are ready to use with oxDNA’s simulation engine for coarse-grained molecular dynamics. Having your structure prepped with sequence and base pairing information from within Adenita saves time and reduces error-prone conversions.
Tips for better exports
- Before exporting, ensure your scaffold and staples are complete and properly assigned (settings for scaffold sequence are in the Adenita Options menu).
- Visualize your structure at the appropriate abstraction scale to make sure you’re exporting what you need.
- Use the
Set Scaffoldfunction to automatically assign complementary bases before export, accessible via this icon:
Conclusion
Whether you’re preparing your DNA origami for manufacturing or running dynamic simulations to study behavior under different conditions, Adenita in SAMSON offers export tools that integrate well with downstream applications. These built-in features help you move from sequences and structures to systems ready for study.
Learn more in the official Adenita documentation: https://documentation.samson-connect.net/tutorials/adenita/adenita/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.