Designing DNA nanostructures in silico is an exciting way to prototype molecular devices before heading to the lab. But one question frequently halts the creative process for many researchers: How can I turn my design into data suitable for simulation?
If you’re designing DNA nanostructures using Adenita within the SAMSON platform, you’re in luck. Adenita includes built-in tools that make it straightforward to export your structures to the oxDNA format, which enables simulations of coarse-grained DNA models for stability analysis, dynamics, and more. Let’s walk through how this process works and why it matters.
Why export to oxDNA?
Simulation plays a crucial role in understanding the feasibility and behavior of DNA nanostructures under realistic conditions. oxDNA is a well-known coarse-grained DNA simulation framework that captures essential thermodynamic and mechanical properties of DNA. Exporting to oxDNA lets you:
- Assess the structural stability of your designs
- Evaluate folding pathways
- Run molecular dynamics simulations without atomic-level overhead
- Experiment with temperature or ionic strength parameters
How to export your design from Adenita
Once your design is ready in Adenita, exporting it to oxDNA format takes just a few clicks. Here’s how:
- Select your full design or the component you want to simulate.
- Click on the Export icon in Adenita’s interface. It looks like this:
- From the export options, choose the oxDNA format.
This will generate a set of files compatible with oxDNA simulators. You’re now ready to import your model into oxDNA and begin simulation!
What gets exported?
The oxDNA export includes:
- A sequence file representing the base information
- A topology file indicating strand connectivity
- A configuration file for the spatial arrangement of nucleotides
If you’ve specified scaffold sequences or used custom strands, Adenita will preserve this information accurately in the export.
Before you simulate: a few tips
While Adenita handles most of the formatting, you’ll want to double-check a few things before starting a simulation in oxDNA:
- Ensure all strands are connected properly. Use the connect and merge tools in Adenita if needed.
- If you’ve used circular strands or non-standard geometries, visualize the exported structure in oxDNA to confirm everything looks correct.
- Set your simulation parameters appropriately (e.g., temperature, ion concentration) when configuring oxDNA.
The bottom line
Exporting DNA nanostructures from Adenita to oxDNA removes a major friction point in the modeling workflow: going from 3D design to plausible dynamics. With a few clicks, you can iteratively refine, validate, and optimize your structures—saving both time and effort in the experimental phase.
Ready to simulate? You’ll find the export option in Adenita’s main interface after selecting your design.
To explore detailed instructions and additional features, visit the Adenita tutorial documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.