Many researchers working with DNA nanostructures face a critical challenge: designing intricate 3D models is only half the journey. The other half is preparing those models for simulations — typically with coarse-grained tools like oxDNA — or sharing them with collaborators in universally understandable formats.
Adenita, a SAMSON Extension dedicated to the modeling and visualization of DNA nanostructures, helps bridge that gap by offering straightforward export options. In this post, we’ll walk through how to export your designed DNA models from Adenita, whether you’re preparing for simulations or compiling genetic sequences.
Why Export Matters
Researchers modeling DNA origami frequently move from CAD-like design environments into simulation tools to test thermodynamic stability, folding pathways, or interaction with proteins. Exporting structured designs in the correct format ensures efficiency and reduces the risk of errors when transitioning between tools.
Export Options in Adenita
Once your structure is complete or partially developed, you can use Adenita’s export functionality. Click on the Export icon (
) in the interface to access several formats:
- Sequence Export (CSV): Outputs a list of nucleotide sequences, which can be used for ordering strands or documenting your design.
- oxDNA Export: Prepares your design for simulation in oxDNA, a popular tool for coarse-grained DNA modeling. This is especially useful if you’re running molecular dynamics to observe DNA behavior under various conditions.
Preparing for oxDNA Simulations
Exporting to the oxDNA format enables you to simulate folding, flexibility, or binding. Here’s a quick checklist to ensure smooth preparation:
- Tag your scaffold and staple strands clearly using Adenita’s tagging functionality.
- Set the 5’ ends of strands explicitly using the Set 5′ tool (
) so simulation tools can interpret strand direction properly. - Use the Calculate icon (
), if you’ve configured ntthal, to determine thermodynamic properties like melting temperature and Gibbs Free Energy for selected regions. This helps predict strand behavior in simulation.
Common Pitfalls & Tips
- Missing strand ends: Ensure every DNA strand has a defined start and end. Tools like oxDNA may misinterpret incomplete strands.
- Visual overlaps: Use Adenita’s different visualization levels to confirm structural clarity before exporting. This avoids geometrical artifacts in simulation.
- Multiple components: If your system includes more than one DNA nanostructure, verify each one is organized in separate components or merged thoughtfully with the
tool.
A Visual Overview
Here’s a snapshot of the export feature you’ll be using:
With these steps, you can take your 3D model of DNA from visual concept to ready-for-simulation reality. The export process in Adenita is designed to be accessible and efficient, so you spend less time translating formats and more time exploring results.
To learn more about using Adenita, including editing tools, interface tips, and other features, visit the full documentation 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.