When working on in silico DNA nanostructure design, a recurring frustration among molecular modelers is the gap between design and simulation. Once a structure is modeled in a visual toolkit, exporting it into the right format for downstream analysis — such as coarse-grained molecular dynamics — often requires tedious formatting or custom scripting. Fortunately, Adenita, a SAMSON Extension for modeling DNA structures, provides a streamlined way to make this transition.
Whether you’re preparing synthetic DNA designs for thermodynamic analysis or for coarse-grained simulations (e.g., in oxDNA), Adenita is equipped to export your models in a compatible and research-friendly format.
Why Exporting Matters
Adenita doesn’t just allow for the visual and conceptual design of DNA nanostructures — it supports a pipeline that takes those designs directly to simulation platforms. This means you save time, avoid format mismatches, and reduce manual intervention when switching from structure building to analysis.
What You Can Export
From Adenita’s interface, you can export your designs in two principal ways:
- CSV Sequence File: Capture nucleotide sequences from the structure, component-by-component. This is ideal if your goal is to synthesize the structure or analyze its sequence features.
- oxDNA Format: A widely used coarse-grained representation of DNA for simulation with the oxDNA engine. Exporting in this format allows you to move from structure to dynamics in just a few steps.
Export options are found in the main interface
How to Export Your Design
To export your DNA nanostructure:
- Open your design in SAMSON and launch Adenita (you’ll find it under Home > Apps).
- In Adenita’s main interface, locate the Export icon (🡕 arrow symbol).
- Click it and select the desired format: CSV for sequence output or oxDNA for simulation-ready models.
- Choose a location to save your file. Adenita will generate the export with the necessary structural and sequence data encapsulated.
These exports are particularly useful if you’re planning to:
- Simulate DNA flexibility and behavior with oxDNA
- Estimate hybridization and binding energies using other tools
- Synthesize DNA sequences through ordering platforms
Bonus Feature: Thermodynamic Calculations
If you specify the path to ntthal in Adenita’s settings under Options, Adenita can also calculate melting temperatures and Gibbs free energies for all binding regions in a selected component. This is accessible via the 
icon.
These features let you build, analyze, and export — all within the same visual environment.
To see more export and calculation options, visit the Adenita Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.