Designing DNA nanostructures is just the beginning. For researchers working in structural DNA nanotechnology, the ability to export a design for further simulation is a critical step in the workflow. Whether you’re preparing input for coarse-grained simulation using oxDNA or simply want to obtain a list of DNA sequences, Adenita — a DNA nanostructure design tool in SAMSON — offers export features tailored to these needs.
Why export matters 🧬➡️🧮
Simulation tools like oxDNA allow you to predict folding behavior, structural stability, and interactions based on your design. Experimental work becomes more efficient when in-silico simulations suggest which designs are viable. This makes exporting a bridge between conceptual design and practical validation.
Export options in Adenita
After building your DNA nanostructure in Adenita, you can export it in formats ready for simulation or analysis:
- DNA sequence list: As a CSV file that provides the sequences of the scaffold and staples based on your design.
- oxDNA format: For use with the oxDNA simulation engine, a popular tool for coarse-grained modeling of DNA and RNA structures.
Using the Export Function
Accessing the export option is direct via Adenita’s main interface. Look for the export icon:
Clicking this icon opens export settings where you can choose how to save your work:
- Save sequences for ordering synthetic DNA strands.
- Export full design files in
.adnformat. - Generate oxDNA input files, ensuring compatibility with simulation workflows.
Simulation-readiness: A few things to keep in mind
Here are some practical tips when exporting:
- Double-check base pairing: Ensure the scaffold and staples align correctly by using the Set Scaffold tool before export.
- Use sequence options: In the Options menu, you can specify which sequence Adenita assigns to scaffolds — useful when working with known sequences or standards.
- Export components or all: Choose to export the entire system or just parts, depending on your focus.
Where this fits in your workflow
Whether you want to prototype DNA shapes, simulate dynamics, or prepare sequences for wet lab synthesis, exporting your design lets you integrate DNA nanostructures into broader research pipelines. Adenita’s seamless options help researchers avoid file conversion headaches and focus on insights rather than formatting.
Try it out
To see this in action or learn how to design from scratch, check out Adenita’s full documentation at this page.
SAMSON and all SAMSON Extensions are free for non-commercial use. To get started, download SAMSON at https://www.samson-connect.net.