One of the most common hurdles for researchers and students working in DNA nanotechnology is moving from an intricate 3D design to physical simulation. Whether you’re studying system stability, strand dynamics, or molecular interactions, having your model in a simulation-ready format like oxDNA is crucial.
This is where Adenita, a SAMSON Extension, can help. Adenita not only allows you to design and visualize DNA nanostructures in 3D, but it also includes native support for exporting your work for oxDNA simulations — a much-needed bridge between interactive modeling and computational analysis.
Why export to oxDNA?
oxDNA is a coarse-grained DNA simulation package that allows you to test the physical behavior of DNA structures under various conditions. Preparing data for oxDNA manually can be time-consuming, especially with complex designs. With Adenita, the process is streamlined directly within the interface.
How it works in Adenita
Once you’ve modeled your DNA nanostructure using Adenita’s intuitive editors — whether you’re working with strands, nanotubes, lattices, or wireframe designs — you can export the structure by clicking the export button:
This opens options including exporting your design as a CSV file containing nucleotide sequences, or directly in oxDNA format for simulation. No extra scripts. No conversion tools. Just one click and your model is ready for simulation.
Benefits of this workflow
- Time-saving: Use Adenita’s editors to drag, connect, and adjust structures visually, then export in simulation-ready format without intermediate steps.
- Consistency: Designing and exporting from the same tool reduces risk of format mistakes or incompatibility.
- Visual feedback: The multiscale interface lets you check structures in both abstract and nucleotide detail levels before exporting.
Tips before exporting
- Assign nucleotide sequences where needed. Using the scaffold editor (
), you can define sequence rules to ensure base pair complementarity. - Make use of the Calculate tool (
) to estimate melting temperatures (if ntthalis configured). This helps when planning which regions may be more thermodynamically stable or less likely to separate during simulations. - Use visualization layers to highlight tags and strand orientations to double-check your selections.
And finally, if you have further processing steps in oxDNA or elsewhere (for example, simulation control files or analysis scripts), exporting from Adenita gives you a clean base to build on.
Try it out
If you’re building DNA nanostructures for simulation purposes, this feature in Adenita can save you a considerable amount of preparation time. For more detailed steps and video tutorials, visit the full Adenita documentation:
https://documentation.samson-connect.net/tutorials/adenita/adenita/
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.