Designing DNA nanostructures is a meticulous process that often doesn’t stop at the visual modeling stage. Many molecular modelers and nanobiotechnologists also need to export their designs for use in simulations or experimental protocols. That’s why understanding how to export your DNA constructs from Adenita, the DNA nanostructure modeling extension for SAMSON, can save you hours of manual conversion and formatting.
Whether you’re preparing to run a coarse-grained molecular dynamics (MD) simulation or need to share DNA sequence data with a colleague, Adenita offers practical export options to streamline your workflow.
Typical Challenge: Going from 3D Models to Simulations
Suppose you’ve just designed a complex 3D DNA nanostructure in Adenita using wireframes or lattices. The next step may be simulating how this structure behaves under experimental conditions, using tools like oxDNA. However, exporting this model into a compatible format without errors or loss of information is not always straightforward.
Using Adenita’s export functionalities, you can:
- Generate nucleotide sequences as
.csvfiles for lab protocols. - Export the model in
oxDNAformat for coarse-grained simulations. - Save your entire design or selected components in custom file formats for repetitive workflows.
How to Export Your Design
After constructing your DNA nanostructure, look for the following tool in Adenita’s main interface:
Export tool
Clicking the Export button will provide two main options:
- CSV Sequence File: This file contains the full DNA sequences from your scaffold and staples, ready to be synthesized or shared with collaborators.
- oxDNA Format: Perfect for importing your geometry directly into oxDNA for simulations. This preserves both the topology and the sequence of your model.
Tips When Exporting
- Check your component selection: Ensure you’re exporting the right components. Components not added through Adenita’s editors won’t be captured.
- Use settings to customize: You can specify scaffold sequences in the Options menu so your exports match your experimental plans.
- Remember to define the 5’ ends: Use the
tool to mark the beginnings of strands clearly, which matters for certain assembly methods and simulations.
Here is an example of where the Export button can be found in the Adenita interface:
Once exported, these files can be pipelined into popular DNA simulation software like oxDNA, or parsed for synthesis ordering platforms. This tight integration of design and export eliminates the need for manual re-entry and reduces error rates.
Learn more about exporting and other functionalities from the Adenita 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.