About Adenita:

Adenita is a 3D visualization and modeling toolkit for the in silico design of static and dynamic DNA nanostructures. Based on a multiscale data model, it visualizes DNA-based structures on different abstraction levels and enable users to load and create DNA origami structures and combine them with proteins.

Adenita: Interactive 3D modeling and visualization of DNA Nanostructures. Elisa de Llano, Haichao Miao, Yasaman Ahmadi, Amanda J. Wilson, Morgan Beeby, Ivan Viola, Ivan Barisic. Pre-print at bioRxiv (849976); 2019. doi: https://doi.org/10.1101/849976


Adenita, currently in the alpha version, is being developed by Elisa De Llano and Haichao Miao.

Adenita: quick-start guide

This document is a quick-start guide to get you started designing DNA nanostructures on Adenita.

  1. Requirements
  2. First steps
  3. Features
  4. Adenita UI
  5. Video tutorials


Adenita is available for Windows and Linux. A dedicated graphics card is recommended.

If SAMSON crashes after having added Adenita, please make sure you have the latest supported Microsoft Visual C++ Redistributable.

First steps

Adenita SAMSON edition is a SAMSON plugin. It is available for SAMSON 0.7.0 and SAMSON 0.8.5. After installing SAMSON, you can select Adenita from a variety of plugins. Adenita can be combined with any of them! If you are unfamiliar with SAMSON, check out their tutorials.

If you encounter any problems while working with Adenita, you can report them here.


Create DNA nanostructures

Use different editors to create dsDNA, nanotubes, lattices or wireframe nanostructures (uses Daedalus algorithm).

Save components of your design, or the entire design

You can save the entire workspace using SAMSON’s save function. If you want to save components of your design for later reuse, use Adenita’s saving function (.adnpart).

Import a DNA nanostructure from Cadnano, or load a previous design

Through the main UI you can load a Cadnano design, or component saved as .adnpart. You can combine as many components as your graphics card and CPU can afford.

Export your design

Besides being saved, you can export your design as a list of sequences or in oxDNA format for simulations.

Adenita UI

Once you have installed Adenita the main UI should be located with other applications:


Different editors can be found on the editor menu:


The user can also set some options:


Main UI

The following functions can be accessed through the main UI:


Video Tutorials

Getting Started:

Creating ssDNA/dsDNA:

Creating Nanotubes and Untwisting:

Creating Square/Honeycomb Lattices and Connecting ssDNA:

Creating DNA Wireframe Structures and Creating All Atom Model:

Load and Visualize Proteins (PDB) & Connect to DNA Wireframe:

Highlighting, Tagging:

Coloring, Melting Temperature (Gibbs Free Energy):

Creating Superstructures (Merging Two DNA Wireframe Structures):

Exporting for Simulation (using oxDNA Format for Coarse-grained Simulation):

Icons from: https://icons8.com/icons.