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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

Note

Adenita is in the alpha version.

It was originally developed by Elisa De Llano and Haichao Miao (see: https://edellano.github.io/Adenita-SAMSON-Edition).

Porting of Adenita to the latest versions of SAMSON and its support are done by the SAMSON team at OneAngstrom.

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

  1. First steps
  2. Features
  3. Adenita interface
  4. Video tutorials
  5. References

First steps#

  1. Install SAMSON from SAMSON Connect.
  2. Add Adenita from SAMSON Connect - Marketplace and then restart SAMSON - it will automatically download and install Adenita for you.
  3. You can find Adenita in Home > Apps or via Find everything....

If you encounter any problems, please let us know at SAMSON Connect Forum. You can also join the Adenita community on Discord at https://s-c.io/dntd.

Features#

Create DNA nanostructures#

Use different Adenita editors to create double-strand DNA (dsDNA), nanotubes, lattices, or wireframe nanostructures (uses Daedalus algorithm).

Save components of your design or the entire design#

You can save the entire workspace into a SAMSON document. If you want to save components of your design for later reuse, use Adenita's saving function (it will save them in .adnpart format).

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

Through the Adenita interface 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's interface#

Once you have installed Adenita, you can find it in Home > Apps or via Find everything....

Adenita's interface

Adenita provides a number of editors that can be accessed either via Adenita's interface or via the editors toolbar on the left-side of the viewport (click on ... at the bottom of the editors toolbar).

Adenita's interface: Editors

You can also access Adenita's settings through its interface - click on Settings.

Adenita's interface: Settings

Main interface#

The following functions can be accessed through the main UI:

  • Load Load a DNA nanostructure from a file. Possible choices are a cadnano design (for cadnano 2.5) as .json, a mesh in .ply (will be loaded using the Daedalus algorithm), or a .adnpart or .adn (custom Adenita formats). This option allows to load a component into a workspace (loading using SAMSON files will create a new document).
  • Save selection The user can chose to save a component for later use in our custom format (.adnpart).
  • Save all The user can save all current DNA nanostructures in a .adn file, systems not handled through Adenita won't be saved.
  • Export Options to export as CSV sequence file or in a format appropiate for oxDNA are available here.
  • Set scaffold All scaffolds from the selection will be assigned a sequence specified through the 'Options' menu, scaffold nucleotide's pairs will also be assigned the complementary base.
  • Set 5' It is possible to set any nucleotide as the new 5' of its single strand.
  • Calculate If a path to ntthal has been specified in the Options menu, it will be used to calculate the melting temperatures and Gibbs free energies of all binding regions of a selected component.

Editors#

  • Break Breaks the bond between two consecutive nucleotides of the same strand.
  • Delete Deletes nucleotides or base pairs, depending on the chosen visualization scale.
  • Connect Merges single or double strands. If strand ends are selected, they will be connected in the appropiate direction (5' to 3'). If nucleotides that are not 5' or 3' are selected, the strands will be broken in order to reconnect them at chosen points. It is also possible to insert a new double or single strand along the connection.
  • Merge Reorganize several components into one, or reassign single and double strands to other components. List of components and strands needs to be updated manually.
  • Twist double-strand Modifies the twist angle of a double-strand along the helical axis.
  • Tag Tag nucleotides or modify its base.
  • Twister Remove entire the twist of a double strand locally to observe the single strands that compose it as parallel lines.
  • Strand creator Add a new single or double strand as a component to the design. They can also be circular.
  • Lattice creator Add a lattice of double strands as a component.
  • Nanotube creator Add a nanotube composed of double strands.
  • Wireframe editor Generate a wireframe from the given shapes and add it to the design (uses the Daedalus algorithm).

Video tutorials#

Note

The videos below were recorded using an old version of SAMSON, so, please be aware that some of the interface has changed.

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 and 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)#

References#

  1. Elisa de Llano, Haichao Miao, Yasaman Ahmadi, Amanda J. Wilson, Morgan Beeby, Ivan Viola, Ivan Barisic. Adenita: Interactive 3D modeling and visualization of DNA Nanostructures. Nucleic Acids Research, Volume 48, Issue 15, September 2020. [paper]
  2. Elisa de Llano, Haichao Miao, Yasaman Ahmadi, Amanda J. Wilson, Morgan Beeby, Ivan Viola, Ivan Barisic. Adenita: Interactive 3D modeling and visualization of DNA Nanostructures. Pre-print at bioRxiv (849976); 2019. [https://doi.org/10.1101/849976]
  3. Haichao Miao, Elisa de Llano, Johannes Sorger, Yasaman Ahmadi, Tadija Kekic, Tobias Isenberg, Meister Eduard Gröller, Ivan Barisic, Ivan Viola. Multiscale Visualization and Scale-adaptive Modification of DNA Nanostructures. IEEE Transactions on Visualization and Computer Graphics, 24(1), January 2018. [paper]
  4. Haichao Miao, Elisa de Llano, Tobias Isenberg, Meister Eduard Gröller, Ivan Barisic, Ivan Viola. DimSUM: Dimension and Scale Unifying Maps for Visual Abstraction of DNA Origami Structures. Computer Graphics Forum, 24(1), 37(3), June 2018. [paper]
  5. Rémi Veneziano, Sakul Ratanalert, Kaiming Zhang, Fei Zhang, Hao Yan, Wah Chiu, Mark Bathe. Designer nanoscale DNA assemblies programmed from the top down. Science, 24 Jun 2016. [paper]
  6. Shawn M. Douglas, Adam H. Marblestone, Surat Teerapittayanon, Alejandro Vazquez, George M. Church & William M. Shih. Rapid prototyping of 3D DNA origami shapes with cadnano. Nucleic Acids Research. [paper]