Along the navigation bar, hover over "Submit a design". You will see two options:
This interface currently supports structures with rotational symmetry only. Thus, geometries can be drawn in an unrevolved representation.
The left-hand side of the window can be used to place nodes. It is a cartesian plane where the horizontal axis corresponds to the circumference of the helical ring and the vertical axis corresponds to the height positioning of the ring. The right-hand side is a live preview of the shape after revolving drawn nodes. Only a half cross-section is displayed to better show the revolved geometry of each node.
Color labeling of nodes are a visual guide to ensure that adjacent helices are anti-parallel. To change the direction of a helix, click on the node using the Right Mouse Button, or in the text input interface, complement the direction bit (1 or 0).
Refer below to Submission Options to continue.
The text input interface is accessible from the same screen as the Draw Input by clicking the Swap Input Interface button.
This input is an alternate representation of drawing nodes with respect to the provided horizontal and vertical axis values. The format of each line is:
Circumference, Height, 5'-3' direction
Note: The 5'-3' direction of adjacent helices must be anti-parallel. 1 and 0 are opposite representations of the 5'-3' direction and should be alternated.
You may paste CSV data into the window to save and load structures. Snapping is not enforced for text input, except if you swap back to Draw Input.
Refer below to Submission Options to continue.
DNAxiS can attempt to automatically determine the profile you would like to revolve into an axially symmetric DNA origami nanostructure. This is best used when you want generated shapes to match existing shapes you are working with elsewhere.
If no changes are intended to be made, refer below to Submission Options to continue.
Several options are available that provide high-level control over the subsequent design process. The basic options are setting the desired staple length ranges and the preferred scaffold sequence. Both are set to common values by default.
A scaffold should be selected such that the structure produces the least length of unused scaffold. If more than the selected scaffold is required, the software will attempt to create a multi-scaffold structure using additional, orthogonal scaffold sequences. If the total structure is larger yet, the process will likely fail. Please submit feedback if you would like to use a longer, custom scaffold.
If you would like a link to download the design files sent to your email, you can optionally choose to provide your email address.
Advanced options are also available, but a set of defaults are provided that can typically produce structures with high reliability.
After setting options, click "Next" and proceed with Staple and Scaffold Routing.
Each of the previous input options proceed into the same following pipeline.
The connections page asks you to declare all helices in the design that should be treated as adjacent. Staple crossovers will also be placed between the helixes as declared by the edges on this page.
An automatic routing is initially provided based on nearest neighbors seen from each helix that is within the interhelical distance. If this is incorrect, you may use the Clear button on the right to clear all edges (nodes will remain). The Undo button will clear the most recently drawn edge.
Click from one node to another to indicate that the algorithm should look for STAPLE crossovers between those two helices. You can also repeat this action to remove a specific edge. Hover over the "Help" button for a reminder on using this step of the interface.
Once you are finished, click "Next" and proceed to the Pathway step.
The pathway page asks you to declare all helices in the design that should be routed in order by the scaffold strand. Adjacent helices as declared in the previous step are recorded and displayed as faint red lines as a reminder.
The node graph here cannot have a cycle. The tail of the scaffold strand is expected to be at the break. The graph must be otherwise fully connected. As before, you may use the Clear button on the right to clear all edges (nodes will remain). The Undo button will clear the most recently drawn edge.
Click from one node to another to indicate that the algorithm should look for SCAFFOLD crossovers between those two helices. You can also repeat this action to remove a specific edge.
The red guidelines indicate where you set staple crossovers in the previous step.
Scaffold crossovers should:
Once you are finished, click "Next", which will submit the job to the server. Simple structures may take no longer than a minute, but larger and complex structures utilizing simulating annealing as the crossover routing algorithm can take up to an hour to complete. If you did not supply an email address, do not close the page. Once the processing is done, the page will be reloaded and provide a download link. The link is unique per job and cannot be recovered if you close the page.
The .conf and .top files that are downloaded as output can be viewed and also further edited in oxView.
To create your generated DNA origami,
Below are several vendors you may consider and regions they serve as well as several example synthesis conditions from :
(Feel free to let us know your preferred vendors and they can also be added to the list.)
Disclaimer: There are not always consistent conditions for synthesizing your DNA origami, and it may be to your benefit to compare several at once.
Annealing buffer, 1XTAE-Mg2+
 Daniel Fu, Raghu Pradeep Narayanan, Abhay Prasad, Fei Zhang, Dewight Williams, John S. Schreck, Hao Yan, John Reif. Automated Design of 3D DNA Origami with Non-Rasterized 2D Curvature. (Under Revision), 2022.