nb-sdouglas

Background

In 2004 William Shih published a paper titled A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron Nature 427, 618-621. This design serves a nice testbed for cadnano development, as it includes several struts based on paranemic (px) crossovers.

Questions

1. What is the exact base-level design of the octahedron?
2. Can we port the octahedron design into cadnano and then export an 'abstract' sequence that matches the original base-pairing relationships, if not exact sequence?

Setup

1. For The base-level design, we will import with the original schematic from Figure 1 into Illustrator, re-arrange it for easier editing, annotate the sequence lengths for every domain of the structure, and create a corresponding Schlegel diagram to keep track of overall arrangement and connectivity of the wireframe struts.
2. Next we can use the schematic as a reference for recreating the same design in cadnano.
3. Cadnano only exports abstract sequences at the moment, which encode the base-pairing relationships but not actual sequences. Downstream the base pairs must still be assigned a specific nucleotides prior to synthesis. We can easily write a python script to determine if a nucleotide sequence is an instance of an abstract sequence.

Schematics made as shih-px-octa.ai, exported as a png: Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

some other text Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

Results

• Schematics made as shih-px-octa.ai, exported as a png:

• Cadnano design created with the schematic as reference. We lose the color information in the cadnano diagram due to the way that strands are currently colored (i.e. joining a source and target strand causes the target strand to inherit the source strand's color. I recorded a mov of connecting all the struts.
• Exported various stages of the cadnano design (.c25 files... I just picked 'c25' as a temporary extension for the current dev version of cadnano).

Comments / Next steps

1. Didn't quite finish the sequence / abstract sequence comparison.