Biomod/2011/Harvard/HarvarDNAnos:caDNAnoFiles

caDNAno File Repository

Dear Members of the DNA Origami Community: Please feel free to upload your .JSON files here!

Structures from the literature

Sphere

• JSON file: Media:Sphere match.json
• Literature reference: [recent Science paper by Han et al.]
• Scaffold sequence propagation instructions: add Media:M13mp18_new.txt‎ as a custom sequence
• See this excel file for a way to map between caDNAno coordinates, Han's coordinate system, theta/phi position, and the direction the staple helix is pointing

Tall Rectangular Origami

• JSON file: Media:rothemund-tallrect.json
• Literature reference: http://www.nature.com/nature/journal/v440/n7082/abs/nature04586.html

Rectangular Origami

• JSON file: Media:rothemund-rect.json
• Literature reference: http://www.nature.com/nature/journal/v440/n7082/abs/nature04586.html

Long Rectangular Origami

• JSON file: Media:jungmann-lro.json
• Literature reference: http://pubs.acs.org/doi/abs/10.1021/nl103427w

Structures from Harvard BioMod 2011

• Barrel: caDNAnoSQ file
• Lid: caDNAnoSQ file
  • Staples: Excel file
• Sphere: caDNAnoSQ file
  • Staples: Excel file

Scaffold Permutation Analysis

For reverse engineering of origami without caDNAno specifications into JSON format

• This Python script can be used to determine if reverse-engineered staples match those provided by the literature reference:
  • Media:Sphere debug.zip
• Guidelines:
  • You'll need to match the file name convention and directory structure in the .zip file

SphereCAD

• See here