Applications & Tools

• SphereCAD
• caDNAno
• CanDo
• Maya 3D Design
• Adobe Illustrator
• Adobe Photoshop
• Nucleic Acid Sequence Massager
• J5 Vector Editor
• NuPack
• WolframAlpha
• XPS 2 PDF
• Shawn Douglas' Excel-to-Wiki Converter

Support

• BioMod
• The Wyss Institute
• Harvard University
• Howard Hughes Medical Institute

Selected Literature

Origami container design

• Andersen (2009) - first paper on a DNA origami box: http://www.nature.com/nature/journal/v459/n7243/full/nature07971.html
  • but with caDNAno and multi-layer origami as a design paradigm, the strategy for making boxes becomes very different
• Han et al. (2011) - spherical origami: "DNA Origami with Complex Curvatures in Three-Dimensional Space"
  • basis for our sphere design

Enzyme-free molecular signal amplification

• Zhang (2007) - entropy-driven DNA catalyst paper: http://www.dna.caltech.edu/Papers/entropy_circuits2007.pdf
  • Supplementary Information: http://www.dna.caltech.edu/Papers/entropy_circuits2007supp.pdf
  • Commentary: http://www.sciencemag.org/cgi/content/summary/318/5853/1078
• Zhang (2010): http://dna.caltech.edu/Papers/DNA_catalyst_characterization2010.pdf
• Zhang (2008): http://dna.caltech.edu/Papers/allosteric_catalyst2008.pdf
• Zhang (2011): http://dna.caltech.edu/Papers/linear_classifier2011_LNCS.pdf
• For comparison, see these references on RT-PCR:
  • http://www6.appliedbiosystems.com/support/tutorials/.../rtpcr_vs_tradpcr.pdf

DNA logic gates

• Ogawa (2008): http://pubs.rsc.org/en/Content/ArticleLanding/2009/CC/b910288d
  • log-in through countway.harvard.edu to download article
• Wang (2011): http://onlinelibrary.wiley.com/doi/10.1002/ijch.201000069/pdf
  • good review article on logic gate design for biosensors

Gold nanoparticles

• Rothemund (2009) - http://www.nature.com/nnano/journal/v5/n2/full/nnano.2009.450.html
  • good protocols for binding AuNP-DNA to origami

Origami applications

• About introducing origami to cells