Biomod/2011/Harvard/HarvarDNAnos:Resources
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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
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:
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
