Biomod/2011/Harvard/HarvarDNAnos:Resources: Difference between revisions
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{{Template:Biomod/2011/Harvard/HarvardDNAnos}} | {{Template:Biomod/2011/Harvard/HarvardDNAnos}} | ||
=Applications & Tools= | =Applications & Tools= | ||
*[[Biomod/2011/Harvard/HarvarDNAnos:SphereCAD | SphereCAD]] | *[[Biomod/2011/Harvard/HarvarDNAnos:SphereCAD | SphereCAD]] | ||
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*[http://www.hhmi.org/ Howard Hughes Medical Institute] | *[http://www.hhmi.org/ Howard Hughes Medical Institute] | ||
=Literature= | =Selected Literature= | ||
==Origami container design== | ==Origami container design== | ||
*Andersen (2009) - first paper on a DNA origami box: http://www.nature.com/nature/journal/v459/n7243/full/nature07971.html | *Andersen (2009) - first paper on a DNA origami box: http://www.nature.com/nature/journal/v459/n7243/full/nature07971.html | ||
| Line 41: | Line 38: | ||
==DNA logic gates== | ==DNA logic gates== | ||
*http://pubs.rsc.org/en/Content/ArticleLanding/2009/CC/b910288d | *Ogawa (2008): http://pubs.rsc.org/en/Content/ArticleLanding/2009/CC/b910288d | ||
**log-in through countway.harvard.edu to download article | **log-in through countway.harvard.edu to download article | ||
*http://onlinelibrary.wiley.com/doi/10.1002/ijch.201000069/pdf | *Wang (2011): http://onlinelibrary.wiley.com/doi/10.1002/ijch.201000069/pdf | ||
**good review article on logic gate design for biosensors | **good review article on logic gate design for biosensors | ||
==Gold | ==Gold nanoparticles== | ||
*Rothemund (2009) - http://www.nature.com/nnano/journal/v5/n2/full/nnano.2009.450.html | *Rothemund (2009) - http://www.nature.com/nnano/journal/v5/n2/full/nnano.2009.450.html | ||
**good protocols for binding AuNP-DNA to origami | **good protocols for binding AuNP-DNA to origami | ||
==Origami | ==Origami applications== | ||
*[http://www.fiercebiotech.com/press-releases/dna-cages-can-survive-inside-living-cells About introducing origami to cells] | *[http://www.fiercebiotech.com/press-releases/dna-cages-can-survive-inside-living-cells About introducing origami to cells] | ||
Latest revision as of 21:54, 1 November 2011
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<html><center><a href='http://openwetware.org/wiki/Biomod/2011/Harvard/HarvarDNAnos'><img src=http://openwetware.org/images/1/1c/Hdnaheader.jpg width=800px></a></center></html>
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
