Biomod/2011/Harvard/HarvarDNAnos:Resources: Difference between revisions
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{{Template:Biomod/2011/Harvard/HarvardDNAnos}} | {{Template:Biomod/2011/Harvard/HarvardDNAnos}} | ||
=Applications & Tools= | |||
*[[Biomod/2011/Harvard/HarvarDNAnos:SphereCAD | SphereCAD]] | |||
*[http://cadnano.org/ caDNAno] | *[http://cadnano.org/ caDNAno] | ||
*[http://cando.dna-origami.org/ CanDo] | *[http://cando.dna-origami.org/ CanDo] | ||
*[http://usa.autodesk.com/maya/ Maya 3D Design] | *[http://usa.autodesk.com/maya/ Maya 3D Design] | ||
*[http://success.adobe.com/en/na/sem/products/illustrator.html?kw=p&sdid=FNRPC&skwcid=TC|22174|adobe%20illustrator||S|b|7724724036 Adobe Illustrator] | *[http://success.adobe.com/en/na/sem/products/illustrator.html?kw=p&sdid=FNRPC&skwcid=TC|22174|adobe%20illustrator||S|b|7724724036 Adobe Illustrator] | ||
*[http://www. | *[http://www.photoshop.com/ Adobe Photoshop] | ||
*[http:// | *[http://greengenes.lbl.gov/cgi-bin/nph-massage.cgi Nucleic Acid Sequence Massager] | ||
*[http://j5.jbei.org/VectorEditor/VectorEditor.html J5 Vector Editor] | |||
*[http://www.nupack.org NuPack] | |||
*[http://www.wolframalpha.com WolframAlpha] | |||
*[http://www.xps2pdf.org/ XPS 2 PDF] | |||
*[http://excel2wiki.net/ Shawn Douglas' Excel-to-Wiki Converter] | |||
= | =Support= | ||
*[http://www.biomod.net BioMod] | *[http://www.biomod.net BioMod] | ||
*[http://wyss.harvard.edu/ The Wyss Institute] | *[http://wyss.harvard.edu/ The Wyss Institute] | ||
*[[ | *[http://www.harvard.edu/ Harvard University] | ||
*[http://www.hhmi.org/ 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: [http://www.sciencemag.org/content/332/6027/342.full "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== | |||
*[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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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