Biomod/2011/Harvard/HarvarDNAnos:Resources: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
No edit summary
 
(11 intermediate revisions by 3 users not shown)
Line 1: Line 1:
{{Template:Biomod/2011/Harvard/HarvardDNAnos}}
{{Template:Biomod/2011/Harvard/HarvardDNAnos}}
<div style="padding: 10px; width: 800px; border: 5px solid #333333;">
=Applications & Tools=
=Applications & Tools=
*[[Biomod/2011/Harvard/HarvarDNAnos:SphereCAD | SphereCAD]]
*[[Biomod/2011/Harvard/HarvarDNAnos:SphereCAD | SphereCAD]]
Line 14: Line 12:
*[http://www.wolframalpha.com WolframAlpha]
*[http://www.wolframalpha.com WolframAlpha]
*[http://www.xps2pdf.org/ XPS 2 PDF]
*[http://www.xps2pdf.org/ XPS 2 PDF]
*[http://office.microsoft.com/en-us/excel/ Microsoft Excel]
*[http://excel2wiki.net/ Shawn Douglas' Excel-to-Wiki Converter]
*[http://excel2wiki.net/ Shawn Douglas' Excel-to-Wiki Converter]


Line 22: Line 19:
*[http://www.harvard.edu/ Harvard University]
*[http://www.harvard.edu/ Harvard University]
*[http://www.hhmi.org/ Howard Hughes Medical Institute]
*[http://www.hhmi.org/ Howard Hughes Medical Institute]
*[[Etiquette|OpenWetWare Etiquette]]
=Literature=
==Fluorophores==
*http://en.wikipedia.org/wiki/Fluorophore
*View fluorescence spectra: http://www.invitrogen.com/site/us/en/home/support/Research-Tools/Fluorescence-SpectraViewer.html
*Order fluorphore-labeled DNA strands: http://www.idtdna.com/Catalog/Modifications/Modificationhome.aspx
==Aptamers==
*Aptamer beacon links
**Design strategies for aptamer-based biosensors: http://www.mdpi.com/1424-8220/10/5/4541/pdf
**A great paper on the kinetics/mechanism: http://www.molecular-beacons.org/download/hall,bb09(103)1049.pdf
**Reminiscent of what Shwinn was talking about with free radicals: http://www.molecular-beacons.org/download/lerga,aca08(610)105.pdf


=Selected Literature=
==Origami container design==
==Origami container design==
*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
**But with caDNAno and multi-layer origami as a design paradigm, the strategy for making boxes becomes very different
**but with caDNAno and multi-layer origami as a design paradigm, the strategy for making boxes becomes very different
*Han et al. Science paper: [http://www.sciencemag.org/content/332/6027/342.full "DNA Origami with Complex Curvatures in Three-Dimensional Space"]
*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==
==Enzyme-free molecular signal amplification==
*Entropy-driven DNA catalyst paper (try to understand the mechanism and driving forces in detail!): http://www.dna.caltech.edu/Papers/entropy_circuits2007.pdf
*Zhang (2007) - entropy-driven DNA catalyst paper: http://www.dna.caltech.edu/Papers/entropy_circuits2007.pdf
**Supp: http://www.dna.caltech.edu/Papers/entropy_circuits2007supp.pdf
**Supplementary Information: http://www.dna.caltech.edu/Papers/entropy_circuits2007supp.pdf
**Commentary: http://www.sciencemag.org/cgi/content/summary/318/5853/1078
**Commentary: http://www.sciencemag.org/cgi/content/summary/318/5853/1078
*http://dna.caltech.edu/Papers/DNA_catalyst_characterization2010.pdf
*Zhang (2010): http://dna.caltech.edu/Papers/DNA_catalyst_characterization2010.pdf
*http://dna.caltech.edu/Papers/allosteric_catalyst2008.pdf
*Zhang (2008): http://dna.caltech.edu/Papers/allosteric_catalyst2008.pdf
*http://dna.caltech.edu/Papers/linear_classifier2011_LNCS.pdf
*Zhang (2011): http://dna.caltech.edu/Papers/linear_classifier2011_LNCS.pdf
*For comparison, see these references on RT-PCR:  
*For comparison, see these references on RT-PCR:  
**http://www6.appliedbiosystems.com/support/tutorials/.../rtpcr_vs_tradpcr.pdf
**http://www6.appliedbiosystems.com/support/tutorials/.../rtpcr_vs_tradpcr.pdf


==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 Nanoparticles==
==Gold nanoparticles==
*include Rothemund paper on hybridizing AuNPs
*Rothemund (2009) - http://www.nature.com/nnano/journal/v5/n2/full/nnano.2009.450.html
**good protocols for binding AuNP-DNA to origami


==Other==
==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

<html> <head> 

 <style>
  1. column-one { display:none; width:0px;}

.container{background-color: #f5f5f5; margin-top:50px} .OWWNBcpCurrentDateFilled {display: none;}

  1. content {width: 0px; margin: 0 auto auto 0; padding: 1em 1em 1em 1em; align: center;}
  2. column-content {width: 0px; float: left; margin: 0 0 0 0;padding: 0;}

.firstHeading {display:none; width:0px;}

  1. globalWrapper{width:1280px; margin:auto}

body {background: #F0F0F0 !important;}

  1. column-one {display:none; width:0px;background-color: #f0f0f0;}
  2. content{border:none;margin: 0 0 0 0; padding: 1em 1em 1em 1em; position: center; width: 800px;background-color: #f0f0f0; }

.container{ width: 800px; margin: auto; background-color: #f0f0f0; text-align:justify; font-family: helvetica, arial, sans-serif; color:#f0f0f0; margin-top:25px; }

  1. bodyContent{ width: 1267px; align: center; background-color: #f0f0f0;}
  2. column-content{width: 1280px;background-color: #f0f0f0;}

.firstHeading { display:none;width:0px;background-color: #f0f0f0;}

  1. header{position: center; width: 800px;background-color: #f0f0f0;}
  2. footer{position: center; width:1280px;}
 </style>

</head> </html>

<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>

Home              Mission              Process              Designs              Results              Resources              Team

Applications & Tools

Support

Selected Literature

Origami container design

Enzyme-free molecular signal amplification

DNA logic gates

Gold nanoparticles

Origami applications

Retrieved from "https://openwetware.org/mediawiki/index.php?title=Biomod/2011/Harvard/HarvarDNAnos:Resources&oldid=560100"