Biomod/2011/Harvard/HarvarDNAnos: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

Origami container design

 * 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. Science paper: "DNA Origami with Complex Curvatures in Three-Dimensional Space"

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
 * Supp: http://www.dna.caltech.edu/Papers/entropy_circuits2007supp.pdf
 * Commentary: http://www.sciencemag.org/cgi/content/summary/318/5853/1078
 * http://dna.caltech.edu/Papers/DNA_catalyst_characterization2010.pdf
 * http://dna.caltech.edu/Papers/allosteric_catalyst2008.pdf
 * 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

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