IGEM:Harvard/2006/DNA nanostructures/Notebook

Daily notebook

<calendar> name=IGEM:Harvard/2006/DNA_nanostructures/Notebook date=2006/07/01 view=threemonths format=%name/%year-%month-%day weekstart=7 </calendar>

Stock Oligos: reconstituted (50uM for non-biotinylated oligos, 200uM for biotinylated) oligos in wells or tubes
Pre-working Stocks: mixtures of 10uM of each oligo needed for a "class" of oligos (ex. core, barrel, lid1, lid2); for non-biot oligos, this requires 10uL of each of the necessary stock oligos, for biot-oligos, this requires 2.5uL of stock oligos + 7.5uL dH2O
Working Stocks: mixtures of however-many-oligos-are-in-each-class uL (ex. if there are 94 oligos in the core class of 3.2's design, use 94uL of the core pre-working stock), diluted to a total of 200uL of solution (each individual oligo will be at 250nM)

what percent gel? 10% to 20% polyacrylamide gels, no SDS (but would make for a good control)
what incubation conditions?
how much protein and DNA? protein at 1 μM, DNA at 2 μM
Coomassie stain

number	thrombin	aptamer	nanotube	DNA-stained prediction	protein-stained prediction
0	-	-	-	no bands	no bands
1	-	-	+	slow band (nanotube)	no bands
2	-	+	-	fast band (aptamer)	no bands
3	-	+	+	slow band (aptamer-nanotube), traces of fast band (aptamer)	no bands
4	+	-	-	no bands	fast band (thrombin)
5	+	-	+	slow band (nanotube)	fast band (thrombin)
6	+	+	-	medium band (aptamer-thrombin), fast band (aptamer)	medium band (aptamer-thrombin), traces of fast band (thrombin)
7	+	+	+	very slow band (thrombin-aptamer-nanotube), slow band (aptamer-nantotube), traces of fast band (aptamer)	very slow band (thrombin-aptamer-nanotube), medium band (aptamer-thrombin), traces of fast band (thrombin)

Macaya's and Bock's selection buffer: 20 mM Tris-acetate, pH 7.4, 140 mM NaCl, 5 mM KCl, 1 mM CaCl₂, 1 mM MgCl₂
Liu's incubation buffer: 40 mM Tris, 20 mM CH₃COOH, 2mM EDTA, 12.5 mM (CH₃COO)₂Mg, pH 8.0
Liu's PAGE buffer: 1x TAE/Mg²⁺