IGEM:Harvard/2006/DNA nanostructures/Notebook

• Project Overview
• Designs
• Notebook
• Protocols
• Presentations
• Literature

<calendar> name=IGEM:Harvard/2006/DNA nanostructures/Notebook date=2006/07/01 view=threemonths format=%name/%year-%month-%day weekstart=14 </calendar>

Thrombin-aptamer experiments

Questions / procedures

• 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

Experiments

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)

Buffers

• 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⁺