IGEM:Harvard/2006/DNA nanostructures/Notebook/2006-7-14

Pre-working stocks

 * Mix 10 of each 50  stock oligo

Make c3.2 working stocks
Final concentration of each oligo in working stocks is 250 nM.

c3.2 Folding Experiment
Reagents Annealing protocol
 * 9 p7308 scaffold = (10 nM)/(44 nM) * 40
 * 16 oligos (3.2.A) = (100 nM)/(250 nM) * 40
 * 4 10x folding buffer (500 mM HEPES pH 7.5, 500 mM NaCl, 100 mM )
 * 11 d
 * total volume: 40
 * start at 80
 * 60 cycles: wait 2 minutes, decrease 1
 * hold at 4

Gel analysis

 * 2% agarose gel supplemented to 10 mM
 * run in 1x TBE supplemented to 10 mM
 * 35 min at 130 V
 * 15 min in 1x TBE, 10 mM, 100 /mL EtBr (forgot to put it in the gel)
 * results
 * ladder, scaffold, and oligos all appear as expected
 * folding reaction mixture shows oligo smear (expected) as well as a band that runs slower than the scaffold