IGEM:Harvard/2006/DNA nanostructures/Notebook/2006-7-16

c3.2 Folding Experiment
Reagents (each expt in respective 0.2 mL PCR tube) Annealing protocol
 * start at 80
 * 60 cycles: wait 2 minutes, decrease 1
 * hold at 4

Latch-closing protocol

 * pipet 20 of expts B and C into respective clean 0.2 mL PCR tubes
 * add 1.0 of 3.2.B and 3.2.C (1.25 mM), respectively
 * incubate at room temp. for 30 min.

Gel analysis

 * 2% agarose gel supplemented to 10 mM
 * 100 mL solution with 5 10 mg/mL EtBr
 * run in 1x TBE supplemented to 10 mM
 * 35 min at 130 V

Results/discussion
 * expts B and C, with and without latches (lanes 4, 5, 7, 8, respectively), may have folded successfully, and run with approximately the same mobility as expt A
 * oligos appear very faintly in lanes 3-10 (appeared brighter before photograph was taken)
 * expts B and C without latches (lanes 4 and 7) appear to have similar motility to the same expts with latches (lanes 5 and 8, respectively), which is not conclusive as to whether the latch design was successful
 * 6-helix bundle (lane 10), as previously observed, has faster motility than p7308 scaffold (lanes 2 and 11)