IGEM:Harvard/2006/DNA nanostructures/Notebook/2006-7-12

Results from 7/11 Thrombin-Binding Experiment
 * gels removed at 10:00 am: appear to have run off the gel (very hard to tell since they were so faint to begin with)
 * removed gels from plastic
 * cut bottom of gel where it sticks out of narrow hole at the bottom
 * pried two plastic sides apart (gel now stuck to one side)
 * loosen top edge by sliding flat tool under it a bit.
 * make sure the very bottom is completely cut
 * run it under water over the a plastic tupperware container - move it back and forth left to right - eventually the gel should come free into the container.
 * hold the gel in the container while you pour the water out.
 * stained with GelCode Blue Stain (Coomassie blue) (in brown bottle in first 4 fridge)
 * pour enough Coomassie blue over it to cover the gel.
 * put the lid on the tupperware and put it on the rocker for about 20 minutes.

Protein- and DNA-staining control experiment
 * goal: to load varying concentrations of thrombin onto a gel and stain with Coomassie blue in an attempt to image the protein, and various concentrations of DNA onto a gel and stain with a yet-to-be determined stain to image the DNA
 * all reagents were mixed in individual 0.2 mL PCR tubes
 * 10-20% Invitrogen polyacrylamide gel run at 25 V for 2.5 h.
 * gel catridge opened and cut between protein and DNA sections
 * was cut before removal from one side of cartridge and led to some tearing during removal from that side, cut after removal next time
 * protein section was rocked in GelCode Blue Stain for 1 hr.
 * DNA section was rocked in 100 mL Tris-glycine buffer with 10 of 10 mg/mL ethidium bromide for 1 hr.
 * results
 * loading dye diffused about 3 mm in all directions into the gel
 * neither the protein nor the DNA imaged on the gel
 * discussion
 * when you don't press the "run/stop" button on the power supply so that the light next to "run" is lit, you're not supplying any power for electrophoresis. we hadn't.