RNA formaldehyde gels

Procedure

Prepare gel box:

• Clean gel box and combs etc with detergent, then dionized water.
• Then incubate the gel box and components in 10% H2O2 (hydrogen peroxide, stored in cold room) for 30 minutes.
• Rinse box thoroughly with DEPC water.

For making gel and preparing samples:

• Your should pour (and ideally run) the gel in the hood, since the gel contains formaldehyde. [see protocol from Maniatis (original edition)—attached.]

Running the gel:

Just before loading the samples:

• Heat your samples (see step 3 Maniatis protocol) for 15 minutes at 65 or 70 C and then put immediately on ice. The add loading buffer (see step 4 Maniatis).
• ALSO, pre-run the gel at 50 V for 10 minutes

• Load samples.
• For mini gels, run at 30V for 4-5 hours. (for best results place the gel on a bed of ice to keep it cold)
• Stain in EtBr 1 hour to overnight ( 5 µl of 10 mg/ml solution per 50 ml DEPC water)
• Destain in DEPC water for 1-2 hours (change water 2x during this time)
• Take picture (Karla's lab has a good digital documentation system)