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From 2012.igem.org

Agarose Gel Electrophoresis

Making the Gel

1. Weigh out the appropriate amount of agarose into a 250 mL conical flask. Add 50 mL of 0.5xTBE , swirl to mix
2. Microwave for about 1 minute to dissolve the agarose (stop it after 45 seconds and give it a swirl is generally a good idea
3. Leave it to cool on the bench for 5 minutes down to about 60°C (just too hot to keep holding in bare hands).
4. Add 1 µL of ethidium bromide (10 mg/mL) and swirl to mix
5. Pour the gel slowly into the tank. Push any bubbles away to the side using a disposable tip.
6. Insert the comb and double check that it is correctly positioned.
7. Leave to set for at least 30 minutes, preferably 1 hour, with the lid on if possible.
8. Pour 0.5x TBE buffer into the gel tank to submerge the gel to 2–5 mm depth. This is the running buffer

The amount of agarose to use in your gel depends on the DNA in question. Use the following table as a rough guide:

Agarose Concentration (g/100mL)	Optimal DNA Resolution (kb)
0.5	1 - 30
0.7	0.8 - 12
1.0	0.5 - 10
1.2	0.4 - 7
1.5	0.2 - 3

Preparing the samples

1. Measure out the appropriate mass of agarose into a beaker with the appropriate volume of buffer (see the documentation for your gelbox -- 50mL makes a good, thick gel for a 7x10cm gelbox).
2. Microwave until the agarose is fully melted. This depends strongly on your microwave, but a 90 seconds at full power or 3 minutes at half power seem to provide decent results. As long as you do not burn the agarose and nothing bubbles over, this step is robust.
3. From here on, a heat protective glove should be used any time the heated flask must be touched!
4. Let the agarose cool on the bench for ~5 minutes.
5. At this point add your DNA visualization reagent, e.g., ethidium bromide at a volume appropriate for the amount of melted agarose. This amount will depend on the concentration of the stock solution of the stain.
6. The flask will cool unevenly (surface first), so you must be careful not to cause ripples and bubbles, and should therefore be periodically swirled while the agarose is cooling.
7. Pour the agarose solution into the gel casting apparatus. A pipette tip should be used to pop or shove to the side any bubbles.
8. After bubbles have been popped, the comb should be inserted, and the gel should be allowed to cool for about 30 minutes, until solid.
9. Because removal of the comb too early can cause the wells to collapse on themselves, one should always poor a gel prior to prepping the samples.