A typical gel for DNA electrophoresis is 1% agarose. (Gels will still be useful within a margin of error, so don't worry if you are a little off in your measurements.)
1. Determine the final volume you will need, based on the number of gels you will pour. We recommend that you use increments of 50 mLs (e.g. 50mL, 100mL, 150mL). A single gel requires only about 50mL of solution, so base your calculations on how many gels you plan to use. Keep in mind that gels can keep for a while if properly stored so consider pouring them in bulk.
2. From your final volume, calculate the mass of agarose that you need. (Remember that 1% translates into 1.0g of solute in 100mL of solution.) Add the powder to a flask and 1X TBE buffer to final volume. (Choose the appropriate size flask; you'll want one that is significantly larger than your goal volume. For example, a 250 ml flask works well with 50 05 100 mL of solution.)
3. Using a microwave or hot plate, heat and stir until fully dissolved and just short of boiling. The solution will turn from opaque to clear when it is ready.
4. Carefully tape the edges of your gel tray to prevent leakage when the agarose is poured. Place the comb for the wells in the notches at the end of the tray.
5. Let the agarose cool on the bench until it is slightly warmer than a baby's bottle. When the agarose is ready, you can pour it into the trays. Don't wait too long or the agarose will clump. Pour slowly to avoid bubbles! The gel depth should be approximately .5 cm (1/4 inch) to permit sufficient well depth and a reasonable rate of electrophoresis.
6. When the gel has solidified, place in the electrophoresis chamber with the bottom of the gel facing the positive electrode and cover the gel with 1X TBE buffer. Gently remove the tape and the comb. You are now ready to load the gel.
For complete instructions on running an electrophoresis gel, click here.
For visual learners, click here.
For background information on how electrophoresis works, click here.
For explanation of Southern blotting, click here.
For the separation of fragments
You're "gelling" now!
BROUGHT TO YOU BY THE ROARING GEL MEISTERS OF THE 2002 SUMMER