For most procedures, a 1% agarose gel is sufficient. If you need to separate smaller pieces of DNA fragments (<1 kb) you may wish to use a 1.5% or 2% gel. If you wish to separate larger fragments, you may wish to use a 0.8% gel.

1. You will need to make enough electrophoresis buffer to make and run the gel. The stock solution is 5X TBE buffer and the running buffer is 0.5X TBE.
2. The rig that we use holds 50mL of agarose and has a 10 well comb. Place the gel-forming tray inside the buffer tank so that the rubber gaskets fit tight against the side of the tank. The sides of the tank will create a dam so that no agarose will leak from the tray.
3. Pour the appropriate amount of 0.5X buffer into a 100mL Erlenmeyer flask. Weigh out the appropriate amount of agarose and add it to the flask. For a 1% gel, use 50mL of buffer and .5g of agarose.
4. Place the flask into the microwave and set the time for one minute. Watch the solution and when it starts to boil, stop the microwave. Do not boil it too long or it will boil over. Use a pair of hot mitts to remove the flask. Gently swirl it and place it back into the microwave. Heat the agarose/buffer until it returns to a boil. Remove and swirl. Repeat process until all agarose has dissolved (look carefully, it may be translucent but not in solution).
5. Put on a pair of gloves and add 1 uL of ethidium bromide per 10 mL gel and swirl. The stock solution is 10 mg/mL. Dispose of the pipet tip in the ethidium bromide trash.
6. Allow the gel solution to cool until you can pick up the flask without using the hot mitts. Pour the gel into the gel forming tray. If there are any bubbles, use comb to pop and/or move them to the end of the gel where it won’t affect how the gel runs. Place the comb in the tray. Cover gel rig in foil.
7. When the gel has solidified (about 20 minutes), gently remove the gel forming tray and turn it 90 degrees. Place it back into the tank.
8. Add 0.5X buffer until the entire gel is covered with about 1 mm of buffer. Using both hands, grasp the top of the comb between your thumb and index finger and slowly pull the comb straight upwards.
9. Mix loading dye with solution – 5uL for every 10uL of solution. Generally, each well can hold about 30uL total. If you are only using the gel for evaluation purposes, 10uL solution with 5uL dye is plenty. If you need to gel-extract, you should do about 20uL solution and 10uL dye, and can even increase this and fill multiple wells to increase yield.
10. Load your DNA samples into the well. You will also want to load a set of standards on the gel. Check the concentration of your ladder to determine how much you should dilute it down with nuclease free water. You should load standards on both sides of the gel in case your gel runs unevenly. If you know you will be gel extracting later, skip a well between different DNA samples to make sure that the DNA doesn’t mix.
11. Place the lid on the electrophoresis chamber, attach the electrodes, and set the power supply for 100V (varies with gel concentration). Depending on the samples, the gel will be done running in approximately one hour. You want it to run about 2/3 along the gel.
12. When the gel has run a sufficient distance, put on a pair of gloves and remove the gel tray from the electrophoresis chamber. Cradle the open sides of the tray with the index finger on each hand. The gel can easily slide out of the tray.
13. If you wish to photograph the gel, proceed to the UV light box at the digital camera set-up. If you are isolating a DNA fragment, use a hand held UV light set to long wave. In both cases, you will need to wear gloves to protect your eyes form the UV light.
14. When you have finished with your gel, dispose of it in the ethidium bromide waste. Dump the running buffer into the sink and rinse the chamber and gel forming tray with deionized water.