Gel Electrophoresis
Gel electrophoresis is a method utilized to visualize DNA and is how we will determine if the PCR reactions yielded the correct results. DNA is pushed through a gel matrix by an electrical current. Because DNA is negatively charged, the positive current will cause the DNA to migrate down the gel toward the positive electrode, separating fragments into discrete bands. These DNA bands are visualized by adding a stain activated by UV light.
Prepare the gel:
1) Measure out the appropriate amount of agarose to create the desired density gel. Add the agarose to a flask.
*For 100mL of 1% gel
– 1 g of agarose
2) Add the appropriate amount of 1x TAE buffer to create the desired density gel.
3) Heat the bottle in the microwave in 1 minute increments. Watch the flask to ensure the agarose does not boil over. Occasionally remove the bottle and swirl it gently to distribute the heat.
*Be careful, as the gel heats it will produce a lot of steam!
4) Allow the agarose to cool until it can be handled comfortably with your bare hand. Do not allow it to over-cool, as it will begin to solidify.
5) As the agarose cools, tape the gel box. Be sure that the tape is well sealed to prevent leaks.
6) Add SYBR Safe dye to the melted gel and swirl it to mix. The gel will be a slightly pink color. Pour it into the gel box.
*1uL of SYBR Safe for every 10mL of gel
7) Allow the gel to completely solidify. It will be slightly opaque and will not move when you tap the gel box.
8) Remove the tape and the comb load it into the gel tray.
9) Add enough 1xTAE buffer to completely cover the surface of the gel.

Running the gel:
1) Prepare the DNA samples
* 2μL of 6x loading dye (blue dye) to 5μL of the DNA sample
2) Carefully load the ladder into the gel. Use 7μL of the ladder.
Use the 1Kb ladder for checking DNA extractions (labeled “1%”)
Use the low range ladder for checking PCR (labeled “2%”)
3) Load the DNA samples into the well of the gel. Be careful not to puncture the bottom of the well and avoid bubbles, as this will cause the sample to float out of the well.
4) Plug in the power supply and turn on the gel. Run the gel for ~20-30 min at 170V or until the dye front has reached the desired position on the gel.
*Position of the dye front is more important than time. It may take more or less time to get your gel to the right position, so check it regularly
5) Visualize the gel using a UV transilluminator.