Preparing Gels for Electrophoresis

• We provide you with agarose to prepare 1% gels for your students (the Teacher’s Guide has instructions for 0.8% gels, either will work). A 1% gel is 1 gram of agarose for every 100 mL of solution.  

• The amount of gel needed depends on your electrophoresis system.

• For this example we are making 25mL per gel, one gel per lab group, for 8 lab groups:

  • 25mL * 1 class * 8 lab groups = 200mL. We’ll make a little extra in case of spills, etc, so we’ll make 220mL of agarose solution.

  • Since we need 1g of agarose for every 100mL of solution, we will need 2.2 g of agarose for a 220mL solution. Measure 2.2g of agarose, then bring it up to volume (220mL) by adding 220mL of 1X SB. 

• Heat the solution carefully on a hot plate or in a lab-only microwave. The solution should come close to, but not reach, boiling. Solution should go from cloudy to clear, with no small particles (lenses) visible when held up to the light. In a microwave, heat one minute, swirl solution, then heat in 15-second intervals swirling the solution in between. Use a wadded up paper towel or small inverted beaker to cover the flask while heating and prevent evaporation but allow heat and pressure to escape

Using GelGreen (Lab 4/4a and PCR ONLY): 

• GelGreen is a DNA stain, used to make the DNA fragments in samples visible. There is no DNA in Lab 1, so please do NOT use GelGreen for that lab.

• GelGreen is temperature- and light-sensitive, so it needs to be stored at room temperature and away from light. We provide GelGreen in an amber-colored microcentrifuge tube, with your dry goods (agarose, autoclave bags, etc). The colored tube prevents light from damaging the GelGreen while it is being stored.

• GelGreen should be added to the agarose solution once it has been prepared and cooled (to about 60C), just before you pour the gels. It is provided at 10,000X concentration and should be used at 1X concentration. This means:

  • 1µL GelGreen per 10mL of agarose solution\

• Once the GelGreen has been added to the flask of agarose solution, gently swirl the flask a few times to mix, then pour the gels. Once the gels have set, they should be stored at room temperature away from light (e.g. in a cabinet, covered with a box, etc.). The GelGreen will degrade with time, even in proper storage conditions. We do not recommend making gels with GelGreen more than two days in advance.