Gel electrophoresis is a method used in the laboratory to separate molecules (either proteins or nucleic acids) by size or some other physical attribute. The smaller the molecule the faster it is, so in the case of the orchids the electrophoresis was used to determine slow (large) or fast (small) alleles.

During electrophoresis the molecules are forced to move through a substance called Agarose Gel by applying electrical current to the gel. This electrical current is attached at both ends of the gel, one end repels the molecules whilst the other end’s electrode is simultaneously attracting the molecules. This causes a frictional force in the gel and the gels acts as a sieve. The smaller molecules through faster than the larger ones so you end up with a graded array of molecules, the largest at the top and the smallest at the bottom.

Agarose is a natural colloid, a chain of sugar molecules extracted from seaweed.

This is a picture of the type of seaweed used to produce agarose.

(Picture from: Biology, 3rd. Edition, by Campbell)

Preparing for electrophoresis isn’t hard but it is specific and there are several stages that have to be gone through with a lot of care and precision.

Stage 1: A glass plate is used eventually to receive the gel you make. This must be sealed at all borders with tape to prevent the liquid gel from leaking out.

Prepare an adequate amount of this buffer solution to fill the electrophoresis tank and to prepare the gel.

Stage 4: Heat the agarose solution in a microwave oven and allow all of the grains to dissolve. This will only happen with heat.

The gel will take 30 to 40 minutes at room temperature to set. Pull out the comb and remove the tape from around the plate.

Stage 6: Place the plate and gel in the electrophoresis tank till it is covered by approximately 2mm of solution. The tops of the wells made by the comb should be submerged.

This is a time consuming and tedious process but not terribly hard once you get a rhythm going. It is important to note the well number and the sample number for later comparison, as it is easy to get the finished gel upside down and all the results will be reversed!

Stage 9: Close the lid of the tank and attach the electrodes, making sure that they are on the correct ends and that the sample is orientated correctly with respect to current flow….DNA always migrates towards the anode and away from the cathode. Turn on the machine and watch to ensure that the voltage is correct. You need enough to make it move but not too much or it will move to fast. If it is working correctly you should see bubbles rising that have formed in the buffer because of the electrical field being generated. Later you will be able to see the dyes running or moving down the gel. The total amount of time it will take for the gel to be finished depends on the voltage running through and the size of the molecules you are trying to separate. On average it should take between 60 – 120 mins.