Visualizing the Results

Once a PCR reaction has been completed, we need to be able to see the results. To do this, a sample of the PCR mixture is loaded into an agarose gel for electrophoresis. The agarose gel contains a matrix of pores which enables it to separate DNA fragments based on their sizes. For details about setting up and running an electrophoresis gel, see  Electrophoresis: How Scientists observe fragments of DNA.

Figure 8 shows a picture of a gel electrophoresis gel that is running. The box on the right contains DNA loaded in the agarose gel. The gel placed in an aqueous solution of electrolytes. Depending on the type of dye used, color bands are a dye that was added to the PCR sample before it was loaded into the sample well. This allows for the tracking of the DNA’s progression through the gel. Hooked up to this gel unit is an electrical power source which provides the force to move the DNA through the gel. Since DNA molecules are negatively charged, they will migrate towards the red, positive electrode. Shorter DNA fragments move faster than longer fragments through the pores in the gel.

After the gel is run, the DNA is stained with a chemical that binds specifically to DNA molecules and then will either reflect a specific color of visible light or fluoresce a specific color when viewed with ultraviolet light. A single 'band' contains thousands of individual DNA fragments, all the same length. Figure 9 illustrates the visual information that can be obtained from an electrophoresis gel after it has run. The electric current uniformly moves all the DNA fragments through a gel in the same direction toward the positive electrode. The sample wells at the top of the gel image thus establish lanes for the DNA samples to move.