Visualizing the Results
Now that a complete 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. An agarose gel looks something like a thin block of jello. It contains a matrix of pores which enables it to separate DNA fragments based on their sizes. See lesson on Electrophoresis: How Scientist observe fragments of DNA
The figure labeled Electrophoresis, shows a picture of a gel electrophoresis set-up. The box on the right contains DNA loaded in the agarose gel, seen by the purple bands. The purple color comes from a dye that was added to the PCR sample in order to track the DNA’s progression through the gel. Hooked up to this gel unit is an electrical power supply source which then draws the DNA through the gel. Since DNA is negatively charged, it will migrate towards the positive electrode. The shorter a DNA fragment is, the faster it will move because it has less resistance when moving through the gel’s pores.
After the gel is run, the DNA is stained with a chemical called ethidium bromide (EtBr). EtBr binds to DNA molecules and fluoresces orange when viewed with ultraviolet light. Therefore, EtBr makes it possible to actually see the DNA bands. A single 'band' contains 1000s of individual DNA pieces, all of the same length . Typically the first lane of a gel is loaded with a molecular weight ladder. Each band in this ladder is of known size. DNA length is measured in units called base pairs (bp), so the following DNA strand would be 10 bp long: ACTGGTACCA TGACCATGGT