PFGE allows investigators to separate much larger pieces of DNA than conventional agarose gel electrophoresis. In conventional gels, the current is applied in a single direction (from top to bottom). But in PFGE, the direction of the current is altered at a regular interval as shown in the animated gif below.
The gray box is the gel, the six sets of 4 black lines represent the 3 pairs of electrodes. Initially, the gel is empty but soon Whole chromosomes mixed with blue loading dye will be placed into the wells. Then the current will be turned on and the direction of the current will change in a regular pattern. This is repeated until the loading dye reaches near the end of the gel Then the gel is soaked in a solution containing ethidium bromide which fluoresces orange when bound to DNA.
Figure 1. Animated Gif of PFGE which will repeat one time.
The red-striped arrows represent the direction of the current.
Figure 2. Example of a real PFGE; drug resistant Staphylococcus aureus.
The molecular weight markers are digested lambda phage (λ) and are given in kb.