It is used as a preparative technique in laboratories for PCR, Southern blotting, genome mapping, and DNA sequencing, and is also used in DNA fingerprinting and plant breeding. Scientists studying molecular biology, microbiology, and biochemistry utilize electrophoresis for studies and experiments in medicine, forensic science, and conservation biology, just to name a few.

Gel electrophoresis is one of the most common electrophoresis methods used.

In these systems, molecular samples are loaded into the electrophoresis apparatus, a type of box or chamber referred to as a gel box. The gel box is filled with an agarose or polyacrylamide gel and is equipped with a gel comb, as well as a negative electrode, or anode, on one side, and a positive electrode, or cathode, on the other. The comb helps form the wells where the samples are placed, and the negative and positive electrodes create an electrical current that generates electrophoretic separation.

The electrical current generated separates the DNA fragments based on their size or charge because, even though DNA molecules have the same amount of charge per mass, longer DNA fragments tend to have a higher molecular weight compared to shorter DNA pieces. That difference means segments move at varying speeds through the gel medium, grouping up according to size.

After gel electrophoresis is performed, the gel is stained with a fluorescent binding dye, which eventually allows the groups that formed to be more easily observed. Having stained the gel, a light source is then used to excite the fluorescent dye so that the DNA bands are visible for post-separation and analysis.

A well-defined group or line of DNA is referred to as a separation band. These separation bands tell us more about the DNA fragments size or charge.