Gel electrophoresis is a laboratory method used for a variety of protocols including sequencing, RFLP analysis, marker analysis, DNA fingerprinting and DNA purification. It is based on two key principles: 1) DNA has an overall negative charge (due to the phosphate backbone) and thus will migrate towards a positive charge. 2) A gel acts as a sort of microscopic sieve; smaller DNA fragments will travel through the gel more rapidly then larger fragments. Thus DNA can be separated based on the length (size) of the DNA segment.

Procedure

Gels are typically made from agarose or acrylamide. They start as liquids that become semi-solid either through cooling or a chemical reaction, thus forming a gel matrix. The liquid agarose or acrylamide is poured into a form and allowed to solidify. The form or mold includes a comb, which creates wells or chambers so that the DNA can be loaded in to the gel.            Once the gel has solidified, the comb is removed and the gel is placed in a running chamber with buffer. The DNA samples are mixed with a dye (so it can be seen as it runs through the gel), loaded into the wells and current is applied to the apparatus. The current pulls the DNA through the gel towards the positive charge, thus separating the fragments according to size. Several methods can be used to visual the DNA bands. Frequently the DNA is tagged with fluorescent molecules or radioactive labels.

Illustration of different steps of gel electrophoresis.