Agarose gel electrophoresis separates DNA fragments according to their size. Typically, a DNA molecule is digested with restriction enzymes, and the agarose gel electrophoresis is used as a diagnostic tool to visualize the fragments. An electric current is used to move the DNA molecules across an agarose gel, which is a polysaccharide matrix that functions as a sort of sieve to help “catch” the molecules as they are transported by the electric current.
This technique has lots of applications. Generally speaking you can analyze DNA fragments that result from an enzyme digestion of a larger piece of DNA to visualize the fragments and determine the sizes of the fragments. In addition to its usefulness in research techniques, agarose gel electrophoresis is a common forensic technique and is used in DNA fingerprinting.
The phosphate molecules that make up the backbone of DNA molecules have a high negative charge. When DNA is placed on a field with an electric current, these negatively charged DNA molecules migrate toward the positive end of the field, which in this case is an agarose gel immersed in a buffer bath. The agarose gel is a cross-linked matrix that is somewhat like a three-dimensional mesh or screen. The DNA molecules are pulled to the positive end by the current, but they encounter resistance from this agarose mesh. The smaller molecules are able to navigate the mesh faster than the larger one, so they make it further down the gel than the larger molecules. This is how agarose electrophoresis separates different DNA molecules according to their size. The gel is stained with ethidium bromide so you can visualize how these DNA molecules resolved into bands along the gel.
Ethidium bromide is an intercalcating dye, which means it inserts itself between the bases that are stacked in the center of the DNA helix. One ethidium bromide molecule binds to one base. As each dye molecule binds to the bases the helix is unwound to accommodate the strain from the dye.
Closed circular DNA is constrained and cannot withstand as much twisting strain as can linear DNA, so circular DNA cannot bind as much dye as can linear DNA.