Gel electrophoresis separates DNA fragments by size in a solid support medium such as an agarose gel. A sample (DNA) is pipetted into the sample wells and an electric current is applied to cause the negatively charged DNA to migrate (electrophoretically) toward the anodic, positive (+) end. Mobility is proportional to size: smaller fragments move faster and end up at the bottom of the gel.

1. Agarose gel electrophoresis allows estimation of the size of DNA fragments after digestion with restriction endonucleases, for example, in restriction mapping of cloned DNA.

2. Analysis of PCR products, e.g., for molecular genetic diagnosis or genetic fingerprinting.

3. Agarose gel electrophoresis is commonly used to resolve circular DNA with different superhelical topologies and to resolve fragments that differ by DNA synthesis.

4. In addition to providing an excellent medium for fragment size analysis, agarose gels can also purify DNA fragments.