19.1.9—Gel electrophoresis

Gel electrophoresis separates DNA fragments by their movement through a gel. DNA has a net negative charge because of its phosphate groups, so an electric field drives it towards the positive electrode; fragment size also affects how far it moves through the gel pores.

1. Prepare the DNA sample and an agarose gel with wells, then submerge the gel in electrolyte solution.
2. Load the DNA fragments into the wells and position the wells at the negative-electrode side.
3. Apply the electric field: negatively charged DNA migrates through the gel towards the positive electrode.
4. Separate the fragments: smaller or shorter fragments move more easily through the pores and therefore travel faster and farther than larger fragments.
5. Make the separated DNA visible using an appropriate stain, fluorescent label or labelled-probe detection method supported by the investigation.
6. Compare the band pattern with a size ladder and suitable control fragments to estimate sizes or assess similarity.
7. Interpret cautiously: a matching pattern supports similarity under the tested preparation and conditions, but band evidence alone does not establish absolute identity.

Direction is set by DNA charge, while separation distance is influenced by fragment length and the gel conditions. A ladder or control provides the reference for comparison; distance is a conditional size estimate, and band brightness is not itself a fragment-length measurement.

The method gives evidence from a band pattern, not an automatic biological conclusion. No voltage, run time or fixed band count is assumed here. Microarrays and bioinformatics are separate cards.