Applications

• Analyzing and separating DNA fragments for molecular cloning

Agarose gel electrophoresis is routinely used to assess the quality, integrity, and conformational state of plasmid DNA. Plasmid DNA can exist in multiple topological forms, including supercoiled, nicked (open circular), and linear conformations, each of which migrates differently through an agarose gel. The supercoiled form is the most compact and therefore migrates fastest, appearing as a lower band on the gel. Nicked or open circular plasmid DNA, resulting from single-strand breaks, adopts a relaxed conformation and migrates more slowly, appearing as an upper band. Linear plasmid DNA, generated by double-strand breaks or restriction enzyme digestion, migrates at an intermediate rate corresponding to its actual molecular size.

• Analysis of mutation, gene duplication, deletions and genetic mapping