How does electrophoresis separate DNA molecules by size?

Electrophoresis separates DNA molecules by size through a process known as gel sieving. Because DNA is negatively charged, it naturally migrates toward the positive terminal (anode) when an electric field is applied across a porous gel matrix, such as agarose or polyacrylamide.12

The gel matrix acts as a physical barrier, or sieve, with pore dimensions comparable to the size of the DNA molecules. As the molecules move through this porous structure, the matrix provides resistance to their migration. Larger, heavier DNA molecules encounter more resistance and move through the pores more slowly, while smaller, lighter molecules navigate the matrix more easily and migrate faster. This differential rate of movement allows the molecules to be resolved and separated based on their molecular weight.12