Gel Electrophoresis

DNA is negatively charged, because its phosphate backbone carries phosphate groups that lose a proton and sit negative at normal pH. Drop DNA fragments into wells cut in a slab of agarose gel, run an electric current through it, and every fragment gets pulled toward the positive electrode, same as any negative charge would be. The gel itself is a tangled mesh of agarose fibers. Small fragments wiggle through the gaps easily and race ahead. Large fragments snag and drag, so they lag behind. After running the current for a set time, you get bands: clusters of same-sized fragments that have all traveled the same distance down the gel.

To read a gel, you load each sample into its own well at the top, including a ladder, a mix of fragments of known sizes, in one lane as a ruler. After running, you compare your unknown bands against the ladder bands at the same distance. Because size relates to migration distance on roughly a log scale rather than a straight line, each equal step down the gel between ladder marks corresponds to fragment size halving, not dropping by a fixed amount. That lets you interpolate: a band sitting halfway between the 500 bp and 1000 bp marks is not 750 bp, it is closer to the geometric middle, around 700 bp.

This technique is the payoff step after cutting DNA with restriction enzymes or amplifying it with PCR: you need gel electrophoresis to actually see and size the fragments those tools produce, which is why it closes out the gene expression and biotechnology unit.