After PCR or after cutting DNA with enzymes, scientists need to see how big the pieces are. Gel electrophoresis sorts DNA pieces by length.
Key idea
DNA is negatively charged, so in an electric field it moves toward the positive end. A gel is a mesh that slows big pieces more than small ones, so shorter pieces travel farther. A ladder of pieces with known sizes, run beside the samples, lets you read each band's size.
Why it works
Every nucleotide has a phosphate group, and each phosphate carries a negative charge. So every DNA piece has about the same charge for each unit of length, and the electric pull per unit of length is the same for all of them. What sets them apart is the gel: a long piece has to snake through many more pores, so it falls behind.
Worked example: Reading a gel
A sample has three bands: 3,000, 1,200 and 400 base pairs (bp). Which band ends up closest to the wells?
- Short pieces move farthest; long pieces stay near the wells.
- The longest piece is 3,000 bp.
Answer: The 3,000 bp band.
Worked example: Cutting, then running
A straight (linear) DNA molecule of 5,000 bp is cut at two places, at 1,000 bp and at 3,500 bp from one end. What bands appear?
- The pieces run from 0 to 1,000, 1,000 to 3,500, and 3,500 to 5,000.
- Their lengths: 1,000, 2,500 and 1,500 bp.
Answer: Three bands: 2,500, 1,500 and 1,000 bp (2,500 nearest the wells).
Gels are used to check that PCR worked, to compare DNA from different sources (a DNA profile compares band patterns at places where people differ in the number of repeats), and to pick out a gene for recombinant DNA. The DNA is invisible on its own, so it is stained with a dye that glows under special light.
Common mistake
Two ideas often get turned around. First, bigger pieces do not travel farther because they are heavier; they travel less far, because the gel holds them back. Second, DNA moves toward the positive electrode, because its phosphates are negative and opposite charges attract. Check: the smallest ladder band is always the one farthest from the wells.