How does gel electrophoresis separate fragments of DNA?

Each nucleotide in DNA carries negative charges on their phosphate group, and because of this all molecules of DNA have a constant mass/charge ratio. This means that in an electric field, every molecule of DNA will feel the same net acceleration toward the positive electrode. However, the larger strands of DNA will snag on the gel polymer more frequently, and longer or larger molecules of DNA will move more slowly than shorter or more compact molecules. So generally, a shorter DNA strand goes faster than a longer one, and a more tightly supercoiled circular DNA molecule will go faster than a less tightly or knicked circular DNA molecule.

DNA fragments carry electrical charges due to their molecular composition. The gel in the electrophoresis is a sort of permeable gel. When a current is introduced to the machine, the DNA fragments naturally repel from their like charge at the top and are attracted to the unlike charge at the bottom. The smaller peices of DNA are able to move further in the gel before getting "stuck".

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Generally 1, size. Speaking from a biochemist's point of view, the charge-to-mass ratio is virtually identical for DNA fragments being separated from each other by gel electrophoresis. Much like for proteins being separated by SDS-PAGE, where mass becomes the primary determinant of migration rate in a gel.

DNA is negatively charged due to the phosphate group which allows for the fragments to move with in the gel. The larger the molecule, the slower it will move though the gel. So the answer is size.

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