Electrophoresis can be used to separate molecules by size, shape, and charge. When DNA samples are run in an electrophoresis gel, the different bands produced generally represent fragments of different sizes. Why is the size of the fragment the most critical factor in determining how far it migrates on a gel when DNA fragments are compared?The charge on DNA is so small that it has a minimal effect on movement in the gel.DNA moves toward a positive charge due to the negative charge on its phosphate groups. The charge is consistent because all DNA nucleotides have a single phosphate group rather than having more diverse patterns of charges. Because the charge is relatively consistent, size is the most important factor determining how far fragments move.The shape of the DNA fragments has an even greater effect on movement than size or charge, so charge is relatively unimportant.A special type of gel is used for DNA electrophoresis to minimize the effects of charge.

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