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charge-to-mass ratio

this ratio significantly affects the mobility of a macromolecule through a solution when driven by an electric field (two molecules of identical mass but different charge will move at different rates in an electric field). Since at neutral pH, the majority of the net charge on DNA is derived from the negatively charged phosphate groups in the DNA backbone, as DNA increases in size, the total charge increases at the same rate. The resulting charge-to-mass ratio therefore remains constant, and DNA fragments of different sizes all move at about the same rate in an electric field. For separation of the fragments according to size, it is necessary to force the fragments to migrate through a molecular sieve or matrix of many small pores that allows the smaller fragments to move faster than the larger fragments. agarose and polyacrylamide gels are most commonly used as a matrix for size separation of DNA and RNA fragments.

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