SDS-PAGE is widely used to analyze the proteins in complex extracts. The most
commonly used methods are derived from the discontinuous SDS-PAGE system first described by
Laemmli (1970). In gel electrophoresis, an electric field is used to move charged molecules through a matrix of a polymerized substance such as agarose or polyacrylamide. The rates at which individual molecules move through the gel depend on the properties of both the separation
system and the molecules themselves. Gel matrices are permeated with networks of pores through
which the molecules move. The amount of resistance that the matrix presents to the movement of
a molecule depends on the diameter of the pore as well as the size and geometry of the molecule.
Researchers can control the size of the pore by adjusting the concentration of gel monomer within
a certain range. In general, smaller, more highly charged molecules migrate more rapidly through
gels than larger or less charged molecules. The mobility of a molecule is also affected by the buffer system and the strength of the electrophoretic field used for the separation.
You have already used agarose gel electrophoresis to separate DNA molecules. Recall that the size of a linear DNA molecule can be estimated from the rate at which it moves through an agarose gel, because DNA molecules have a uniform charge to mass ratio. Protein electrophoresis is somewhat more complicated than DNA electrophoresis. Proteins are much smaller than DNA molecules, so polyacrylamide gels are used for their separation.