During gel electrophoresis, long elastic polymers, such as DNA chains, and even large polystyrene spheres, become so entangled during their passage through the gel as ultimately to stop migrating. A change in the direction of the electric field can liberate these species from their entanglement. Net migration in one direction can be accomplished by alternating the field direction in pulses. The periodic change in the direction of the field also provides a mechanism for separation based on size; the longer chains are more sluggish in following the periodic changes of field direction than the shorter ones. Pulsed field gel electrophoresis (PFGE) of large DNA is based on the two mechanisms of liberation from entanglement and size separation (1).
Strictly, this is not a gel electrophoretic separation method because the separation is not directly related to the concentration of the gel; the gel acts as an anticonvection medium and, more importantly, as an array of obstacles entangling, stretching, and releasing the elastic, reptating DNA chain (2).
A pulsed power supply can also be used to advantage in the electrophoresis of proteins to provide improved resolving capacity. This presumably functions by suppressing the band spreading that would occur as a result of effective heat dissipation during the off-power phase in cases of inadequate joule heat dissipation capacity of the apparatus.
