PFGE stemmed from the observation that DNA molecules elongate upon application of an electric field and return to an unelongated state upon removal of the electric field; this relaxation rate is dependent on the size of the DNA.
When the orientation of the electric field is changed during electrophoresis, the DNA molecules must return to their elongated form prior to reorientation, thus affecting the migration rate. This effect can be used to greatly extend the size range over which electrophoretic DNA separations are possible.
When the electrical field is applied to the gel, the DNA molecules elongate in the direction of the electrical field. The first electrical field is then switched to the second field according to the run specifications. The DNA must change conformation and reorient before it can migrate in the direction of this field.
As long as the alternating fields are equal with respect to the voltage and pulse duration, the DNA will migrate in a straight path down the gel (see below).
Time-lapse representation of DNA molecules undergoing PFGE.
The large size of DNA molecules to be separated by PFGE imposes certain constraints on sample preparation and handling. High molecular weight DNA is easily cleaved through shearing and imparts very high solution viscosity. For these reasons, DNA samples for PFGE are generally prepared by embedding in gel medium. Cellular source material is suspended in low gelling agarose and the gelled suspension is poured into molds. All subsequent manipulations (for example, cell lysis, protein removal, and restriction digestion) are performed by diffusing reagents into the resultant gel plugs. The processed gel plugs are then carefully loaded into wells of an agarose gel used for PFGE.
Find more information on troubleshooting PFGE gels, plug preparation, preparing and running a gel, image analysis, PFGE size standards, restriction enzyme digestion, and critical parameters in optimizing sample resolution in the Protocols section below.
Klotz LC and Zimm BH (1972). Retardation times of deoxyribonucleic acid solutions. II. Improvements in apparatus and theory. Macromolecules 5, 471–481.
Schwartz DC and Cantor CR (1984) Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell 37, 67–75.