Larger fragments of DNA, > 50 kilobases (kb), cannot be separated with AGE or PAGE in routine electrophoresis systems; the gel pore sizes are too small for their migration. Fragment separation can be achieved with alternately applying the power to different pairs of electrodes. The most common method alternates the positive and negative electrodes in cycles during electrophoresis. The DNA fragments must reorient to a new field direction in each cycle. These changing pulses and reorientations separate the large size DNA fragments.
Sample runs require longer time periods, some 24 hours or more, special gel boxes, different electrodes and controls for switching the electric fields during electrophoresis.
Pulsed-field gel electrophoresis patterns of Staphyloccocus aureus strains. Reference: CDC's Emerging Infectious Disease Website.