Translational motion: DNA motion in gel electrophoresis

Gel electrophoresis is a commonly used method to separate DNA fragments. In Classic Gel Electrophoresis (CGE), negatively-charged DNA fragments are loaded into lanes in a block of agarose gel. A constant electric field is applied to the system, which causes the DNA fragments to migrate toward the opposite end of the block. DNA fragments are separated because shorter fragments can move through pores in the agarose gel more quickly than longer fragments. Groups of DNA fragments of the same length migrate together and can be visualized as bands in the gel.

Figure 1: Schematic Representation of CGE. The arrow indicates the direction of net DNA migration. Dark bands in the gel represent groups of DNA molecules of identical length. ‘A’ indicates the site of DNA loading. ‘B’ indicates the area through which DNA molecules migrate.

CGE can only separate DNA fragments between 5 and 20,000 base pairs in length. Pulsed Field Gel Electrophoresis (PFGE) is a powerful technique that can separate DNA fragments differing by as many as 106 base pairs. There are several variants of PFGE, all of which share the essential characteristic that the orientation of the electric field is abruptly changed thousands of times during the procedure. As the electric field changes direction, the DNA molecules reorient themselves before migrating in a new direction. Typically, smaller molecules are able to reorient themselves more quickly and therefore migrate farther. One currently available PFGE apparatus utilizes electrodes arranged in a hexagonal array, in which each electrode can be controlled independently. The electrodes are turned on in alternating arrangements to produce straight, distortion-free, lanes of DNA migration.

Figure 2: Example electrode array for PFGE. The small bars at the top of the block show where DNA loading would occur. ‘A’ shows the relative electrode potentials when the -45° field angle is activated. ‘B’ shows the relative electrode potentials when the +45° field angle is activated.