High-resolution separation and accurate size determination in pulsed-field gel electrophoresis of DNA. 3. Effect of electrical field shape.

The resolution of pulsed-field gel electrophoresis is dramatically affected by the number and configuration of the electrodes used, because these alter the shape of the applied electrical fields. Here we present calculations and experiments on the effect of electrode position in one of the most commonly used pulsed-field gel electrophoresis configurations. The goal was to explore which aspects of the electrical field shape correlate with improved electrophoretic resolution. The most critical variable appears to be the angle between the alternate electrical fields. The most effective electrode configurations yield angles of more than 110 degrees. A continually increasing angle between the fields produces band sharpening that greatly enhances the resolution.