Effect of spike pulses on the orientation of the agarose gel matrix

The orientation of the agarose gel matrix in two-part, “stair-step” electric fields has been studied by transient electric birefringence. Stair-step electric fields are those in which a pulse of a given amplitude is immediately followed by a short, higher voltage “spike” pulse of the same polarity. A single stair-step pulse orients the agarose gel matrix as though the two portions of the pulse were individually applied to the gel. However, a series of consecutive stair-step pulses causes an anomalous increase in the amplitude of the birefringence, suggesting that increased numbers of agarose fiber bundles are orienting in the electric field. Spike pulses ≥ 10 V/cm appear to cause junction zone breakdown, freeing large numbers of agarose fiber bundles and microgel domains from the constraints of the gel matrix. The implications of these results for pulsed field gel electrophoresis are discussed.