As current is applied, the proteins start to migrate downward through the stacking gel
toward the positive pole, since they are negatively charged by the bound SDS. Since the
stacking gel is very loose, low and average molecular weight proteins are not impeded
in their migration and move much more quickly than in the running gel. In addition, the
lower ionic strength of the stacking gel (weak buffer) creates a high electrical resistance,
(i.e., a high electric field V/cm) to make proteins move faster than in the running gel
(high ionic strength, lower resistance, hence lower electric field, V/cm). Remember that
applied voltage results in current flow in the gel through the migration of ions. Hence
low ionic strength means high resistance because fewer ions are present to dissipate the
voltage and the electric field (V/cm) is increased causing the highly polyanionic
proteins to migrate rapidly.