Methods for manipulating separation media

A method of electrophoresis is provided that does not require complete replacement of an electrophoresis medium, for example, an acrylamide polymer, between each electrophoresis run. Only a small percentage of the electrophoresis medium, for example, less than 5% of the total electrophoresis medium in a capillary can be replaced in the capillary of a capillary electrophoresis apparatus prior to an electrophoresis run and show little or no degradation in the analytic capabilities of the electrophoresis system. A polymer-displacement pump system can be used for reciprocating a pump piston in a first direction to draw fresh fluid into a chamber, and reciprocating the pump piston in a second direction to cause the fresh fluid to exit the chamber and fill at least one capillary electrophoresis capillary or an array of such capillaries.