Abstract: An apparatus and method for the preparation of large DNA molecules from cells which have been cast in agarose. Specifically, the invention provides for a processing chamber that allows agarose plugs to be molded and processed within the same apparatus. This greatly reduces the amount of manipulation required of such DNA samples and reduces the loss of material due to agarose plug breakage. The mold has a filling port for agarose and a slot for at least one retainer for preventing the molten agarose from exiting through openings in the mold through which DNA processing solutions later access the molded agarose plugs.