The DNA, RNA, or proteins that must be separated in this method are run through a gel that contains small pores. The molecules are driven through the gel by an electric field. The molecules pass through the pores of the gel, and the speed of movement is inversely proportional to their respective lengths. Therefore, molecules with a lower molecular size will move faster than molecules with a higher molecular weight. The electric field is generated by the difference in charge at two ends of the gel. One end contains a positive charge, and the other end contains a negative charge.
In horizontal gel electrophoresis, the gel is present in a horizontal orientation and is immersed in a continuously operating buffer that is present within the gel box itself. In vertical gel electrophoresis, the buffer system is vertically oriented and discontinuous with two chambers present at the top and bottom with a cathode and an anode, respectively. This is the key difference between horizontal and vertical gel electrophoresis.