Protein Separation By SDS Polyacrylamide Gel Electrophoresis Lab General Theory Electrophoresis is a very useful technique for the separation of macromolecules. Any charged particle will migrate when placed in an electrical field. This is most simply understood for DNA, which has a negative charge on the phosphate group of the backbone for each nucleotide present. This macromolecule moves toward the positive electrode.
Proteins can be negatively or positively charged or neutral.
Of course, the charge on the protein depends on the pH of the solution. Thus, in its native state, the direction of migration of the protein depends on its charge. The extent of migration also depends on the resistance that the molecule encounters along the way. If the electrophoresis is taking place in solution, little resistance is encountered. Normally, electrophoresis is perfromed in a support medium such as a gel of agarose or polyacrylamide.