Electrophoresis A method of separating large molecules (such as DNA fragments, peptides or proteins) from a mixture of similar molecules. An electric current is passed through a medium containing the mixture, and each kind of molecule travels through the medium at a different rate, depending on its electrical charge and size. Separation is based on these differences; typically smaller fragments travel farther through the media (gel) in which separation is carried out. Agarose and acrylamide gels are the media commonly used for electrophoresis of proteins and nucleic acids.