Gel electrophoresis is used to separate things (DNA, RNA, or proteins) by their size. Gel electrophoresis is used to separate things (DNA, RNA, or proteins) by their size. For example, say you have a sample of protein that you have prepared accordingly and want to separate by size. You would run it through a gel, and after a designated amount of time, would view the progress that the protein has made through the gel, and then image the gel.