Because of ionized phosphate groups, both DNA and RNA will migrate in an electrical field with an appropriate buffer. They are negatively charged and will migrate to the anode. The speed of migration and separation achieved is based upon size with smaller molecules traveling faster. The shape of macromolecules, type of support medium, and electrophoresis method also vary the separation results. The isolated nucleic acid can be single-stranded or double-stranded and can fold into other structures.
AGE, PAGE, and CE are the most common electrophoresis methods used in analysis of nucleic acids. Pulsed electric fields are needed to separate large fragments. The electrophoresis employed in blotting techniques enhance these discrimination techniques.