Agarose-gel electrophoresis is used to separate DNA molecules on the basis of size and shape (1-4). Since DNA is negatively charged, the charge-to-mass ratio is constant. Thus, migration through agarose is inversely proportional to the size of the molecule. However, the electrophoretic mobility of DNA in agarose is also affected by the shape of the DNA, the pore size of the matrix (agarose concentration), temperature, the ionic strength of the electrophoresis buffer, the applied voltage/field strength, and the presence of intercalators (reviewed in 5,6).
