Southern, the blot is a fast way of analysing a small number of DNA fragments which may be present in a complex mixture. For instance, the sickle cell mutation is a point mutation in the beta globin gene which changes a single amino acid in the beta globin polypeptide. In homozygotes, in conditions of low oxygen concentration the mutant globin polymerises forcing the cell into a bizzarre shape. Suppose that we wish to ask whether the sickle cell mutation is present in an individual and the only material which we have available is a DNA sample. DNA is first digested with a restriction endonuclease and then separated according to the size of DNA fragments by electrophoresis through an agarose gel.
Small fragments are able to migrate more quickly through the gel than are long fragments.
Most restriction enzymes will digest human DNA into about a million fragments. We will want to compare only those which contain the human beta globin gene. A probe is made. In this example, sample 1 seems to be homozygous for the slower moving allele, sample 3 is homozygous for the faster allele and sample 2 is a heterozygote. As a consequence the size of the restriction fragment containing the 5 end of the gene is altered from 1.15kb to 1.35kb.