Analysis of DNA by the Southern Blot technique

    DNA is applied to an agarose gel, and  electrophoresis separates the fragments of DNA according to size. The gel is then placed atop a thin sponge wick resting in a dish of salt solution, and a special filter (typically nitrocellulose) is placed on top of the gel. A stack of absorbent material (typically paper towels) is placed on top of this stack. The absorbent material draws the salt solution from the dish into the wick and through the gel by capillary action, which transfers the DNA fragments into the filter. The procedure is called a "Southern transfer" after the Eric Southern who invented the procedure. The filter now contains the DNA fragments in the same pattern as the gel, but is more easily manipulated.

    The filter is placed in a standard "seal-a-meal" bag, containing a solution of radioactively-labelled DNA probe [~~~~~] for a particular gene sequence. The probe binds to the filter only where a complementary DNA sequence is located. After washing to remove unbound probe, a piece of X-ray film is placed over the hybridized filter and left for several hours to several days. The radioactive label produces a black band on the film where it has stuck to the complementary DNA, producing an autoradiogram. If a labelled size marker has been used, the exact sizes of the fragments can be determined.

    The Southern Blot technique is useful for identifying a DNA sequence that appears only once or twice in the genome, the typical situations with nuclear loci. Note that in this example, the electrophoresis gel shows a continuous "smear" of DNA of all fragment sizes, whereas the autoradiogram identifies exactly three fragments, of three different sizes.


Figure 2000 by Griffiths et al. ; text 2013 by Steven M. Carr