Analysis of DNA by the Southern Blot technique
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
the gel by capillary action, which transfers the DNA fragments
the filter. The procedure is called a "Southern transfer" after
who invented the procedure. The filter now contains the DNA
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
of DNA of all fragment sizes, whereas the autoradiogram
exactly three fragments, of three different sizes.
[A related technique
separates RNA in a gel and probes it with DNA. Since
base-pairing is in a sense the reverse of a "southern"
experiment, this technique
is referred to as a "northern blot"].