Southern Blotting

SOUTHERN BLOTTING

Southern blotting is a technique that combines the use of restriction enzymes, electrophoresis, and DNA probes to generate, separate, and detect pieces of DNA.

Figure 33.12 Southern blotting procedure. [Note: Nonradiolabeled probes are now commonly used.]

A. Experimental procedure

This method, named after its inventor, Edward Southern, involves the following steps (Figure 33.12). First, DNA is extracted from cells, for example, a patient’s leukocytes. Second, the DNA is cleaved into many fragments using a restriction enzyme. Third, the resulting fragments are separated on the basis of size by electrophoresis. [Note: Because the large fragments move more slowly than the smaller ones, the lengths of the fragments, usually expressed as the number of base pairs, can be calculated from comparison of the position of the band relative to standard fragments of known size.] The DNA fragments in the gel are denatured and transferred (blotted) to a nitrocellulose membrane for analysis. If the original DNA represents the individual’s entire genome, the enzymic digest contains a million or more fragments. The gene of interest is on only one (or a few if the gene itself was fragmented) of these pieces of DNA. If all the DNA segments were visualized by a nonspecific technique, they would appear as an unresolved blur of overlapping bands. To avoid this, the last step in Southern blotting uses a probe to identify the DNA fragments of interest. The patterns observed on Southern blot analysis depend both on the specific restriction endonuclease and on the probe used to visualize the restriction fragments. [Note: Variants of the Southern blot have been facetiously named “Northern” (electrophoresis of mRNA followed by hybridization with a specific probe), and “Western” (electrophoresis of protein followed by detection with an antibody directed against the protein of interest), neither of which relates to anyone’s name or to points of the compass.]

B. Detection of mutations

Southern blotting can detect DNA mutations such as large insertions, deletions, or rearrangements of nucleotides. It can also detect point mutations (replacement of one nucleotide by another;) that cause the loss or gain of restriction sites. Such mutations cause the pattern of bands to differ from those seen with a normal gene. Longer fragments are generated if a restriction site is lost. For example, in Figure 33.12, Person 2 lacks a restriction site present in Person 1. Alternatively, the point mutation may create a new cleavage site with the production of shorter fragments. [Note: Most sequence differences at restriction sites are harmless variations in the DNA.]