Southern blot: DNA detection by gel transfer and hybridization

In 1975, molecular biologists could cut genomic DNA into fragments with restriction enzymes and separate those fragments by size on an agarose gel. What they could not do was identify which band among hundreds contained a specific sequence of interest. Edwin Southern, at the Medical Research Council's Mammalian Genome Unit in Edinburgh, solved that problem with a simple approach: transfer the fragments from the gel onto a membrane that could then be probed with radioactive RNA complementary to the target sequence.

The mechanics of the Southern blot relied on capillary action. A stack of absorbent paper drew buffer upward through the gel, carrying the DNA fragments with it and depositing them on a nitrocellulose membrane placed directly above. The membrane was then incubated with a radiolabeled RNA probe that stuck only to the complementary sequence. Autoradiography revealed the position of the target band. Southern published the method in the Journal of Molecular Biology in 1975; thirty years later it was the most highly cited paper in that journal's history.

DNA diagnosis before blotting was crude: in 1976 Yuet Wai Kan and colleagues diagnosed alpha-thalassemia before birth by measuring, through solution hybridization, how many alpha-globin genes the fetal DNA carried. Blotting let researchers see individual fragments. In 1978 Kan and Andree Dozy found that a 13.0-kilobase HpaI fragment carrying the beta-globin gene, instead of the usual 7.6-kilobase fragment, often traveled with the sickle mutation, and they used it to diagnose sickle cell trait in DNA from amniotic fluid cells. They proposed such restriction-site differences as a new class of genetic marker for linkage studies.

The name prompted a tradition of naming analogous techniques geographically. Northern blotting, which applies the same transfer-and-hybridize logic to RNA, and Western blotting, which does so for proteins after SDS-PAGE separation, were named by analogy. Neither technique was developed by anyone named Northern or Western. Southern himself went on to conceive DNA microarrays, tiny arrays of short DNA sequences that allow many hybridization tests to run in parallel.

Alec Jeffreys used Southern blotting to develop DNA fingerprinting, first applied in 1985 to an immigration case in which it showed that a boy facing deportation was his mother's son. Fingerprinting was soon used to solve crimes and settle paternity disputes. Blotting was also used heavily in mapping the human genome, and in 2005 Southern and Jeffreys shared the Lasker Award for Clinical Medical Research.