Southern blot
/ SUTH-ern blot /
A gel may have thousands of DNA fragments smeared down it, and you want to know whether one particular sequence — say, a specific gene — is present and how big the fragment carrying it is. The gel alone cannot tell you; every fragment looks the same. The Southern blot is a clever way to ask, 'where in this gel is my sequence?' and get a clear answer.
The method has four moves. First, separate DNA fragments by size on a gel. Second, transfer (blot) them out of the soft gel onto a sturdy membrane, preserving their positions — capillary action wicks buffer up through the gel and carries the DNA onto the membrane like ink onto blotting paper. Third, bathe the membrane in a labelled probe: a single-stranded piece of DNA complementary to the sequence you are hunting. The probe hybridizes — base-pairs — only to fragments that contain a matching sequence. Fourth, detect the probe (by radioactivity or a colour or light signal), which lights up exactly the band carrying your sequence. So the blot converts an invisible needle in a haystack into a single visible band at a known size.
The Southern blot, invented by Edwin Southern in 1975, was a landmark — the first way to detect a specific DNA sequence within a complex genome. For decades it was the standard for confirming a gene's presence, counting its copies, detecting mutations or rearrangements, and DNA fingerprinting in forensics. PCR and sequencing have largely replaced it for everyday work, but its core idea — separate, blot, hybridize a probe, detect — is the template for its named relatives: the Northern blot (for RNA) and the Western blot (for protein).
To test whether a patient carries a gene deletion, you digest their genomic DNA, run it on a gel, blot it to a membrane, and hybridize with a probe for that gene. A healthy person shows the expected band; if the gene is deleted, no band lights up — the absence is the answer.
A labelled probe lights up only the DNA band carrying its match.
The mnemonic is not a coincidence of geography: 'Southern' is the inventor's surname, and Northern and Western were named as playful puns on it — they are not actual compass directions.