Difference between northern & Southern blotting

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Difference between northern & Southern blotting
Southern blotting prints DNA. (Stockbyte/Stockbyte/Getty Images)

The Southern blot is a method to isolate a specific DNA sequence. It gets its name from Ed Southern, who invented the technique in 1975. J.C. Alwine invented a similar method from isolating RNA in 1977. Rather than naming the RNA blotting method after himself, he named it the “northern blot” as a pun on the earlier “Southern blot.” The extension of the term didn’t end there. W. Neal Burnette based a technique to identify antigens (proteins) on the northern blot method. He named his technique the “western blot.” As the Southern blot is named after someone it is usually capitalised. The northern blot and western blot aren’t.

Southern blot

The Southern blot produces the image of DNA that is now commonly known. In it, different DNA sequences appear as dark bands on a lighter background. A specific sequence appears in a specific position. This technique is used in paternity testing because the presence of specific DNA strands are inherited. Matches of specific patterns show relationships between people.

Northern blot

The northern blot uses the same method as the Southern blot, but applies it to RNA instead of DNA. DNA hold genetic information and RNA manages the conversion of information contained in the DNA to form proteins. So RNA implements DNA’s data. RNA manages the growth of a foetus and so the northern blot is used to track the development of particular genes during the development of an embryo.


In the Southern blotting process, DNA strands are fragmented and mixed into an added gel in a gel electrophoresis chamber. This gel is then pressed against a membrane to create a print of the DNA sequences. The most common technique to transfer the DNA sequence is through a capillary effect. The gel is placed on top of filter paper or a sponge which sits in a tray of salt solution. The membrane is placed on top of the gel and a stack of paper towels sits on top of that. The stack is pressed by a weight. Salt solution rises up through the sponge and passes through the gel and the membrane to be absorbed by the paper towels. The traces of DNA do not pass through the membrane, and so imprint on its surface.


Although the same technique applies in Southern and northern blotting, RNA is a more delicate material than DNA and so results are harder to achieve. The gel used in northern blotting needs to contain formaldehyde to prevent the RNA clotting -- a process that does not occur with DNA. An RNA blot is more prone to contamination and so greater effort has to be taken in northern blotting to ensure a sterile environment.

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