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Southern, Northern, Western, and Eastern blots

In 1975, British biologist Edwin Southern published a method for detecting specific DNA fragments after separating them by size. The DNA was first treated with restriction enzymes to make the fragments, then subjected to agarose gel electrophoresis to separate them by size, then denatured in situ and transferred to a nitrocellulose membrane by virtue of sucking volumes of buffer through the gel and the membrane, using stacks of paper towels to blot up the buffer. The membrane could then be analyzed with labeled DNA probes that would hybridize to specific sequences.

Overnight, sales of paper towels to molecular biology labs skyrocketed. 

Not long after, while still a graduate student, I attended a seminar wherein the investigator demonstrated the use "Southern blots" to diagnose genetic diseases. 

"Isn't that great?" enthused Tony Hunter, the Salk Institute scientist sitting next to me, clearly overjoyed (inasmuch as his English reserve would allow him) that molecular biology lab techniques were being used for something so obviously medically useful. Now, of course, the Southern blot has also been adapted for forensic DNA analysis. A number of prisoners have been released from Death Row on the basis of DNA assays performed years after their original trial.  Southern's technique has literally become an industry.

Very rapidly, a similar technique was developed to analyze RNA by James Alwine, David Kemp, and George Stark at Stanford.  Molecular biologists being punny fellows, this was immediately dubbed the Northern blot. Northern blots were invaluable for detecting and quantifying specific mRNAs, thus determining the activity of different genes. This is particularly important in problems of gene regulation, such as embryogenesis and the concomitant cell differentiation. Blotbase, from medicalgenomics.org, is a free database of mRNA sequences quantified by Northern blots from various cell types and tissues.

The pun was stretched even further to include Western blots, also developed in the Stark laboratory. Proteins are separated by one or two-dimensional polyacrylamide gel electrophoresis--usually by isoelectric point in one dimension, and by size, in the presence of denaturing detergent, in the other direction. The proteins are then transferred onto a membrane and probed with specific antibodies. Like Southerns, Western blots are also used for diagnostic assays, for instance, the confirmation of HIV infection.

As the only direction remaining, the term "Eastern blotting" has been fought over extensively. Many different techniques have been variously described as Eastern blotting, most of which involve using different types of probes to detect post-translational modifications of proteins, for instance the use of lectins to probe a protein-blotted membrane in search of specific carbohydrates.   

There is a whole menagerie of variations on the Southern's original theme: Far-Western blots, Far-Eastern blots, Middle Eastern blots, Southwestern blots etc. that will not be described here. 

Southern's simple strategy of transferring size-separated macromolecules to a membrane for assay purposes was certainly clever, but did not seem like high technology, even in 1975. It is by little tricks that technology grows, and with it, science. 

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Steven A. Edwards, Ph.D.