Southern and Northern Blots
*This web page was created for Biology 361, an undergraduate course at Davidson College*



The process of Southern Blotting was created in the 1970’s by Edward M. Southern, a scientist at Edinburgh University in Edinburgh, Scotland. Southern blotting is designed to locate a particular sequence of DNA within a large, complex sample of DNA. For example, Southern Blotting can locate a single specific gene within an entire genome (Khalsahttp, 2000).


The first process of the Southern blot is agarose gel electrophoresis, a technique that separates DNA fragments by size. A mixture of DNA is digested with restriction enzymes, which cut the DNA into small pieces of various sizes, and placed into different lanes of an agarose gel. An electric current, which is run through the gel, forces the DNA fragments to move through the agarose matrix. Since the smaller fragments are able to navigate through the matrix faster than the larger ones, the DNA sections are separated by size (Khalsahttp, 2000).

Next, the size-fractionated DNA, while still on the gel, is chemically denatured and blotted onto a sheet of nitrocellulose paper. The nitrocellulose is then heated so that the single stranded DNA fragments are permanently adhered to its surface. The Southern blot is now ready to be analyzed. A radioactive single stranded probe is hybridized with the DNA in question. The probe anneals to the DNA wherever a complementary sequence of genetic code exists. After the radioactive probe has been allowed to bond with the denatured DNA on the nitrocellulose paper, an X-ray is taken of the nitrocellulose sheet. Only the areas where the probe binds to the denatured DNA will show up on the X-ray film. This allows researchers to identify the spatial location and frequency of the specific genetic sequence contained by the probe (Brinton and Lieberman, 1994).


A Northern blot is very similar to a Southern blot except that it is mRNA rather than DNA which is extracted, run on a gel, and transferred to a filter membrane. Since mRNA is made during gene transcription, a Northern blot is used to determine the temporal and spatial locations where a specific genetic sequence is expressed in an organism (Gilbert, 2000).


In regards to genetically modified organisms, Southern blotting is used as a definitive test to ensure that a particular section of DNA of known genetic sequence has been successfully incorporated into the genome of the host organism. Southern blotting is especially effective when a selectable marker gene cannot be used in the gene transformation process.

Since Northern blotting is used to look at the expression patterns of a particular section of genetic code, scientists use Northern blots to identify where and when a specific section of DNA of known sequence is being transcribed. For example, this allows scientists to determine whether a specific promoter naturally found in a potato plant works when introduced in a banana tree.

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Figure 1: Step-by-step diagram of Southern blot technique



Brinton, Kate, Lieberman, Kim-An. Basics of dna fingerprinting. 1994. 9/8/02. <>

Khalsahttp, Guruatma. Mama ji's molecular kitchen. 2000. 9/8/2002.<>

Gilbert, Scott F.(2000). Developmental Biology 6th ed. (New York: Sinauer publishers). pp. 92-93.


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