The basis of PCR amplification or RNase protection assay is, DNA and RNA probe will selectively hybridize with the molecules of nucleic acid of complementary sequence in a given sample which is usually unknown. The main difference between Southern and Northern blotting is, southern blot is used when we want to find out the presence of a particular DNA fragment in a given sample. On the contrary northern blotting is a technique used for detecting RNAs which are separated by the process of electrophoresis.
Southern blotting was introduced by E.M. Southern in 70’s. In southern blotting what happens is, a DNA is extracted from the human cell which is of interest and then it is cut into fragments with the help of restriction enzyme. Once these fragments are separated using the process of electrophoresis, they are transformed into bands which contain many copies of that DNA. We can also make these bands invisible by using specific staining. Then these bands are transferred to nitrocellulose filter. Here the solution is made to pass through gel and filter to paper towel. This whole process produce nitrocellulose filter with DNA fragments transferred to the filter. This filter is then exposed to radioactively labeled probes and this probe hybridize with a short sequence of DNA. At last filter is exposed to X-ray film and the gene is identified by a band on developed film.
Northern blotting was introduce by Alwine and his colleagues in 70’s. RNA is extracted in this procedure from a given sample. Electrophoresis occurs and RNA is eventually separated by the size. After this, this RNA is transferred to the membrane and fixed to it with the help of UV light and heat. labeled probes are applied on it which helps in visualization of labeled RNA over X-ray film. In Northern blotting, extraction of RNA is followed by electrophoresis and then hybridization to a labeled DNA probe.
- Southern introduced this technique of southern blotting. Northern blotting was introduced by Alwine.
- Separation of DNA occurs in southern blotting, separation of RNA occurs in northern blotting.
- Denaturation is not needed in northern blotting but it is required in southern blotting.
- Nitrocellulose filter membrane is used in southern blotting but not in northern.
- DNA-DNA hybridization occurs in southern blotting. RNA-DNA hybridization occurs in northern blotting.
- Amino benzoyloxymethyl filter paper is used in northern blotting but not in southern.