Southern Blot - Applications

Applications

Southern transfer may be used for homology-based cloning on the basis of amino acid sequence of the protein product of the target gene. Oligonucleotides are designed that are similar to the target sequence. The oligonucleotides are chemically synthesised, radiolabeled, and used to screen a DNA library, or other collections of cloned DNA fragments. Sequences that hybridise with the hybridisation probe are further analysed, for example, to obtain the full length sequence of the targeted gene.

Second, Southern blotting can also be used to identify methylated sites in particular genes. Particularly useful are the restriction nucleases MspI and HpaII, both of which recognize and cleave within the same sequence. However, HpaII requires that a C within that site be methylated, whereas MspI cleaves only DNA unmethylated at that site. Therefore, any methylated sites within a sequence analyzed with a particular probe will be cleaved by the former, but not the latter, enzyme.