Question

You have a hypothesis that another gene, "W", might play a role in muscle cell differentiation. As a first step towards testing this hypothesis, you want to do a DNase I digest assay and a Northern blot, just like what was done for genes X and Y.

You search in the lab freezer and find 2 tubes left behind by a former student. Each tube contains a unique antisense DNA oligonucleotide probe for gene "W". The first probe will bind an upstream regulatory region of the "W" promoter, while the second probe will specificalley recognize the second exon of "W" gene. Will either of these probes work for BOTH the Southern and Northern blots? Explain your reasoning.

Answer 1

Souther blotting is the molecular biology technique in which the binding of a hybridization probe takes place to a target DNA sequence for identification of a specific sequence in a given pool of DNA. On the other hand, Northern blotting is the molecular biology technique in which the binding of a hybridization probe takes place to a target RNA sequence for identification a particular target sequence of mRNA which has been undergone transcription against a target DNA.

This suggests that whereas Souther blotting has utility in identification of a target gene, Northern blotting has utility in identification of transcript of a target gene.

Here, it must be carefully noted that the DNA and the RNA have complementary sequences to each other. Thus, this fact of complementarity makes the sense that the probe which is suitable for, say, Souther blotting, will not be suitable for Norther blotting since it will have same nucleotide sequence as the target mRNA or any RNA and thus, no complementary hybridization will take place. This is why specific probes are artificially synthesized with high accuracy to conduct a Southern or Northern blotting experiment.

Thus, according to the information, the available probes have hybridization sequences against the upstream regulatory sequence and the exon. It must be noted here that the upstream regulator is not transcribed and the exon will have complementary sequence in Northern blotting. Thus, based upon the above given explanation, none of the probes will work against both Souther and Northern blots.