A limitation of this technology is that very small probe (20 nucleotides) contains only a small number of biotinylated sites, limiting the intensity of signal obtained. III has been solved by adding long 'tails' of biotinylated nucleotides to the probes through enzymatic methods. Sometime the probe does not need to be labelled with biotin, but only coupled with a tail.
Another disadvantage of biotin labelled probes is that the cytochemical visualization reaction lead to precipitation of insoluble material which can not be removed and therefore, the filter can not be reused, while in radiolabelled probes, the filters can be used repeatedly for hybridization with a number of probes one at a time
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