Figure 4. Deletion Amplification Assay (DADA) PCR. DADA-PCR is used to specifically detect the presence of a gene deletion allele that is present at a low frequency or is otherwise difficult to detect in a mixed population of mutant and WT phage. The DADA-PCR primer is designed such that the 3′ end anneals across the new junction created by the joining of the two DNA ends flanking the deleted region. When this primer anneals to the WT allele, this creates mismatch (shown an ‘x’ in the figure) through which a high fidelity DNA polymerase cannot synthesize under stringent PCR conditions. However, the DADA-PCR primer is complementary to the deletion allele, and with an appropriate down- (or up-) stream primer, will only generate a product if the mutant allele is present.