Simple plaque hybridization method for the detection of differentially represented repetitive DNA

A differential DNA hybridization method of detecting moderately repetitive strain-specific or species-specific DNA is described. Two Drosophila melanogaster strains, one with and one without transposable elements, were utilized as a model system to demonstrate the effectiveness of this procedure. A genomic library was constructed from flies of the pi 2 strain, which contains both P and hobo transposable elements. Duplicate plaque lifts of this library were probed with DNA from the same strain and with DNA from the Canton-S strain, which contains neither of these two families of transposable elements. Plaques that hybridized stronger to the genomic DNA that contained elements were noted, and then the filters were stripped and reprobed with P and hobo element DNA. Many of the differentially hybridizing plaques were shown to contain DNA homologous to one of the two known elements. This method should allow the isolation and cloning of any repetitive DNA present in one species or isolate, but absent or present in reduced copy number in another species or isolate. By analogy to the recent invasion of D. melanogaster by P elements, such differentially represented DNA is likely to represent recently invading transposable elements that are actively mobile.