Regular arrangement of restriction sites in Drosophila DNA.

When DNA of Drosophila melanogaster is digested to completion with Hemophilus aegyptius restriction endonuclease, the majority of the products are DNA segments whose lengths fits a random distribution with an average of 350 base pairs. However, some 10% of the DNA is recovered as various segments of discrete lengths, ranging from 30,000 to 365 base pairs. These segments arise from the regular spacing of the enzyme restriction sites in limited portions of the Drosophila genome. Three segments have been shown to originate from mitochondrial DNA, while all the others can be assigned to one or more isopycnic density classes of nuclear DNA. Five of the discrete fragments display modular lengths, each being an integral multiple of a 365 base pairs subunit. The relative frequencies of these multiple segments suggest that they are derived from DNA originally containing restriction sites every 365 base pairs, and that approximately 25% of these sites have been randomly inactivated.