Inverted repeat sequences in the Drosophila genome.

The properties of inverted repeat (foldback) sequences in Drosophila melanogaster DNA have been studied by HAP chromatography and electron microscope methods. Electron microscope observations show that there is a broad distribution of lengths of the duplex regions of the inverted repeats from very short to greater than 15 kb, with number and weight average values of 1.35 kb and 5.0 kb respectively. About 20% of the inverted repeats are separated by a single-strand spacer with lengths too short to observe, but the other 80% have spacers, P, with lengths ranging from 0.5 kb to greater than 30 kb. The number average and weight average spacer lengths for the total sample are 2.7 kb and 6.1 kb. With respect to the lengths of the spacers, P, between inverted repeats, the Drosophila genome differs from that of most organisms which have been studied where the spacers P are mostly too short to be measured. EM and HAP studies suggest that the average center-to-center spacing between sets of inverted repeats is 40-80 kb. The HAP studies show that there is a broad range of thermal stabilities for the duplexes formed by reassociation of inverted repeat sequences. Kinetic analysis shows that all of the frequency components of the Drosophila genome are present in the inverted repeats, the loops P, and the flanking sequences. There is a somewhat larger proportion of middle repetitive DNA in those inverted repeat duplexes which are resistant to digestion by Mung Bean Endonuclease I. These enzyme resistant duplexes comprise about 3% of the entire genome. It is estimated that there are approximately 2000-4000 inverted repeat pairs in the entire genome.