Structure and distribution of inverted repeats (palindromes)

The size and distribution of renatured inverted repeats (palindromes) in D. melanogaster DNA were studied by electron microscopy (EM). The results of these studies differ from the previously published observations regarding the number, distribution and the size of inverted repeats (ir) present in DNA. -1. In contrast to the previous published observation almost all (96%) of the ir were found in crowded clusters. The DNA strands with clustered palindromes contained 2-21 palindromes (4-42 ir), with an average of 7.25 palindromes (14.5 ir) per strand. No correlation could be found between the length of the DNA strands and the number of ir per strand. -2, Also contrary to some previously published results, most (80%) of the ir formed on renaturation unlooped palindromes and these were always clustered. Looped palindromes (hairpins, formed by renaturation of ir separated by a non-homologous sequence long enough to be seen in EM as single-stranded loop) were found 1-2 per DNA strand, as part of clusters or as solitary palindromes in a DNA strand. The average spacing length (inside clusters) between centers of all palindromes was 2.349 kb, and between centers of looped palindromes 7.6 kb. - 3. The length of the ir was found to be smaller than documented in most of the previously published results. The majority, 80-90%, of the ir found in the unlooped and looped palindromes, respectively, belonged to one main-size class with a range of 30-210 bp and an average length of 100 bp, but longer ir were also observed. The average length of the ir in unlooped palindromes was 124 bp, in looped 244 bp, and the total average was 148 bp - 4. It was calculated that there are about 30,000 palindromes (60,000 ir) in the D, melanogaster genome, of which about 24,000 are unlooped and 6,000 looped, with the spacing between centers of all palindromes averaging about 4.4 kb in length.