Purine.pyrimidine (pur.pyr) DNA tracts are prevalent in eukaryotic genomes. They can adopt a triplex conformation in vitro under conditions that may exist in vivo, suggesting that triplex (H-) DNA may exist naturally in chromosomes. To explore this possibility and gain insight concerning potential functions, the distribution of triplex DNA was studied in fixed polytene chromosomes of Chironomus tentans and Drosophila melanogaster by indirect immunofluorescence microscopy using an anti-triplex DNA monoclonal antibody (Jel 318). Chromosomes stained with this antibody exhibited immunopositive regions corresponding to condensed chromatin bands; interbands were less immunofluorescent. These results imply that there is more triplex DNA in bands than in interbands. In Chironomus, nucleolar organizer regions and Balbiani rings were immunonegative, indicating that triplex DNA is not present in decondensed, transcriptionally active chromatin. A few specific bands in both Chironomus and Drosophila were intensely immunofluorescent. In Drosophila, one such region was 81F on chromosome 3 R. Competition during staining with exogenously added sequences corresponding to a constituent 1.672 g/cm3 statellite DNA in region 81F failed to abolish the immunofluorescence, suggesting that the satellite DNA does not fortuitously react with Jel 318 and implying that unidentified pur.pyr sequences forming triplex DNA are also present at this location. Region 81F exhibits ectopic pairing with nonrelated chromosome regions that have also proven to be intensely immunopositive; this suggests that the formation of triplex DNA between common, shared pur.pyr sequences in these otherwise nonhomologous bands might account for the ectopic pairing phenomenon. Together with our previous results, these data are consistent with the hypothesis that triplex DNA may play a role in chromosome organization by participating in regional chromatin condensation.
