Nucleosome core particles inhibit DNA triple helix formation

We have used DNase I footprinting to examine the formation of DNA triple helices at target sites on DNA fragments that have been reconstituted with nucleosome core particles. We show that a 12 bp homopurine target site, located 45 bp from the end of the 160 bp tyr T(46A) fragment, cannot be targeted with either parallel (CT-containing) or antiparallel (GT-containing) triplex-forming oligonucleotides when reconstituted on to nucleosome core particles. Binding is not facilitated by the presence of a tripler-binding ligand. However, both parallel and antiparallel triplexes could be formed on a truncated DNA fragment in which the target site was located closer to the end of the DNA fragment. We suggest that intermolecular DNA triplexes can only be formed on those DNA regions that are less tightly associated with the protein core.