DNA triple-helix formation on nucleosome core particles - Effect of lengthof the oligopurine tract

We have used DNase I footprinting to examine the formation of intermolecula r triplexes on DNA fragments which have been complexed with nucleosome core particles. We have prepared five DNA fragments, based on the 160-bp tyrT s equence, which contain different length oligopurine tracts (up to 25 bp) at two different positions along the fragment, and have examined their availa bility for triple-helix formation after reconstituting onto nucleosome core particles. These results are compared with the formation of shorter triple xes in the same regions. In general we find that increasing the length of t he complex does not facilitate nucleosomal tripler formation and that the m ost important factor affecting tripler formation is the position of the tar get site within the nucleosome-bound fragment. In some instances we find th at longer oligonucleotides inhibit tripler formation. Although successful t ripler formation was achieved on the longest nucleosome-bound oligopurine t racts, this was accompanied by changes in cleavage pattern that suggest oli gonucleotide-induced changes in nucleosome structure.