Both chromatin structure and formation of triplex DNA at expanded GAA TTC repeats have been shown to regulate the FXN gene silencing, which causes Friedreich's ataxia. Recent studies have suggested that the presence of heterochromatin at the long expanded GAA TTC repeats, which is enriched in hypoacetylated histones, deters the transcription of the FXN gene. However, neither direct histone binding nor the effect of histone acetylation on the GAA TTC duplex or the GAA GAA TTC triplex has been measured in vitro. In this study, GAA TTC repeating DNAs derived from the human FXN gene, and the GAA GAA TTC triplex, were examined for their ability to assemble single nucleosomes and nucleosome arrays. Competitive nucleosome reconstitution assays demonstrated that the GAA TTC duplex excludes nucleosomes (53% decrease compared to the pUC control DNA) and that the GAA GAA TTC triplex further lowers the nucleosome assembly efficiency (82% decrease compared to the duplex DNA). The difference in assembly efficiency is amplified more significantly when hypoacetylated histones are used, compared to assembly with hyperacetylated histones. By analyzing the formation of nucleosome arrays on GAA TTC-containing plasmids, the triplex structure was shown to destabilize the ability of adjacent sequences to assemble nucleosomes. These results provide the first direct binding measurements for the GAA TTC duplex and the GAA GAA TTC triplex, and on the effect of histone acetylation, towards dissecting the role of chromatin structure in silencing of the FXN gene. These findings suggest that these sequences could profoundly alter local chromatin structure, and the discrepancy between in vivo and in vitro results supports recent studies showing that, in addition to DNA sequences, other factors such as epigenetic marks could be involved in the mechanism for inhibition of FXN gene expression.