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Nucleic Acids Research, 1995, Vol. 23, No. 12 2184-2191
© 1995

MOLECULAR BIOLOGY

Triple helix DNA alters nucleosomal histone-DNA interactions and acts as a nucleosome barrier

Lorelei Westin, Patrik Blomquist, John F. Milligan1 and Örjan Wrange*,

Laboratory of Molecular Genetics, Department of Cellular and Molecular Biology, Medical Nobel Institute Karolinska Institute, S-17177 Stockholm, Sweden 1Gilead Sciences 346 Lakeside Drive, Foster City, CA 94404, USA

* To whom correspondence should be addressed

Received February 28, 1995. Revised May 1, 1995. Accepted May 1, 1995.

Oligonucleotides which form triple helical complexes on double-stranded DNA have been previously reported to selectively inhibit transcription both In vitro and In vivo by physically blocking RNA polymerase or transcription factor access to the DNA template. Here we show that a 16mer oligonucleotide, which forms triple helix DNA by binding to a 16 bp homopurine segment, alters the formation of histone-DNA contacts during In vitro nucleosome reconstltution. This effect was DNA sequence-specific and required the oligonucleotide to be present during In vitro nucleosome reconstitution. Binding of the triple helix oligonucleotide on a 199 bp mouse mammary tumour virus promoter DNA fragment with a centrally located triplex DNA resulted in interruption of histone-DNA contacts flanking the triplex DNA segment. When nucleosome reconstitution is carried out on a longer, 279 bp DNA fragment with an asymmetrically located triplex site, nucleosome formation occurred at the border of the triple helical DNA. In this case the triplex DNA functioned as a nucleosome barrier. We conclude that triplex DNA cannot be accommodated wtthin a nucleosome context and thus may be used to site-specifically manipulate nucleosome organization.


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