Site-directed cleavage of DNA by a linker histone-Fe(II) EDTA conjugate: Localization of a globular domain binding site within a nucleosome

The globular domain of linker histones specifically recognizes and binds to the nucleosome core. However, the exact location of the binding site of the globular domain has not been definitively elucidated. To address this issue, a linker histone has been specifically modified at a site adjacent to the globular domain with a radical-based DNA cleavage reagent. The linker histone-Fe(II) EDTA conjugate was bound to reconstituted nucleosomes containing a Xenopus 5S RNA gene, and the resulting cleavage of DNA was used to precisely map the location of the linker histone binding site. The results indicate that the binding site is located on the inside of the superhelical gyre of DNA, just inside the periphery of the nucleosome core region. The implications of these results for the binding of linker histones within native chromatin complexes are discussed.