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Site-directed histone-DNA contact mapping for analysis of nucleosome dynamics.
Methods Enzymol
March 2004
Department of Biochemistry & Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois 62901-4413, USA.
Structural features of transcription factor IIIA bound to a nucleosome in solution.
Mol Cell Biol
January 2004
Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14625, USA.
Assembly of a DNA fragment containing a Xenopus borealis somatic-type 5S RNA gene into a nucleosome greatly restricts binding of the 5S gene-specific transcription factor IIIA (TFIIIA) to the 5S internal promoter. However, TFIIIA binds with high affinity to 5S nucleosomes lacking the N-terminal tail domains of the core histones or to nucleosomes in which these domains are hyperacetylated. The degree to which tail acetylation or removal improves TFIIIA binding cannot be simply explained by a commensurate change in the general accessibility of nucleosomal DNA.
View Article and Find Full Text PDFNature of full-length HMGB1 binding to cisplatin-modified DNA.
Biochemistry
March 2003
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA.
HMGB1, a highly conserved non-histone DNA-binding protein, interacts with specific DNA structural motifs such as those encountered at cisplatin damage, four-way junctions, and supercoils. The interaction of full-length HMGB1, containing two tandem HMG box domains and a C-terminal acidic tail, with cisplatin-modified DNA was investigated by hydroxyl radical footprinting and electrophoretic gel mobility shift assays. The full-length HMGB1 protein binds to DNA containing a 1,2-intrastrand d(GpG) cross-link mainly through domain A, as revealed by footprinting, with a dissociation constant K(d) of 120 nM.
View Article and Find Full Text PDFSite-directed chemical probing of histone-DNA interactions.
Methods Mol Biol
July 2000
Department of Biochemistry and Biophysics, University of Rochester Medical Center, NY, USA.
hSWI/SNF disrupts interactions between the H2A N-terminal tail and nucleosomal DNA.
Biochemistry
June 1999
Department of Biochemistry and Biophysics, University of Rochester Medical Center, New York 14642, USA.
We have employed a site-specific core histone-DNA cross-linking approach to investigate the mechanism of hSWI/SNF remodeling of a nucleosome. Remodeling results in the complete loss of canonical contacts between the N-terminal tail of H2A and DNA while new interactions are detected between this domain and DNA near the center of the original nucleosome. The data are consistent with a model in which remodeling results in the unraveling of a region of DNA from the edge of the nucleosome, leading to a repositioning of the H2A/H2B dimer to a noncanonical position near the center of the remodeled complex.
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