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Department of Molecular, Cell, and Cancer Biology

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Amino Acids, Peptides, and Proteins | Biochemistry | Cell Biology | Cells | Fungi | Genetic Phenomena | Investigative Techniques | Laboratory and Basic Science Research | Microbiology | Molecular Biology


Nucleosomes are the fundamental unit of eukaryotic chromosome packaging, comprised of 147 bp of DNA wrapped around two molecules of each of the core histone proteins H2A, H2B, H3, and H4. Nucleosomes are symmetrical, with one axis of symmetry centered on the homodimeric interaction between the C-termini of the H3 molecules. To explore the functional consequences of nucleosome symmetry, we designed an obligate pair of H3 heterodimers, termed H3X and H3Y, allowing us to compare cells with single or double H3 alterations. Our biochemical validation of the heterodimeric X-Y interaction included intra-nucleosomal H3 crosslinking using dimethyl suberimidate (DMS). Here, we provide a detailed protocol for the use of DMS to analyze yeast nucleosomes.


Chromatin, Crosslink, Histone, Nucleosome, Protein-protein interaction, Streptavidin affinity chromatography

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Copyright Ichikawa and Kaufman. This article is distributed under the terms of the Creative Commons Attribution License (CC BY 4.0).

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Bio Protoc. 2018 Mar 20;8(6). doi: 10.21769/BioProtoc.2770. Link to article on publisher's site

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Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.