Nucleosome Structure

The histone proteins interact with each other, to form a histone octamer, wrapped by approximately 146 base pairs of DNA, 1.7-1.8 times in a left-handed superhelix, to build a nucleosome (Kornberg and Lorch, 1999). Additional linker DNA between neighboring nucleosomes varies in length depending on cell type (McGhee and Felsenfeld, 1980). Properties of octamer formation were determined by ion concentration-dependent interactions. In the absence of DNA or salt the core histones form dimers of H2A and H2B, and tetramers of two H3/H4 dimers. With addition of DNA or NaCl, the core histone proteins combine to form the histone octamer. DNA-histone octamer interactions occur through the neutralization of negatively charged backbone phosphate groups by direct interactions and water-mediated hydrogen bonds with lysines and arginines. Additionally, hydrophobic interactions occur between residues such as threonine, proline, valine, and isoleucine and the deoxyribose groups of DNA (Luger et al., 1997). The lack of specific interactions with the nitrogenous base pairs corresponds with the lack of nucleotide-sequence specificity of histone-DNA interactions. Also of note, the major grooves of the two turns of DNA on each side of the nucleosome line up, forming a channel, allowing the tails of H2B and H3 to escape while the tails of H2A and H4 pass through the minor groove. Finally, the nucleosome can accommodate DNA with a slightly altered twist, allowing for potential mechanisms to shift nucleosome positions along the DNA sequence (Luger et al., 1997).

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