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The structure of DNA in the nucleosome core

Abstract

The 1.9-Å-resolution crystal structure of the nucleosome core particle containing 147 DNA base pairs reveals the conformation of nucleosomal DNA with unprecedented accuracy. The DNA structure is remarkably different from that in oligonucleotides and non-histone protein–DNA complexes. The DNA base-pair-step geometry has, overall, twice the curvature necessary to accommodate the DNA superhelical path in the nucleosome. DNA segments bent into the minor groove are either kinked or alternately shifted. The unusual DNA conformational parameters induced by the binding of histone protein have implications for sequence-dependent protein recognition and nucleosome positioning and mobility. Comparison of the 147-base-pair structure with two 146-base-pair structures reveals alterations in DNA twist that are evidently common in bulk chromatin, and which are of probable importance for chromatin fibre formation and chromatin remodelling.

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The authors declare that they have no competing financial interests.

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Acknowledgements

We thank I. Berger and D. Sargent for comments on the manuscript. This study was supported by the Swiss National Science Fund.

Author information

Competing interests

The authors declare that they have no competing financial interests.

Correspondence to Timothy J. Richmond.

Supplementary information

Supplementary Figure 1: Schematic diagrams of base-pair and base-pair-step parameters (JPG 45 kb)

Supplementary Methods: Calculation of DNA curvature, base pair and base-pair-step parameters, and backbone geometry. (DOC 28 kb)

Supplementary Information: Comparison of mean roll angles for NCP147 and oligonucleotide DNA. (DOC 28 kb)

Supplementary Tables: 1.) DNA mean conformational parameters. 2.) Principle components of DNA conformational parameters. 3.) Deviation of DNA phosphate group position for homologous histone motifs. (DOC 86 kb)

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Further reading

Figure 1: Superhelical path and base-pair-step parameters for NCP147 DNA.
Figure 2: DNA bending in the NCP147 DNA.
Figure 3: Oscillation of the base-pair-tip parameter for NCP147 DNA.
Figure 4: Structural alignments of the histone-fold DNA-binding motifs and bound-phosphate groups.

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