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Rapid spontaneous accessibility of nucleosomal DNA

Nature Structural & Molecular Biology volume 12, pages 4653 (2005) | Download Citation

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Abstract

DNA wrapped in nucleosomes is sterically occluded, creating obstacles for proteins that must bind it. How proteins gain access to DNA buried inside nucleosomes is not known. Here we report measurements of the rates of spontaneous nucleosome conformational changes in which a stretch of DNA transiently unwraps off the histone surface, starting from one end of the nucleosome, and then rewraps. The rates are rapid. Nucleosomal DNA remains fully wrapped for only 250 ms before spontaneously unwrapping; unwrapped DNA rewraps within 10–50 ms. Spontaneous unwrapping of nucleosomal DNA allows any protein rapid access even to buried stretches of the DNA. Our results explain how remodeling factors can be recruited to particular nucleosomes on a biologically relevant timescale, and they imply that the major impediment to entry of RNA polymerase into a nucleosome is rewrapping of nucleosomal DNA, not unwrapping.

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Acknowledgements

We are grateful to S. Huang for valuable discussions and comments on the manuscript. We thank J. Little for the LexA expression plasmid, and the Keck Biophysics Facility at Northwestern University for the use of instruments. This work was supported by US National Institutes of Health (NIH) grants GM54692 and GM58617 to J.W., and by NIH grant GM32543, and US Department of Energy grants DE-AC03-76DF00098, GTL2BN Microscopies of Molecular Machines, and SNANOB Design of Autonomous Nanobots to C.B.

Author information

Affiliations

  1. Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, Illinois 60208-3500, USA.

    • Gu Li
    •  & Jonathan Widom
  2. Department of Physics, University of California, Berkeley, California 94720, USA.

    • Marcia Levitus
    •  & Carlos Bustamante
  3. Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.

    • Carlos Bustamante
  4. Biophysics Graduate Group, University of California, Berkeley, California 94720, USA.

    • Carlos Bustamante
  5. Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA.

    • Marcia Levitus
    •  & Carlos Bustamante

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Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Jonathan Widom.

Supplementary information

PDF files

  1. 1.

    Supplementary Fig. 1

    Stopped-flow FRET as a function of [LexA].

  2. 2.

    Supplementary Fig. 2

    Cooperative nonspecific binding by LexA.

  3. 3.

    Supplementary Fig. 3

    Stopped-flow FRET at elevated [Na+].

  4. 4.

    Supplementary Table 1

    Summary of kinetic analyses.

  5. 5.

    Supplementary Data

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DOI

https://doi.org/10.1038/nsmb869

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