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Preprint

Hydroxyl radical-mediated cleavage of nucleosomal DNA

GK George A. Kassavetis
GC Grisel Cruz-Becerra
JK James Takuro Kadonaga

Last updated date: Oct 22, 2022 Views: 445 Forks: 0

original An abbreviated version of this protocol was published in eLife in Oct, 2019
The tardigrade damage suppressor protein binds to nucleosomes and protects DNA from hydroxyl radicals
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  1. We wrote a detailed method for the reconstitution of nucleosomes in BioProtocol: Cruz-Becerra, G., and Kadonaga, J. T. (2021).  Reconstitution of chromatin by stepwise salt dialysis.  Bio Protoc. 11, e3977.  PMCID: PMC8054172
  2. A more detailed method for hydroxyl radical-mediated cleavage of DNA (naked DNA or nucleosomes) is attached.  The authors are George A. Kassavetis, Grisel Cruz-Becerra, and James T. Kadonaga.  Department of Molecular Biology, University of California, San Diego.  La Jolla, CA 92093 USA.
  3. Please also note that we followed the methodology that was developed in the pioneering work of Tom Tullius and colleagues: Tullius TD, Dombroski BA, Churchill ME, Kam L. 1987. Hydroxyl radical footprinting: a high-resolution method for mapping protein-DNA contacts. Methods in Enzymology 155:537–558. DOI: https://doi.org/10.1016/0076- 6879(87)55035-2, PMID: 2828876
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How to cite：
Readers should cite both the Bio-protocol preprint and the original research article where this protocol was used:
  1. Kassavetis, G A, Cruz-Becerra, G and Kadonaga, J T(2022). Hydroxyl radical-mediated cleavage of nucleosomal DNA. Bio-protocol Preprint. bio-protocol.org/prep2005.
  2. Chavez, C., Cruz-Becerra, G., Fei, J., Kassavetis, G. A. and Kadonaga, J. T.(2019). The tardigrade damage suppressor protein binds to nucleosomes and protects DNA from hydroxyl radicals. eLife. DOI: 10.7554/eLife.47682

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