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Albany 2019: 20th Conversation - Abstracts

category image Albany 2019
Conversation 20
June 11-15 2019
Adenine Press (2019)

Investigating the structural dynamics of DNA in nucleosome core particles

DNA is tightly packaged around nucleosome core particles (NCPs) for efficient storage, yet must remain readily accessible for processing. Our interest is in developing experimental tools that reveal the global structure(s) of DNA in NCPs, to understand the molecular mechanisms by which release is affected by factors including histone or DNA sequence variations or the action of partner molecules, such as remodelers or chaperones. To accomplish this goal, we must be able to detect the global structure(s) of the DNA in the presence of protein partners. Contrast variation small angle x-ray scattering is an ideal probe of the conformation of the nucleic acid component of a protein-nucleic acid complex(1). This method can be implemented in either static (2) or time-resolved studies (3). As a proof of principle, we studied the salt dependent conformations of DNA in NCPs, in both equilibrium and time resolved studies. Data were analyzed using an ensemble optimization method that yields plausible structural ensembles present under each different solution condition or at different time during a dynamic release experiment. Initially, we employed the tightly positioning Widom 601 DNA sequence and canonical histones (2,3); we recently expanded our studies to account for DNA sequence using sequence specific models to create ensembles(4), histone variants, and finally the addition of chaperones such as the Chd-1 remodeler (5).

LP’s research on NCPs is supported by NIH under: R35GM122514.

References

    1. Tokuda JM, Pabit SA, Pollack L (2016) Protein-DNA and ion-DNA interactions revealed through contrast variation SAXS. Biophys Rev:1–11.

    2. Chen YJ, et al. (2014) Revealing transient structures of nucleosomes as DNA unwinds. Nucleic Acids Res 42(13):8767–8776.

    3. Chen Y, et al. (2017) Asymmetric unwrapping of nucleosomal DNA propagates asymmetric opening and dissociation of the histone core. Proc Natl Acad Sci U S A 114(2):334–339.

    4. Mauney AW et al., (2018) Local DNA Sequence Controls Asymmetry of DNA Unwrapping from Nucleosome Core Particles. Biophys. J. 115(5):773-781.

    5. Tokuda JM, et al. (2018) The ATPase motor of the Chd1 chromatin remodeler stimulates DNA unwrapping from the nucleosome. Nucleic Acids Res. 46(10):4978-4990.

Lois Pollack

School of Applied and Engineering Physics
Cornell University
Ithaca, NY 14853 US

Email: lp26@cornell.edu

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Possible conformations of DNA in an NCP, in the presence of a remodeling protein. With contrast variation SAXS, only the structure of the DNA is measured, even though the proteins are present. Structures from work described in Ref. 5.