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    Relative Contributions of Base Stacking and Electrostatic Repulsion on DNA Nicks and Gaps

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    relative contribution.pdf
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    Type
    Article
    Authors
    Harris, Paul D.
    Hamdan, Samir cc
    Habuchi, Satoshi cc
    KAUST Department
    Biological and Environmental Sciences and Engineering (BESE) Division
    Bioscience Program
    Laboratory of DNA Replication and Recombination
    Single-Molecule Spectroscopy and Microscopy Research Group
    KAUST Grant Number
    UFR/1/3764-01-01
    Date
    2020-11-12
    Embargo End Date
    2021-11-12
    Submitted Date
    2020-07-29
    Permanent link to this record
    http://hdl.handle.net/10754/665998
    
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    Abstract
    In duplex DNA, the continuous sugar phosphate backbones prevent the double helix from significant bending, but breaks in the duplex such as nicks, gaps, and flaps present points at which significant bending is possible. The conformational dynamics of these aberrant structures remains poorly understood. Two factors can maintain the duplexlike conformation of these aberrant structures, these being the hydrophobic and aromatic stacking interactions of the nucleobases, and the electrostatic repulsion of the negatively charged backbones. Using confocal single-molecule Förster resonance energy transfer on nicked and gapped DNA structures, we compare the relative contributions of these two factors by modulating the electrostatic repulsion through mono- and divalent cation concentrations. Base stacking interactions dominate the dynamics of nicked DNA, making it behave essentially like duplex DNA. Gapped structures have weaker base stacking and thus backbone electrostatic repulsion becomes important, and shielding from cations results in an average increase in bending around the gap. This bending of gapped structures could be interpreted by increased flexibility of unstacked structures, transient unstacking events, or a combination of the two. Burst variance analysis (BVA) and analysis by photon-by-photon hidden Markov modeling (H2MM), methods capable of detecting submillisecond dynamics of single molecules in solution, only revealed a single state, indicating that dynamics are occurring at time scales shorter than microseconds.
    Citation
    Harris, P. D., Hamdan, S. M., & Habuchi, S. (2020). Relative Contributions of Base Stacking and Electrostatic Repulsion on DNA Nicks and Gaps. The Journal of Physical Chemistry B. doi:10.1021/acs.jpcb.0c06941
    Sponsors
    The authors thank Dr. Eitan Lerner for his invaluable help using FRETBursts, for writing the Jupyter notebooks used to analyze the data, and for consultation on best background thresholds and H2 MM parameters. We also thank Vlad-Stefan Raducanu for his consultation regarding labeling procedures and data interpretation. The research reported in this publication was supported by King Abdullah University of Science and Technology (KAUST), and the KAUST Office of Sponsored Research (OSR) under Award No. UFR/1/3764-01-01.
    Publisher
    American Chemical Society (ACS)
    Journal
    The Journal of Physical Chemistry B
    DOI
    10.1021/acs.jpcb.0c06941
    PubMed ID
    33179916
    Additional Links
    https://pubs.acs.org/doi/10.1021/acs.jpcb.0c06941
    ae974a485f413a2113503eed53cd6c53
    10.1021/acs.jpcb.0c06941
    Scopus Count
    Collections
    Articles; Biological and Environmental Science and Engineering (BESE) Division; Bioscience Program

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