Binding of Nucleoid-Associated Protein Fis to DNA Is Regulated by DNA Breathing Dynamics

@inproceedings{NowakLovato2013BindingON,
  title={Binding of Nucleoid-Associated Protein Fis to DNA Is Regulated by DNA Breathing Dynamics},
  author={Kristy Nowak-Lovato and Ludmil B. Alexandrov and Afsheen Banisadr and Amy L. Bauer and Alan R. Bishop and Anny Usheva and Fangping Mu and Elizabeth Hong-Geller and Kim {\O}. Rasmussen and William S. Hlavacek and Boian S. Alexandrov},
  booktitle={PLoS Computational Biology},
  year={2013}
}
Physicochemical properties of DNA, such as shape, affect protein-DNA recognition. However, the properties of DNA that are most relevant for predicting the binding sites of particular transcription factors (TFs) or classes of TFs have yet to be fully understood. Here, using a model that accurately captures the melting behavior and breathing dynamics (spontaneous local openings of the double helix) of double-stranded DNA, we simulated the dynamics of known binding sites of the TF and nucleoid… CONTINUE READING
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