Binding of nucleoid-associated protein fis to DNA is regulated by DNA breathing dynamics.

ABSTRACT: 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-associated protein Fis in Escherichia coli. Our study involves simulations of breathing dynamics, analysis of large published in vitro and genomic datasets, and targeted experimental tests of our predictions. Our simulation results and available in vitro binding data indicate a strong correlation betwee

SUBMITTER: Nowak-Lovato K 

PROVIDER: S-EPMC3547798 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature