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Proc Natl Acad Sci U S A. 2017 Apr 18;114(16):E3251-E3257. doi: 10.1073/pnas.1701884114. Epub 2017 Mar 31.

Facilitated dissociation of transcription factors from single DNA binding sites.

Author information

1
Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208.
2
Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208.
3
Department of Materials Science and Engineering, Northwestern University, Evanston, IL 60208.
4
Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208; m-olvera@northwestern.edu john-marko@northwestern.edu.
5
Department of Chemistry, Northwestern University, Evanston, IL 60208.
6
Department of Biological Chemistry, David Geffen School of Medicine at the University of California, Los Angeles, CA 90095.
7
Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208; m-olvera@northwestern.edu john-marko@northwestern.edu.

Abstract

The binding of transcription factors (TFs) to DNA controls most aspects of cellular function, making the understanding of their binding kinetics imperative. The standard description of bimolecular interactions posits that TF off rates are independent of TF concentration in solution. However, recent observations have revealed that proteins in solution can accelerate the dissociation of DNA-bound proteins. To study the molecular basis of facilitated dissociation (FD), we have used single-molecule imaging to measure dissociation kinetics of Fis, a key Escherichia coli TF and major bacterial nucleoid protein, from single dsDNA binding sites. We observe a strong FD effect characterized by an exchange rate [Formula: see text], establishing that FD of Fis occurs at the single-binding site level, and we find that the off rate saturates at large Fis concentrations in solution. Although spontaneous (i.e., competitor-free) dissociation shows a strong salt dependence, we find that FD depends only weakly on salt. These results are quantitatively explained by a model in which partially dissociated bound proteins are susceptible to invasion by competitor proteins in solution. We also report FD of NHP6A, a yeast TF with structure that differs significantly from Fis. We further perform molecular dynamics simulations, which indicate that FD can occur for molecules that interact far more weakly than those that we have studied. Taken together, our results indicate that FD is a general mechanism assisting in the local removal of TFs from their binding sites and does not necessarily require cooperativity, clustering, or binding site overlap.

KEYWORDS:

DNA–protein interactions; biomolecule binding; chemical kinetics; facilitated dissociation; transcription factor

PMID:
28364020
PMCID:
PMC5402408
DOI:
10.1073/pnas.1701884114
[Indexed for MEDLINE]
Free PMC Article

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