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Sequence-specific minor groove binding by bis-benzimidazoles: water molecules in ligand recognition

Nucleic Acids Research
Oxford University Press
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gkq1140 2249..2259 Concentration-dependent exchange accelerates turnover of proteins bound to double-stranded DNA John S. Graham1,*, Reid C. Johnson2 and John F. Marko1,3 1Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208-3500, 2David Geffen School of Medicine at UCLA, Department of Biological Chemistry, Los Angeles, CA 90095-1737 and 3Department of Physics, Northwestern University, Evanston, IL 60208-3112, USA Received August 30, 2010; Revised October 19, 2010; Accepted October 23, 2010 ABSTRACT The multistep kinetics through which DNA-binding proteins bind their targets are heavily studied, but relatively little attention has been paid to proteins leaving the double helix. Using single-DNA stretching and fluorescence detection, we find that sequence-neutral DNA-binding proteins Fis, HU and NHP6A readily exchange with themselves and with each other. In experiments focused on the Escherichia coli nucleoid-associated protein Fis, only a small fraction of protein bound to DNA spon- taneously dissociates into protein-free solution. However, if Fis is present in solution, we find that a concentration-dependent exchange reaction occurs which turns over the bound protein, with a rate of kexch = 6�104 M�1s�1. The bacterial DNA-binding protein HU and the yeast HMGB protein NHP6A display the same phenomenon of protein in solution accelerating dissociation of pre- viously bound labeled proteins as exchange occurs. Thus, solvated proteins can play a key role in facilitating removal and renewal of proteins bound to the double helix, an effect that likely plays a major role in promoting the turnover of proteins bound to DNA in vivo and, therefore, in controlling the dynamics of gene regulation. INTRODUCTION Many small proteins, such as transcription factors, bind the DNA double helix so as to control chromosome function and dynamics. Understanding the kinetic pathways through which such proteins find their binding sites is a subject of intense study, with 3D and 1D

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