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LexA-DNA Bond Strength by Single Molecule Force Spectroscopy

F. Kühner ^*, L. T. Costa  , P. M. Bisch , S. Thalhammer , W. M. Heckl  and H. E. Gaub ^*

^* Lehrstuhl für Angewandte Physik and Center for Nano-Science, 80799 Munich, Germany; Department for Geo- and Environmental Sciences and Center for Nanoscience, Ludwig-Maximilians-University, Munich, Germany; and Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil

Correspondence: Address reprint requests to Ferdinand Kühner, E-mail: ferdinand.kuehner{at}physik.uni-muenchen.de.

The SOS system of Escherichia coli is coordinated by two proteins: LexA, a repressor protein of several unlinked genes, and the coprotease RecA. As known to date LexA controls 31 genes with slightly different DNA binding motifs allowing for a variable degree of repression from one gene to the other. Besides the SOS system LexA plays an important role in the regulation of transcription. The protein regulates transcription by using particular motifs to bind DNA, the helix-turn-helix motif. Here, we employed AFM-based single molecule force spectroscopy to characterize the interaction of LexA protein with two different DNA motifs: recA and yebG. We measured the dissociation rates to be 0.045 s^–1 for recA and 0.13 s^–1 for yebG, respectively, which is in accordance with the predicted higher affinity between LexA-recA compared to LexA-yebG. The widths of the binding potentials were determined to be 5.4 ± 1 Å and 4.9 ± 0.5 Å, respectively. This short-ranged potential is characteristic for a stiff hydrogen-bonding network between protein and DNA. The unbinding occurs in a breakup rather than a gradual sliding.

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