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LexA-DNA bond strength by single molecule force spectroscopy.

F Kühner1, L T Costa, P M Bisch

  • 1Lehrstuhl für Angewandte Physik and Center for Nano-Science, 80799 Munich, Germany. ferdinand.kuehner@physik.uni-muenchen.de

Biophysical Journal
|September 30, 2004
PubMed
Summary

The LexA protein in E. coli binds DNA with higher affinity to recA than yebG motifs. This interaction, characterized by force spectroscopy, reveals a strong, short-range binding potential crucial for gene regulation.

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Genetics

Background:

  • The SOS system in Escherichia coli is regulated by LexA (repressor protein) and RecA (coprotease).
  • LexA controls at least 31 genes, exhibiting variable repression based on DNA binding motifs.
  • LexA utilizes helix-turn-helix motifs for DNA binding and transcription regulation.

Purpose of the Study:

  • To characterize the interaction between the LexA protein and two distinct DNA motifs (recA and yebG).
  • To quantify the binding affinity and unbinding dynamics of LexA to these DNA sequences using single-molecule force spectroscopy.

Main Methods:

  • Atomic Force Microscopy (AFM)-based single-molecule force spectroscopy.
  • Measurement of protein-DNA dissociation rates.
  • Determination of binding potential widths.

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Main Results:

  • LexA exhibited a lower dissociation rate (0.045 s⁻¹) for the recA motif compared to the yebG motif (0.13 s⁻¹), indicating higher affinity for recA.
  • Binding potential widths were measured at 5.4 ± 1 Å for recA and 4.9 ± 0.5 Å for yebG.
  • The short-ranged binding potential suggests a stiff hydrogen-bonding network, with unbinding occurring abruptly.

Conclusions:

  • LexA demonstrates a preferential binding affinity for the recA DNA motif over the yebG motif.
  • The biophysical characteristics of LexA-DNA interaction support a direct, strong binding mechanism.
  • These findings provide insights into the molecular mechanisms of LexA-mediated gene regulation within the SOS response.