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Individual lac repressor (LacI) proteins slide along DNA, frequently hopping between grooves. This sliding mechanism speeds up DNA search but can lead to bypassing target sequences, revealing a speed-accuracy trade-off.

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Genetics

Background:

  • Proteins binding specific DNA sequences utilize 3D diffusion and 1D sliding on non-specific DNA.
  • Understanding the dynamics of this 1D sliding is crucial for comprehending genome exploration.

Purpose of the Study:

  • To characterize the DNA exploration dynamics of individual lac repressor (LacI) molecules during 1D sliding.
  • To investigate the rotational motion and groove-hopping behavior of LacI on DNA.

Main Methods:

  • Utilized real-time single-molecule confocal laser tracking combined with fluorescence correlation spectroscopy (SMCT-FCS) to monitor LacI rotation on the microsecond timescale.
  • Employed single-molecule fluorescence resonance energy transfer (smFRET) to directly observe sequence bypassing events.

Main Results:

  • LacI exhibits rotation-coupled sliding, traversing approximately 40 base pairs (bp) per revolution, exceeding DNA's helical pitch.
  • Observed LacI hopping one to two grooves (10-20 bp) every 200-700 μs, indicating frequent bypassing of target sites.
  • Demonstrated a trade-off between sliding speed and search accuracy due to weak non-specific protein-DNA interactions.

Conclusions:

  • LacI's 1D sliding mechanism involves frequent groove hopping, balancing search speed with potential target bypassing.
  • The developed SMCT-FCS technique offers a powerful tool for investigating microsecond-timescale molecular dynamics in biological interactions.