Slip sliding away: new insights into DNA-protein recognition

@article{Dahlquist2006SlipSA,
  title={Slip sliding away: new insights into DNA-protein recognition},
  author={Frederick W. Dahlquist},
  journal={Nature Chemical Biology},
  year={2006},
  volume={2},
  pages={353-354}
}
  • F. Dahlquist
  • Published 2006
  • Physics, Medicine
  • Nature Chemical Biology
DNA-binding proteins accomplish the remarkable feat of finding their correct target sequences within a sea of genomic DNA. A new study uses NMR spectroscopy to show the mechanism by which proteins may hop between and slide along DNA as they search for their target binding sites. 
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References

SHOWING 1-5 OF 5 REFERENCES
Direct observation of enhanced translocation of a homeodomain between DNA cognate sites by NMR exchange spectroscopy.
TLDR
Rapid translocation at high concentrations of free DNA observed directly by NMR exchange spectroscopy reconciles the long half-lives of protein-DNA complexes measured by biochemical analysis in vitro with the highly dynamic behavior of such complexes observed in vivo. Expand
How do site-specific DNA-binding proteins find their targets?
TLDR
A simplified version of the 'facilitated diffusion' model of Berg, Winter and von Hippel is presented, showing how non-specific DNA-protein interactions may account for accelerated targeting, by permitting the protein to sample many binding sites per DNA encounter. Expand
Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor--operator interaction: kinetic measurements and conclusions.
TLDR
The experimental data is concluded that the experimental data for the "faster-than-diffusion-controlled" interaction of repressor and operator can be quantitatively modeled by a two-step process in which sliding is the dominant transfer mechanism. Expand
Facilitated target location in biological systems.
In this minireview we have attempted to provide some overall perspective on the question of how various forms of diffusion in reduced dimensions, or diffusion within a nonspecifically bound state,Expand
Detecting transient intermediates in macromolecular binding by paramagnetic NMR
TLDR
It is shown that intermolecular paramagnetic relaxation enhancement (PRE) provides a means of directly detecting the presence of, and investigating the nature of, low population transient intermediates under equilibrium conditions. Expand