Slip sliding away: new insights into DNA-protein recognition

  title={Slip sliding away: new insights into DNA-protein recognition},
  author={Frederick W. Dahlquist},
  journal={Nature Chemical Biology},
  • 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. 
Reaction-Diffusion kinetics of Protein DNA Interactions
This thesis uses various aspects of reaction-diffusion theory to solve the challenge of rapidly finding one specific binding site among millions of nonspecific sites on the chromosomal DNA. Expand
Protein sliding along DNA: dynamics and structural characterization.
The presented model that captures various experimental features of facilitated diffusion has the potency to address other questions regarding the nature of DNA search, such as the sliding characteristics of oligomeric and multidomain DNA-binding proteins that are ubiquitous in the cell. Expand
Physical signals for protein-DNA recognition.
Findings show that current promoter prediction programs (PPPs) based on DNA physical properties may suffer from lots of false positives because other functional sites such as splice sites and replication origins have similar physical signals as promoters do. Expand
New Insights into DNA Recognition by Zinc Fingers Revealed by Structural Analysis of the Oncoprotein ZNF217*
The structure of a ZNF217-DNA complex is determined and it is shown that although the overall position of the ZFs on the DNA closely resembles that observed for other ZFs, the side-chain interaction pattern differs substantially from the canonical model. Expand


Direct observation of enhanced translocation of a homeodomain between DNA cognate sites by NMR exchange spectroscopy.
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?
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.
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
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