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Journal of Biomolecular NMR

, Volume 56, Issue 1, pp 41–49 | Cite as

Sliding and target location of DNA-binding proteins:an NMR view of the lac repressor system

  • Karine Loth
  • Manuel Gnida
  • Julija Romanuka
  • Robert Kaptein
  • Rolf BoelensEmail author
Article

Abstract

In non-specific lac headpiece-DNA complexes selective NMR line broadening is observed that strongly depends on length and composition of the DNA fragments. This broadening involves amide protons found in the non-specific lac-DNA structure to be interacting with the DNA phosphate backbone, and can be ascribed to DNA sliding of the protein along the DNA. This NMR exchange broadening has been used to estimate the 1D diffusion constant for sliding along non-specific DNA. The observed 1D diffusion constant of 4×10−12 cm2/s is two orders of magnitude smaller than derived from previous kinetic experiments, but falls in the range of values determined more recently using single molecule methods. This strongly supports the notion that sliding could play at most a minor role in the association kinetics of binding of lac repressor to lac operator and that other processes such as hopping and intersegment transfer contribute to facilitate the DNA recognition process.

Keywords

Protein-DNA interaction One-dimensional diffusion NMR relaxation Exchange broadening Sliding 

Notes

Acknowledgments

We are grateful to Babis Kalodimos for useful discussions in an early stage of the project. This work was financially supported by NWO-Chemical Sciences (NWO-TOP and instrument funding for the 900 MHz NMR and TCI cryoprobe) and by European Commission funding through the SPINE2-Complexes (contract LSHG-CT-2006-031220) and BioNMR (contract 261863) projects. Manuel Gnida gratefully acknowledges financial support by the Deutsche Forschungsgemeinschaft.

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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Karine Loth
    • 1
    • 2
  • Manuel Gnida
    • 1
    • 3
  • Julija Romanuka
    • 1
    • 4
  • Robert Kaptein
    • 1
    • 5
  • Rolf Boelens
    • 1
    Email author
  1. 1.Bijvoet Center for Biomolecular Research, NMR SpectroscopyUtrecht UniversityUtrechtThe Netherlands
  2. 2.Centre de Biophysique MoléculaireCNRS, UPR4301, Affiliated to University of OrléansOrléans Cedex2France
  3. 3.Department of ChemistryPaderborn UniversityPaderbornGermany
  4. 4.Shell Global Solutions InternationalRijswijkThe Netherlands
  5. 5.Novosibirsk State UniversityNovosibirskRussia

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