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Cooperative non-specific DNA binding by octamerizing lambda cI repressors: a site-specific thermodynamic analysis

T R Pray1, D S Burz, G K Ackers

  • 1School of Medicine, Washington University, St Louis, MO, 63110, USA.

Journal of Molecular Biology
|October 1, 1998
PubMed
Summary

Bacteriophage lambda cI repressor oligomerization correlates with non-specific DNA binding. Only octamers showed significant non-specific DNA binding, suggesting assembly state regulates DNA sequence affinity.

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Genetics

Background:

  • Previous studies characterized wild-type and mutant cI repressors' dimerization and site-specific binding at bacteriophage lambda DNA's right operator (OR).
  • The roles of higher-order oligomers (tetramers and octamers) in cI repressor DNA interactions remained unclear.

Purpose of the Study:

  • To establish a correlation between cI repressor oligomerization and non-specific DNA-binding activity.
  • To investigate how repressor assembly state influences DNA binding specificity.

Main Methods:

  • Quantitative DNase I footprint titration to assess non-specific DNA binding by cI repressor oligomers on OR-flanking lambda DNA.
  • Modeling non-specific DNA binding using one-dimensional Ising lattice and multivalent lattice approaches.

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Main Results:

  • A strong correlation was found between repressor oligomerization and non-specific DNA binding.
  • Only repressors capable of octamerization exhibited significant non-specific DNA-binding activity.
  • Non-specific DNA binding by repressor oligomers is highly cooperative and energetically independent of site-specific binding at OR.

Conclusions:

  • The assembly state of the cI repressor molecule modulates its affinity for specific and non-specific DNA sequences.
  • Higher-order oligomers (tetramers and octamers) may preferentially bind non-specific DNA, while dimers favor specific OR sites.
  • Allosteric regulation, involving information transfer from the C-terminal to the N-terminal domain, governs these binding specificities.