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

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.

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.