Effect of salt concentration on TTF-1 HD binding to specific and non-specific DNA sequences

The Thyroid Transcription factor 1 (TTF-1) recognizes specific DNA sequences by a Homeodomain (TTF-1 HD). The TTF-1 HD DNA-binding properties with both specific and non-specific DNA sequences were investigated. TTF-1 HD exists as a monomer in solution and as a monomer binds DNA. At 75 mM KCl, its relative binding affinity with a specific DNA sequence is about 50 fold higher than with a non-specific DNA sequence. Increase of KCl concentration reduces the apparent binding affinity both to specific and non-specific DNA sequences. However, non-specific binding is more sensitive than specific binding to the increase of salt concentration. When DNA-binding reactions are performed at temperature and salt concentration close to the intracellular environment, TTF-1 HD binds the specific sequence with an affinity at least 1000 fold higher respect to the non-specific sequence.