Final answer:
In DNase Footprinting, binding affinity is estimated by the equilibrium dissociation constant, also known as KD. A small KD value indicates a strong interaction, while a large KD value reflects a weak interaction.
Step-by-step explanation:
Binding affinity in DNase Footprinting is estimated by the equilibrium dissociation constant, also known as KD. A small KD value indicates a strong interaction between the ligand and the protein, while a large KD value reflects a weak interaction. To measure binding affinity, one of the reactants (ligand or protein) is kept at a constant low concentration while the other reactant is varied. To determine binding affinity, the fraction of the ligand bound to the protein is plotted against the concentration of the other reactant, and the KD value is determined at the concentration that forces 50% binding.
The fraction of the ligand bound to the protein is then plotted against the concentration of the other reactant, and the KD value is determined at the concentration that forces 50% binding.