Fluorescence anisotropy studies on the Ku-DNA interaction: Anion and cation effects

DNA non-homologous end joining starts with the binding of Ku heterodimers to double strand breaks. In this work, we characterized the thermodynamics of the Ku-DNA interaction by fluorescence anisotropy of the probe-labeled DNA. We determined that the microscopic dissociation constant (k_d) for the binding of Ku to a DNA binding site of the proper length (>20 bp) ranges from 22 to 29 nM at 300 mM NaCl. The binding isotherms for DNA duplexes with two or three heterodimers were analyzed with two independent models considering the presence and absence of overlapping binding sites. This analysis demonstrated that there is no or very weak nearest-neighbor cooperativity among the Ku molecules. These models can most likely be applied to study the interaction of Ku with duplexes of any length. Furthermore, our salt dependence studies indicated that electrostatic interactions play a major role in the binding of Ku to DNA and that the k_d decreases ∼60-fold as the salt concentration is lowered from 300 to 200 mM. The slope (T_salt) of the plot of log k_d versus log[NaCl] is 12.4 ± 0.1. This value is among the highest reported in the literature for a protein-DNA interaction and suggests that ∼12 ions are released upon formation of the Ku-DNA complex. In addition, comparison of the slope values measured upon varying the type of cation and anion indicated that approximately nine cations and three anions are released from DNA and Ku, respectively, when the complex is formed.