Similar DNA binding properties of free P70 (KU) subunit and P70/P80 heterodimer

The Ku antigen consists of 70 and 80 kDa protein subunits (p70 and p80, respectively) that form the DNA binding component of a DNA-dependent protein kinase (DNA-PK). It is controversial whether the interaction of Ku with DNA is mediated by p70 alone or requires formation of p70/p80 dimers. In the present studies, the DNA binding properties of p70/p80 heterodimers and full-length human p70 expressed in the absence of p80 were investigated. The binding of free p70 and p70/p80 heterodimers to DNA showed similar sensitivity to high ionic strength buffers. Competitive DNA binding studies revealed that free p70, like the p70/p80 heterodimer, bound preferentially to linear double stranded DNA fragments, whereas tRNA and closed circular DNA molecules competed poorly with the radiolabeled linear DNA for binding to Ku. These studies suggest that free p70 and p70/p80 heterodimers have similar DNA binding properties, and that the interaction of Ku with DNA may depend primarily on the p70 subunit, possibly with implications for the assembly and function of DNA-PK.