Ku is a heterodimeric protein comprising 70-and 80-kDa subunits that participate in the non-homologous end-joining (NHEJ) repair pathway for rejoining DNA double strand breaks. We have analyzed the pre-steady state binding of Ku with various DNA duplex substrates and identified a redox-sensitive Ku-DNA interaction. Pre-steady state analysis of Ku DNA binding was monitored via intrinsic Ku quenching upon binding DNA and revealed that, under fully reduced conditions, binding occurred in a single-step process. Reactions performed under limited reduction revealed a two-step binding process, whereas under fully oxidized conditions, we were unable to detect quenching of Ku fluorescence upon binding DNA. The differential quenching observed under the different redox conditions could not be attributed to two Ku molecules binding to a single substrate or Ku sliding inward on the substrate. Although only modest differences in Ku DNA binding activity were observed in the stoichiometric anisotropy and electrophoretic mobility shift assay studies, as a function of redox conditions, a dramatic difference in the rate of Ku dissociation from DNA was observed. This effect was also induced by diamide treatment of Ku and could be abrogated by dithiothreitol treatment, demonstrating a reversible redox effect on the stability of the Ku-DNA complex. The redox-dependent alteration in Ku-DNA interactions is manifested by a redox-dependent alteration in Ku structure, which was confirmed by limited proteolysis and mass spectrometry analyses. The results support a model for the interaction of Ku with DNA that is regulated by redox status and is achieved by altering the dissociation of the Ku-DNA complex.
DNA double strand breaks (DSBs)2 can be a lethal type of DNA damage. Cells have developed two major pathways in which to remove such damage, homologous recombination and NHEJ (1). The Ku autoantigen is an essential component of the NHEJ pathway. Ku shows a high affinity for double strand DNA termini (2), and once bound to the DNA end, increases the affinity of the DNA-PK catalytic subunit (DNA-PKcs) for the DNA termini (3). To accommodate the large 469-kDa DNA-PKcs, Ku translocates inward on the DNA in an ATP-independent manner, ultimately forming the active DNA-PK complex (3, 4). Activated DNA-PK then phosphorylates target proteins, including Artemis (5), Mre11/Rad50/NBS1 complex (6), and DNA ligase IV/XRCC4 (7), all of which participate in either signaling events in response to DNA damage or completing the repair process.The crystal structure of free Ku and the Ku-DNA complex has been solved and reveals a novel DNA binding structure comprising a base, two pillars, and a bridge through which the duplex DNA can thread (8). The Ku70 and -80 subunits share minimal sequence homology, yet adopt similar three-dimensional structures, with each subunit contributing to the base, pillars, and bridge (8). This ring-like structure of Ku provides the structural basis for the DNA termini requirement for binding as well as the energy-independent ability...