Inhibition of the catalytic activity of DNA-PKcs in XRCC4 deficient cells does not prevent the processing of DSB ends into ssDNA. (A) GM16147 (XRCC4 deficient) cells were incubated with 50 μM NU7026 and the DNA was extracted with the warm or cold protocol at different repair times after irradiation. The number of DNA fragments was determined by PFGE and normalized to the number of DNA fragments at 0 h by the cold protocol. Error bars represent the SD of three experiments. *Denotes significant difference with paired t-test (p < 0.05) between warm and cold extraction. (B and C) BrdU corresponding to ssDNA was detected 4 h after irradiation in GM16147 cells treated with 50 μM NU7026 and cells were scored as belonging to one of the following categories: I. Weak BrdU staining in the whole nucleus; II. Increased BrdU staining in the nucleus compared to I or > 20 strong dots in the nucleus; III. Strong dots in the whole nucleus and background staining in the whole nucleus. At least 100 cells in three experiments were scored. Error bars represent the SD.