FIG. 3.
Ku and DNA-PK bind to DNA with hairpin ends. (A) Ku and DNA-PK binding to open-ended DNA. A 70-bp open-ended DNA probe was incubated with increasing amounts of 70% pure DNA-PK (0.37, 1.1, and 3.3 Promega units in lanes 1 to 3, respectively) or purified Ku (14, 42, and 126 ng in lanes 4 to 6, respectively) or without added protein (lane 7) and resolved by nondenaturing polyacrylamide gel electrophoresis. Positions are indicated for free DNA probe (F), complexes containing one, two, or three Ku molecules, and a DNA-PK complex containing Ku and DNA-PKCS. (B) DNA-PK binding to hairpin- and open-ended DNA. DNA-PK (1.1 U) was incubated with DNA probes consisting of either a 68-bp hairpin-ended molecule (lanes 1 to 7) or a 70-bp open-ended molecule (lanes 8 to 14). For each probe, incubations were also done with unlabeled competitor DNA consisting of either the hairpin-ended molecule (lanes 2 to 4 and 9 to 11) or the open-ended molecule (lanes 5 to 7 and 12 to 14) in increasing amounts of 0.04, 0.20, and 1.0 ng.