FIG. 4.

PabRNase HII specifically cleaves the fully annealed RNA strand of Okazaki fragment-gapped intermediates but not a 5′ RNA flap. (A) Structures of substrates S4, S5, and S6. The thick line and the closed circle represent the RNA portion and the fluorescent label, respectively. (B) The indicated amounts of PabRNase HII were incubated with the S4 substrate (lanes 1 to 4), the S5 substrate (lanes 5 to 8), and the S6 substrate (lanes 9 to 12). An 18-nt ladder was used (lane 13). Fluorescently labeled products were visualized with a Mode Imager Typhoon 9400 (GE Healthcare), and quantification was performed using ImageQuant 5.2 software.