FIG. 3.

PabRNase HII specifically cleaves RNA-initiated DNA segments fully annealed to a DNA template. (A) Structures of substrates S1, S2, and S3. 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 S1 substrate (lanes 2 to 5), the S2 substrate (lanes 6 to 9), and the S3 substrate (lanes 10 to 13). A base-hydrolyzed ladder (lane 1) was prepared as explained in Materials and Methods. Fluorescently labeled products were visualized with a Mode Imager Typhoon 9400 (GE Healthcare), and quantification was performed using ImageQuant 5.2 software.