Figure 5.

Single-stranded nuclease footprinting of Pf9. (A) 5′-end labelled Pf9 was digested with indicated concentrations of RNase A (lanes 3, 4) or RNase T1 (lanes 5, 6). The cleavage products were separated on a denaturing 20% acrylamide gel. Lane 1 is undigested RNA and lane 2 is a size marker generated by alkaline hydrolysis (OH). Strong cleavages at nucleotides in the upper stem region are indicated with red arrowheads. (B) Summary of Pf9 RNA cleavages by single-stranded nucleases in the context of the predicted secondary structure of Pf9 RNA (as in Figure 1). Upper stem region is boxed in red.