Figure 3.

Application of the high-resolution northern blotting in monitoring RNA reagents expressed in cells. A) Processing of antisense-sense and sense-antisense shRNAs (L-shSCA3 and R-shSCA3, respectively). The 5' and 3' strands of each shRNA were analyzed by detection with probes complementary to either siRNA strand, as indicated in the figure. One probe detected L-5' and R-3' strands (dotted line) while the other probe detected L-3' and R-5' strands (dashed line). B) ssRNA CUG9 and shRNA CAG/CUG7 transcribed from vectors, having either 4T or 6T at their termination sites. M denotes size markers; M1 denotes end-labeled 17, 19, 21, 23, and 25-nt synthetic RNA oligonucleotides and M2 denotes RNA Low Molecular Weight Marker (USB). Quantitative representations of siRNA length variants are shown in the bottom panel, using peaks obtained from phosphorimaging analyses.