Fig. 4

Structural requirements of Type I stem-loops for RNA cleavage. a Analysis of the structural conservation of the Type I stem-loops located in IR1, IR5, and IR10, in which there are two 2-GC-pair regions, respectively, located at the bottom (GC1) and top (GC2) of stems. b, c Effect of deletion of the 2-GC-pair region of IR1-SL1 in the dual-fluorescence reporter system, as analyzed by Northern blotting (b) and qRT-PCR (c). d, e Effect of the arrangement of GC1 in IR1-SL1, as analyzed by Northern blotting (d) and qRT-PCR (e). f, g Effect of deletion of the 2-GC-pair region of IR5-SL1, as analyzed by Northern blotting (f) and qRT-PCR (g). h, i Effect of deletion of the GC3 of IR5-SL1 (h) and replacement of two 2-GC-pair region of IR10-SL (i) was analyzed by Northern blotting. j, k Stem-loop of Type I was designed employing the stem-loop SLx (j) and its function was analyzed by Northern blotting (k). Black arrows highlight the positions of bands that correspond to transcripts as indicated on the right side of the panel of Northern blotting results. 16S rRNA was used as a loading control. Error bars indicate the standard deviation of the mean from experiments done in triplicate