Nuclease V1 and hydroxyl radical (Fe(II)-EDTA) cleavage of 5'-32P-labeled LBS1 and LBS3 RNAs. (a) LBS1 was treated with nucleases under the conditions minimizing self-cleavage or (b) incubated at 50°C for 60 min and 32P-labeled product of self-cleavage was analyzed directly in the mixture. Samples (a) and (b) were analyzed as described in legend for Figure 2 except that for ribonucleases T1 and A only sequencing markers are shown. (c) LBS3 RNA and (d) its post-cleaved 5'-product re-purified by electrophoresis were subjected to ribonuclease V1 and Fe(II)-EDTA cleavage and analyzed as described under Material and Methods (See Additional file 8). (e) The results of experiments shown in Figures 4(a)-(d) and of others not shown are summarized on the proposed secondary structures for pre-cleaved and post-cleaved LBS RNA. Squares indicate the cut sites for V1 nuclease in pre-cleaved and ellipses in post-cleaved RNA. Only V1 nuclease-sensitive sites qualitatively judged to be strongly cut under the conditions stated are shown. The relative intensity of squares corresponds to the relative intensity of electrophoretic bands. Green color indicates stacking area before self-cleavage, raspberry color indicates stacking area which appears after self-cleavage. Blue and black colors indicate P1 and P4 stems, respectively.