FIGURE 3.

Chemical structure mappings verify folding prediction RNA. (A) 11Dr8, (B) 11Dr7 short, (C) 11Xl16, and (D) 12Xl5 were subjected to chemical modifications with DMS, CMCT, and kethoxal, and were transcribed reversely together with two sequencing reactions. Three to five experiments were done independently. Sites that were consistently accessible to modification and thus represent unpaired regions were marked on the secondary-structure prediction plot by different symbols, as indicated. A representative gel of the mapping of RNA 11Dr7 short is given in B. The primer used for RT reaches into loop 2. The folding predictions for the full-length sequence of 11Dr7 (not shown) could be verified independently.