Base-pairing models for tertiary interactions in B. stearothermophilus trp leader RNA. Models 1 and 2 contain interactions between the single-stranded TRAP binding site (ssTBS) and both the 5′ and 3′ sides of the pyrimidine-rich internal loop (See Fig. 3). In contrast, models 3 and 4 contain only interactions between the ssTBS and the 5′ side of the pyrimidine-rich internal loop. Models 3 and 4 may also have interactions to the 3′ side of the internal loop, but are not shown here. Models 1 and 2 have similar pairings at the top of the structure, as do models 3 and 4, whereas models 1 and 3 have similar pairings at the base of the structure, as do models 2 and 4. Note that models 1, 3, and 4 have the potential for an A+•C base-pairing interaction, which is stabilized by lower pH. Mutants used to test the models are shown, and numbering is from the start of transcription.
