Figure 1.

Secondary structures of WT and mutant 5′ BC1 domains. A, Secondary structure of the WT 5′ BC1 domain was established by chemical and enzymatic probing (Rozhdestvensky et al., 2001). GA motif, unpaired U22, and the basal internal loop (IL) are indicated. Noncanonical purine·purine pairs are symbolized by •, standard WC pairs by = (GC) or − (AU), wobble WC pairs by ·. The noncanonical GA core motif resides in an A-form helix in the 5′ BC1 stem–loop domain (Muslimov et al., 2006, 2011). The GA core is clamped by canonical base pairs which are mostly G=C standard WC. The following 5′ domain mutations were introduced into full-length BC1 RNA. B, The WC mutation abolishes the 5′ BC1 GA motif by conversion to WC base pairing. C, Mutant 5′ BC1 ΔU22 lacks the unpaired U residue at position 22. D, In mutant 5′ BC1 ΔIL, the basal internal loop has been eliminated by conversion to WC base pairing. Substitution mutations are indicated in red.