Tolerance of the pseudoknot structure to stem and loop length. (A) Mutations of the pseudoknot stem lengths. Mutated nucleotides are shown in lowercase and the mutants are boxed in colors according to their translation activity, as defined in the legend. Deletions of nucleotides are shown as Δ. (B) Primer extension inhibition and toeprinting of stem length mutants. The positions of the major stops are indicated at the right of each gel and are defined in Figure 2, A and B. (C) Mutants of the pseudoknot loop lengths and base pairing at the terminus of SI, with the mutations and the activities represented as in A. (D) Primer extension inhibition and toeprinting of SI terminus base pair mutants, labeled as in B.
