Figure 3.
Secondary structure models for the STMV RNA ex virio. (A) SHAPE-directed model. Maximum allowed base pairing distance was 600 nucleotides.22 The start and stop codons for the capsid protein are boxed. (B) Linked stem-loop model, created using SHAPE data and parameters designed to force formation of short stem-loop motifs by restricting the maximum base pairing distance to ≤50 nucleotides. Nucleotides are colored by SHAPE reactivity (see legend); gray indicates no data were obtained. Calculated lengths of major structural features in each structure are shown (in nanometers).