FIGURE 1.

Models of a 16S rRNA domain (the 126–235 RNA). (A–C) Secondary structure derived from SHAPE data (1D-data-guided) on the solution RNA, from mutate-and-map (2D-data-guided) of the solution RNA, and from crystallography in the context of the full ribosome. Colored helices are pairings under question, as described in the text and presented with the same color-coding in subsequent figures. P2* consists of noncanonical base pairs in the crystallographic model, while it is predicted as Watson-Crick-paired in 1D- and 2D-data-guided modeling. (D) Comparisons of independent SHAPE reactivity measurements of 126–235 RNA. SHAPE data presented in prior study (Deigan et al. 2009) within the full-length 16S ribosomal RNA extracted from E. coli (prior [full-length]); for a construct isolating the 126–235 domain (prior [126–235]); and from this work (current [126–235]). Standard deviations (SD) are shown, N = 7.