Figure 2.

DsrA–RNA interactions in the middle stem-loop. (A) Computer sequence alignment of the hns coding sequence depicted as a coaxial stack with regions of DsrA. The two regions of DsrA complementary to hns are depicted as boxed (region 2.1) and as white letters on a black background (region 2.2). Nuclease susceptibility (black lollipops) and numbers over stem-loops are as in Fig. 3. (B and C) Other RNAs modeled as coaxial stacks. The argR (B) and ilvIH (C) RNAs of E. coli with DsrA complementarity. Because of overlap in the DsrA complementary sequences, there is potential for different pairings within coaxial stacks (lowercase letters). Vertical lines represent base pairs verified by compensatory mutagenesis (4); dashed vertical lines represent base pairs predicted by informatic or biochemical analyses; a colon (:) represents a G:U base pair; ○ represents a G:A base pair. Start codons are circled; stop codons are boxed.