Skip to main content
. Author manuscript; available in PMC: 2013 Jan 20.
Published in final edited form as: J Mol Biol. 2011 Nov 4;415(3):489–502. doi: 10.1016/j.jmb.2011.10.046

Figure 2.

Figure 2

Primary and predicted secondary structures of RNA constructs used in this work. a. ACD, central domain of 16S rRNA from A. aeolicus. The ACD helices are labeled (italic) as the homologus secondary structure of E. coli 16S rRNA. Identical bases in the central domains of A. aeolicus, T. thermophilus, and E. coli are printed in black. A. aeolicus bases identical to E. coli, T. thermophilus, or neither are printed in green, orange, and gray respectively. The italic bases indicate non-ribosomal nucleotides included in the sequences for ease of transcription. The helical region corresponding to the minimal site for specific binding of E. coli S8 is boxed in red. The smallest sequence of RNA mapped to a picomolar Kd for AS8 is boxed in blue. b. AFr1 is the A. aeolicus 16S rRNA construct that was previously identified with a picomolar Kd for AS8. c and d. ΔH21 and ΔH23 were used in EMSA experiments to map the smallest RNA with a picomolar Kd for AS8 (blue box in Figure 2a). e. Minimal 16S rRNA construct required for specific binding to AS8. Protein binding to this site was monitored by both competition EMSA and fluorescence anisotropy assays. The position of the fluorescein label on the minimal RNA construct is labeled Fl.