Different RNA recognition by ProQ and FinO depends on the sequence surrounding intrinsic terminator hairpins

Comparison of FinP, FinP-U-UAU₄, and FinP-U-U₆ binding to ProQ^NTD, and to FinO. (A) Secondary structures of FinP, FinP-U-UAU₄, and FinP-U-U₆, which were predicted using RNAstructure software (Reuter and Mathews 2010). The nucleotides from malM-3′ which were substituted into FinP are shown in black underlined font. The lowercase g denotes guanosine residue added on 5′ ends of RNA molecules to enable T7 RNA polymerase transcription. (B) The respective binding data for ProQ^NTD and FinO are shown on the graphs below each RNA. The fitting of the quadratic equation into FinP-U-UAU₄ data provided a K_d value of 4.6 nM for binding to ProQ^NTD, and 184 nM for binding to FinO. The fitting of FinP-U-U₆ data using the quadratic equation provided a K_d value of 11 nM for binding to ProQ^NTD, and 160 nM for binding to FinO. The data shown for FinP are the same as in Figure 1. Gels corresponding to the data in the plots are shown in Supplemental Figure S10. Average K_d values are shown in Table 1.