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

Comparison of malM-3′, malM-3′-A-GU₆, and malM-3′-A-GAU₅ binding to ProQ^NTD, and to FinO. (A) Secondary structures of malM-3′, malM-3′-A-GU₆, and malM-3′-A-GAU₅, which were predicted using RNAstructure software (Reuter and Mathews 2010). The nucleotides from FinP which were substituted into malM-3′ are shown in red 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 malM-3′-A-GU₆ data provided a K_d value of 1.8 nM for binding to ProQ^NTD, and 151 nM for binding to FinO. The fitting of the quadratic equation into malM-3′-A-GAU₅ data provided a K_d value of 122 nM for binding to FinO, while the K_d value for binding to ProQ^NTD was estimated as higher than 200 nM. The data shown for malM-3′ are the same as in Figure 1. Gels corresponding to the data in the plots are shown in Supplemental Figure S7. Average K_d values are shown in Table 1.