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

Comparison of malM-FinP and FinP-malM chimeras binding to ProQ, ProQ^NTD, and FinO. (A) Secondary structures of malM-FinP and FinP-malM chimeras, which were predicted using RNAstructure software (Reuter and Mathews 2010). The sequences originating from malM-3′ are shown in black font and the sequences from FinP in red 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, the ProQ^NTD, and FinO are shown on the graphs below each RNA. The fitting of the quadratic equation into malM-FinP data provided a K_d value of 85 nM for binding to ProQ and 83 nM for binding to FinO, while the K_d value for binding to ProQ^NTD was estimated as higher than 200 nM. The fitting of the quadratic equation into FinP-malM data provided a K_d value of 27 nM for binding to ProQ, 4.9 nM for binding to ProQ^NTD, and 327 nM for binding to FinO. Gels corresponding to the data in the plots are shown in Supplemental Figure S6. Average K_d values are shown in Table 1.