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

Comparison of RepX, RepX-malM chimera, and malM-RepX chimera binding to ProQ^NTD, and to FinO. (A) Secondary structures of RepX, RepX-malM chimera, and malM-RepX chimera, which were predicted using RNAstructure software (Reuter and Mathews 2010). The sequences originating from RepX are shown in orange font, and the sequences from malM-3′ in black 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 RepX data provided a K_d value of 79 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 RepX-malM data provided a K_d value of 3.0 nM for binding to ProQ^NTD, and 148 nM for binding to FinO. The fitting of the quadratic equation into malM-RepX data provided a K_d value of 137 nM for binding to FinO, while the K_d value for binding to ProQ^NTD was estimated as higher than 200 nM. Gels corresponding to the data in the plots are shown in Supplemental Figure S15. Average K_d values are shown in Table 1.