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

Comparison of cspE81-3′, cspE81-FinP chimera, and cspE81-FinP-stem chimera binding to ProQ^NTD, and to FinO. (A) Secondary structures of cspE81-3′, cspE81-FinP chimera, and cspE81-FinP-stem chimera, which were predicted using RNAstructure software (Reuter and Mathews 2010). The sequences originating from cspE81-3′ are shown in dark blue 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^NTD and FinO are shown on the graphs below each RNA. The fitting of the quadratic equation into cspE81-3′ data provided a K_d value of 2.7 nM for binding to ProQ^NTD, while the K_d value for binding to FinO was estimated as higher than 200 nM. The fitting of the quadratic equation into cspE81-FinP data provided a K_d value of 5.0 nM for binding to ProQ^NTD, and 99 nM for binding to FinO. The fitting of the quadratic equation into cspE81-FinP-stem data provided a K_d value of 55 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 S13. Average K_d values are shown in Table 1.