The sequence and structure of the lower part of the terminator hairpins explain differences in the binding of ProQNTD and its mutants by cspE-3′ and SibB RNAs. (A–D), The secondary structures of RNA molecules are shown above the corresponding plots of fraction-bound data for WT ProQNTD (NTD) or its R69A mutant. The RNA secondary structures were predicted using RNAStructure software (Reuter and Mathews 2010). The changes introduced into the sequence of SibB are marked in red font. The data sets in which the maximum fraction bound was above 40% were analyzed by fitting to the quadratic equation. Data for SibB and cspE-3′ are the same as in Figure 3. The obtained Kd values are shown in Table 2, and raw gel data are presented in Supplemental Figure S15.
