## 3 Results
### Hfq-CTR Stabilizes the C-Stretch Region of ColE1 Plasmid DNA  
Finally, we also analyzed the effects of CTR on the dsDNA C-stretch region of the ColE1 plasmid. First, we checked, as we did for the ColE1 origin sequence, if CTR was able to melt dsDNA (Figure 10). We observed that CTR stabilized the structure of the dsDNA region as the signal at \(\sim\)185 nm increased slightly. SRCD analysis allows measurement at 185 nm of an apparent catalytic kinetic constant k\({}_{\rm cat}\)\({}^{\rm APP}\) of 0.069 mdeg.M\({}^{-1}\).min\({}^{-1}\). To confirm this effect, we analyzed the melting curves of the duplex ColE1 C-stretch. As shown in Figure 11, we observed that the T\({}_{\rm m}\) in the presence of CTR is 10 \({}^{\circ}\)C higher than that measured for dsDNA alone. We thus confirm that Hfq-CTR significantly stabilizes the dsDNA duplex in this region of regulation of the plasmid. Note that in the case of the dsDNA C-stretch region oppositely to dsDNA origin region, we can observe a slight effect of the CTR on the kinetics of annealing. This indicates that Hfq-CTR slightly changes this C-stretch region, reinforcing the helical parameters of the dsDNA.  
Figure 8: Melting curves of RNA I-RNA II complex in the presence of Hfq-CTR (**A**) or without Hfq-CTR (**B**). The increase in CD signal, in particular at 188 nm, indicates that RNA I-RNA II complex is considerably more stable in the presence of Hfq-CTR at high temperatures (**C**). This is not the case for RNA I-RNA II complex without CTR, which melts at increasing temperatures (**D**). Blue curves show CD signal at 188 nm; red curves are at 275 nm. The T\({}_{\rm m}\) of RNAI:RNAII duplex (without CTR) is estimated \(\sim\)110 \({}^{\circ}\)C, which is remarkably high. As for Figures 3 and 4A, SRCD values in Figures 7 and 8A cannot be compared due to molecular alignment and the influence of the SRLD signal.  
Figure 10: Hfq-CTR does not melt the C-stretch region of ColE1 plasmid DNA. Rather, Hfq-CTR appears to stabilize the dsDNA structure. Spectra of the kinetics are from blue (taken 2 min after the wavelength (nm)).  
Figure 9: Observation of RNA II structure stabilization by Hfq-CTR using SRCD (**A**), while for RNA I, the CTR does not have a significant effect (**B**). Spectra in blue are with Hfq-CTR; those in green are without Hfq-CTR. The stabilization is observed by the increased amplitudes at \(\sim\)185 and 270 nm. Around 270 nm, the CD signal shows base-pairing and base-stacking [42], while the positive band at 185 nm together with the negative band around 200 nm are indicative for the formation of RNA double-stranded right-handed helix [50]. Secondary structures of RNAs corresponding to relevant spectra are also shown.  
addition of the CTR) to red (80 min after the addition of the CTR). This can be observed by the evolution of the spectra, mainly at 185 nm. Inset: kinetics of annealing at 185 nm. Kinetic constants \(\mathrm{k_{cat}}^{\mathrm{app}}\) is 0.069 mdeg.M\({}^{-1}\).min\({}^{-1}\). This indicates that Hfq-CTR stabilizes the dsDNA, as confirmed below (see Figure 11). Note that we suspect that the effect could be quasi-instantaneous after binding but cannot be analyzed during the first seconds of the kinetics due to deadtime to load the cell.