As previously said, the mesoscopic model (see Sec. 3.4) with the UO NNBP energies provides a prediction of the unzipping FDC that does not quantitatively reproduce the experimental FDCs. Figures 5.1a,b show the comparison. Note that the sawtooth pattern is well reproduced by the model, in the sense that the number of slopes and force rips coincide with the experimental measurements. However, there is an evident difference in the mean unzipping force: the UO prediction overestimates this value. Moreover, there is a misalignment between the positions of the slopes and the force rips. Such differences cannot be attributed to calibration errors.
Figure 5.1c shows the comparison of the mean unzipping force for several salt concentrations of the buffer (10 mM [NaCl] - 1 M [NaCl]). This discrepancy between the UO prediction and the unzipping experiments is systematic at all salts. Besides, the sign of such discrepancy is the same for both DNA sequences.
The fit of the NNBP energies can make the mesoscopic model quantitatively match the experimental FDC. In order to do so, the FDC of a few molecules is measured at different salt concentrations. Each FDC is fit to the model and the resulting NNBP energies are averaged over all the molecules to give a final estimation of the energies at each salt. From these results, we can infer the rules to correct the NNBP energies at different salt concentrations.
In order to proceed with the fit of the FDCs, we must take into account several considerations. Next section discusses all them.
JM Huguet 2014-02-12