6.2 Detection of metastable intermediate states

Using the same analysis technique developed in Sec. 4.1, here we identify and classify the experimental points measured in the FDC$ _f$ into the most probable state to which they might belong. This gives us information about the intermediate states observed during the unzipping at CF.

As a short reminder, the analysis consists in: 1) determine the origin of coordinates of the FDC by using the elastic response of the ssDNA when the molecule is fully open; 2) calculate the family of curves that give the elastic response of the partially unzipped molecule with $ n$ open base pairs and 3) associate each experimental point with the curve $ n$ that passes closest to this point. Finally, a histogram is computed with the list of associated states. The peaks of the histogram (see Fig. 6.4) indicate the metastable states in which the molecule is retained during the unzipping.

Figure 6.4: Histogram of intermediate states at CF of a 2.2 kbp sequence unzipped/rezipped at a loading rate of 0.05 pN$ \cdot $s$ ^{-1}$.

As expected from the clear differences between the FDC$ _f$ and the FDC$ _x$, the histograms of intermediate states are also significantly different (compare Figs. 6.4 and 4.7a). Here, the number of intermediate states is much lower and they are much more localized at the beginning of the molecule during unzipping, and at the end of the molecule during rezipping. Indeed, the sizes of opening base pairs are smaller and they are concentrated at the beginning of the FDC$ _f$. Summing up, we get less information from the sequence of DNA.

JM Huguet 2014-02-12