5.2 Parameters defining the theoretical FDC

The theoretical FDC computed in Sec. 3.4.1 requires the knowledge of several (theoretical and empirical) parameters. The equations that determine the total extension (Eq. 3.23) and the total energy (Eq. 3.22) implicitly depend on:

Figure 5.2: Dependence of the theoretical FDC on the experimental parameters for the 2.2 kbp sequence. (a) Trap stiffness. The three cases have the same mean unzipping force, so the curves have been displaced vertically $ \pm 2$ pN for convenience. There are no significant differences between the 60 and the 80 pN/$ \mu $m curves. However if the trap is orders of magnitude stiffer, the sawtooth pattern is appreciably different at short distances. As the ssDNA is released, the effective stiffness of the system decreases and the FDC looks like the other two cases. (b) Elasticity of the handles. The persistence length ($ l_p$) of the dsDNA hardly changes the shape of the FDC ($ <0.05$ pN). (c) Elasticity of the ssDNA. The Kuhn length ($ b$) of the ssDNA (which is directly related with the rigidity) changes the mean unzipping force. The higher the rigidity, the lower the unzipping force. (d) NNBP energies. A global increment or decrement of the NNBP energies modifies the mean unzipping force.

In order to obtain an estimation of the NNBP, all the other parameters must be fixed. The stiffness of the optical trap and the elastic properties of the handles can be determined easily. However, some experiments must be carried out in order to determine the elastic properties of the ssDNA. Apart from this, there are two more issues that have to be addressed before proceeding with the fit of the NNBP. The following sections deal with them.

JM Huguet 2014-02-12