The force feedback of the instrument follows a proportional protocol (see Eq. C.2) that corrects the position of the optical trap to keep the force constant. The feedback runs at 4 kHz but the natural bandwidth of the wiggler is about kHz . It means that the electronic controller can give orders faster than the time spent by the wiggler to reposition the optical trap. Strictly speaking, the bandwidth of the wiggler limits the chances to perform unzipping at CF. In addition, the thermal force spectrum of a polystyrene bead surrounded by distilled water in a trap stiffness of 75 pNm has a corner frequency of about 1 kHz. Our force feedback has a similar bandwidth and it is not capable of canceling out the noise of the thermal forces. Nevertheless, we are not really interested in having the thermal forces constant. Instead, we want to control the force when the opening of base pairs is produced during unzipping, which is a phenomenon that occurs at a time scale of 1 s (=1 Hz). Because of the difference in time scales, the force feedback is useful to perform our experiments.
Figure 6.1 shows the typical measurements in a CF unzipping experiment performed on a 2.2 kbp sequence. These experiments are characterized by the loading rate, which is 0.05 pNs in this particular example. The force is the control parameter that increases monotonically while the distance evolves according to the opening of base pairs of the DNA molecule. We compare the new measurements with a previous ones with controlled trap position.
JM Huguet 2014-02-12