The unzipping of long molecules of DNA requires the design and synthesis of molecular constructs that can be pulled with optical tweezers. Optical tweezers use beads to apply forces on the molecules. Therefore, the DNA molecules have to be synthesized with labeled ends, so that the DNA can be bonded to the beads. In our case, the labels must be positioned in the and extremities of the handles.
The synthesis of DNA constructs involves a series of simple steps such as cleavage, electrophoresis or annealing among others. Protocols to carry out these steps are commercially available and are highly efficient. Our protocol of synthesis starts from -DNA molecules which is then cut into several fragments. Latter, the desired fragments are selected and the labeled handles are added. Two different sequences of DNA have been used in our experiments. The first one has a length of 6.8 kbp and the second one has 2.2 kbp. In what follows, we describe the procedure to synthesize the 6.8 kbp sequence.