The DNA is probably the most relevant biomolecule in living systems. Its structure allows it to carry out the tasks devoted to the storage, copy and transmission of the genetic information hardcopied into the base-pairs. In order to have access to the sequence, the two strands of DNA have to be split apart, in a process called unzipping. Cells have a specific machinery to produce the unzipping of DNA, whenever it is necessary. Nevertheless, the unzipping of DNA can be produced artificially by using single-molecule techniques such as optical tweezers. These experiments provide information about the thermodynamics and the kinetics of DNA duplex formation.
The unzipping of DNA using optical tweezers can be easily reproduced thanks to the great advance in molecular biology tools. DNA molecules can be synthesized with the required features in order to be pulled with optical tweezers (handles, loops, etc.).
The FDC is the characteristic measurement obtained with optical tweezers. Since the FDC is sequence-dependent, the FDC is a fingerprint of the DNA molecule. The FDC can be obtained with controlled position or controlled force protocols, which induce a different behavior in the opening of base-pairs. At controlled position, the NN model combined with a mesoscopic description of the other elements of the experiment (optical trap, handles, etc.) is able to accurately describe the quasistatic unzipping of DNA. Such mesoscopic model is quite versatile offering new insights on the physical phenomenon of unzipping. One interesting magnitude that can be calculated is the free energy landscape, which allows us to illustrate the unzipping mechanism.
Next chapters use the model and the methodology explained here to extract relevant information from DNA unzipping experiments. The results shown in those chapters reinforce the statements made here.
JM Huguet 2014-02-12