The end loop of the molecule is a group of 4 bases that forms a different structure from the Watson-Crick base-pairs. The loop is a motif in which the backbone of the ssDNA molecule bends and twists itself. This induces a change in the orientation of the backbone that permits the formation of the DNA duplex (see Fig. 5.6a). The loop is quite useful in unzipping/rezipping experiments because the two strands of DNA are not completely split apart after unzipping, which facilitates the rezipping. Moreover, the end loop allows us to measure the elastic response of a ssDNA above pN, which is an important piece of information to infer the NNBP energies from unzipping experiments (see Fig. 5.3c,d).
The free energy formation of the loop gets contributions from the bending energy, the stacking of the bases in the loop and the loss of entropy of the ssDNA. The energy formation of the loop is positive, meaning that the loop is an unstable structure at zero force. Upon decreasing the total extension, the formation of complementary base pairs along the sequence reduces the total energy of the molecule and the loop can be formed.
The effect of the loop is appreciated only in the last rip of the FDC. It introduces a correction to the free energy of the fully extended ssDNA molecule and modifies the force at which the last rip is observed (Fig. 5.6b).
JM Huguet 2014-02-12