QCM-based rupture event scanning technique as a simple and reliable approach to study the kinetics of DNA duplex dissociation

Rupture Event Scanning (REVS) is applied for the first time within the approach based on dynamic force spectroscopy. Using of model DNA duplexes containing 20 pairs of oligonucleotides including those containing single mismatches, we demonstrated the possibility of reliable determination of the kinetic parameters of dissociation of biomolecular complexes: barrier positions, the rate constants of dissociation, and the lifetime of complexes. Within this approach, mechanical dissociation of DNA duplexes occurs according to the mechanism similar to unzipping. It is shown that this process takes place overcoming a single energy barrier. In the case if a mismatch is located at the farthest duplex end from QCM surface, a substantial decrease in the position of the barrier between the bound and unbound states is observed. We suppose that this is due to the formation of an initiation complex containing 3-4 pairs of bases, and this is sufficient for the start of duplex unzipping.