Figure 5.

Geometrical considerations. (A) The mechanical unbinding path is suggested to be similar to the thermal dissociation path: Starting from a B-DNA helix, representing the energy minimum, thermal fluctuations will open the helix at the ends and drive the system over the reduced energy barrier E-Fx. Here, the transition state has one base pair and stretched single-stranded ends that would lead (as an upper limit) to a separation increase x of 3.6 Å per base pair. (B and C) A nick (B) (located far away form the helix ends) experiences a force that should be independent of the geometry of the force at the helix ends—i.e., if the force is applied via the 3′- or 5′-ends. Therefore, the melting on stretching of a DNA (B) corresponds to the unbinding of the DNA duplex on loading via both 5′-ends (C). (C and D) The difference in the unbinding geometry of the 5′-end to 3′-end (D) and the 5′-end to 5′-end (C) separation of a DNA duplex leads to different unbinding forces because the length gained on opening one base pair is ≈2× bigger in the first compared with the second case.