Figure 5.

Calculation of mean basepair free energies from unzipping measurements. The configuration of the experimental setup at two different distances (λ₁, λ₂) is shown above the FDC. The sawtooth pattern (inset) is approximated by a straight line corresponding to the mean unzipping force (f_p). The force equals f_p at λ₁ and λ₂, so the extension of trap and molecular handles (x_T, x_h) stays constant. Different distances λ correspond then to different ssDNA extensions. The reversible work necessary to drive the system reversibly from λ₁ to λ₂ corresponds to the area in the dashed rectangle. Along this transition, n basepairs are disrupted, and the corresponding free-energy change involves both the basepairing free energy and the free energy due to stretching 2n bases of ssDNA. The basepair free energy can be recovered once the elastic contribution arising from stretching the ssDNA is subtracted from W (as detailed in the main text). To see this figure in color, go online.