Biological Applications of Dynamic Force Spectroscopy - Dynamic Force Spectroscopy and Biomolecular Recognition - page 221

(a) (b)

AFM
Cantilever

Linker

DNA

Linker

FIGURE 6.9 Sketch of the experimental setup used to measure by DFS the unbinding forces
between complementary single DNA strands. (a) DNA was anchored to both the AFM tip
and a substrate through a PEG linker. By approaching the tip to the substrate, a DNA duplex
may be formed. (b) An unbinding process of DNA duplex occurs by retracting the tip from
the substrate. (Adapted from Strunz, T. et al. 1999. Proc. Natl. Acad. Sci. U.S.A , 96:11277-
11282.)

scaling of the unbinding forces. Schumakovitch et al. have successively extended
the study of the unbinding process between DNA strands to include an analysis at
different temperatures (Schumakovitch et al., 2002). They found that the dissociation
rate increases with the temperature whereas the energy barrier width decreases (see
Table 6.4). The temperature dependence of the dissociation rate has been observed
to be in good agreement with the data obtained in bulk solution by the temperature
jump technique. From the Arrhenius plot, they have extracted the activation enthalpy
for the dissociation process by finding a value again consistent with that extracted
by bulk experiments. Such an agreement has been put into relationship to the use
of a slow pulling rate in DFS experiments, which allows to more correctly probe
the energy barrier. At variance, the observed temperature dependence of the energy
barrier width, which is assumed to be constant in the framework of the Bell-Evans
model, has been tentatively ascribed to an entropic contribution to the process. In
this respect, they have remarked that possible discrepancies among DFS data might
arise from temperature effects that are not accounted for by the Bell-Evans model,
and whose effective impact on the final results should be instead taken into account.
Eckel et al. have explored the DFS capabilities to investigate the interaction of
a synthetic peptide with a double-stranded DNA sequence (Eckel et al., 2005). The