Abstract
Nanopore force spectroscopy is used to study the unzipping kinetics of two DNA hairpinmolecules with a 12 base pair long stem containing two contiguous stretches of six GC andsix AT base pairs in interchanged order. Even though the thermodynamic stabilities ofthe two structures are nearly the same, they differ greatly in their unzippingkinetics. When the GC segment has to be broken before the AT segment, theunfolding rate is orders of magnitude smaller than in the opposite case. We alsoinvestigated hairpins with stem regions consisting only of AT or GC base pairs. Thepure AT hairpins translocate much faster than the other hairpins, whereas thepure GC hairpins translocate on similar timescales to the hairpins with only aninitial GC segment. For each hairpin, nanopore force spectroscopy is performed fordifferent loading rates and the resulting unzipping distributions are mathematicallytransformed to a master curve that yields the unfolding rate as a function of appliedvoltage. This is compared with a stochastic model of the unfolding process for thetwo sequences for different voltages. The results can be rationalized in termsof the different natures of the free energy landscapes for the unfolding process.
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