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Published on: June 3, 2019
Probing DNA base pairing energy profiles using a nanopore
Virgile Viasnoff1, Nicolas Chiaruttini, Ulrich Bockelmann
1Laboratoire de Nanobiophysique, CNRS, ESPCI ParisTech, 10 rue Vauquelin, 75005 Paris, France. virgile.viasnoff@espci.fr
Abstract:
We experimentally show that the voltage driven unzipping of long DNA duplexes by an alpha-hemolysin pore is sensitive to the shape of the base pairing energy landscape. Two sequences of equal global stability were investigated. The sequence with an homogeneous base pairing profile translocates faster than the one with alternative weak and strong regions. We could qualitatively account for theses observations by theoretically describing the voltage driven translocation as a biased random walk of the unzipping fork in the sequence dependent energy landscape.

