Probing DNA base pairing energy profiles using a nanopore.
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.
Viasnoff
Virgile
V
Laboratoire de Nanobiophysique, CNRS, ESPCI ParisTech, 10 rue Vauquelin, 75005 Paris, France. virgile.viasnoff@espci.fr
Chiaruttini
Nicolas
N
Bockelmann
Ulrich
U
D010582:Bacteriophage lambda; D020029:Base Pairing; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure; D004586:Electrophoresis / Q000379:methods*; D006460:Hemolysin Proteins / Q000737:chemistry*; D008958:Models, Molecular; D009691:Nucleic Acid Denaturation; D044367:Phase Transition; D013816:Thermodynamics
D006460:Hemolysin Proteins; D004247:DNA