  The transport of DNA polymers through nanoscale pores is central to many
biological processes, from bacterial gene exchange to viral infection. In
single-molecule nanopore sensing, the detection of nucleic acid and protein
analytes relies on the passage of a long biopolymer through a nanoscale
aperture. Understanding the dynamics of polymer translocation through
nanopores, especially the relation between ionic current signal and polymer
conformations is thus essential for the successful identification of targets.
Here, by analyzing ionic current traces of dsDNA translocation, we reveal that
features up to now uniquely associated with knots are instead different
structural motifs: plectonemes. By combining experiments and simulations, we
demonstrate that such plectonemes form because of the solvent flow that induces
rotation of the helical DNA fragment in the nanopore, causing torsion
propagation outwards from the pore. Molecular dynamic simulations reveal that
plectoneme initialization is dominated by the applied torque while the
translocation time and size of the plectonemes depend on the coupling of torque
and pulling force, a mechanism that might also be relevant for in vivo DNA
organization. Experiments with nicked DNA constructs show that the number of
plectonemes depends on the rotational constraints of the translocating
molecules. Thus, our work introduces plectonemes as essential structural
features that must be considered for accurate analysis of polymer transport in
the nanopore.
