  DNA unzipping by nanopore translocation has implications in diverse contexts,
from polymer physics to single-molecule manipulation to DNA-enzyme interactions
in biological systems. Here we use molecular dynamics simulations and a
coarse-grained model of DNA to address the nanopore unzipping of DNA filaments
that are knotted. This previously unaddressed problem is motivated by the fact
that DNA knots inevitably occur in isolated equilibrated filaments and in vivo.
We study how different types of tight knots in the DNA segment just outside the
pore impact unzipping at different driving forces. We establish three main
results. First, knots do not significantly affect the unzipping process at low
forces. However, knotted DNAs unzip more slowly and heterogeneously than
unknotted ones at high forces. Finally, we observe that the microscopic origin
of the hindrance typically involves two concurrent causes: the topological
friction of the DNA chain sliding along its knotted contour and the additional
friction originating from the entanglement with the newly unzipped DNA. The
results reveal a previously unsuspected complexity of the interplay of DNA
topology and unzipping, which should be relevant for interpreting
nanopore-based single-molecule unzipping experiments and improving the modeling
of DNA transactions in vivo.
