Malleable DNA knot translocation in single-digit nanopores*

Knots in long DNA molecules, prevalent in vivo, serve as a model for studying the properties of biopolymers. Here, using solid-state nanopores, we study the translocation dynamics of knots in 48.5 kbp long lambda DNA molecules in a new regime of nanoscale confinement, large driving forces applied over short timescales. We demonstrate that DNA knots translocate in an isomorphic fashion, typically retaining their morphology by quickly compressing laterally once captured in the nanopore. We see an absence of knot tightening and jamming, and only a scant effect of sliding of knots in small nanopores of 5 nm diameter. We understand the observed malleability of knots using full-atom molecular dynamics simulations that reveal a transient, localized melting of strands in the high bending regime. Our results are useful for understanding DNA packaging and regulation in vivo, physics of biopolymers under nanoconfinement, and the development of sequencing technologies based on nanopores.