Prevalence of loose and tight knots in DNA investigated by a nanopore sensor

The knotting of long DNA chains is an important effect in fundamental biological processes such as DNA replication, viral DNA packaging, and transcription. Knots also become a technological challenge in the single molecule sequencing of long DNA segments. Despite being ubiquitous, there is no consensus in the literature regarding basic physical properties of equilibrium knots due to limitations of the existing experimental methods. Nanopore sensing is a new technique for investigating knots that affords high-throughput, single molecule interrogation of molecular conformations at a wide range of length-scales. Here we report a new implementation of nanopore sensing and a classification scheme, which allows us to map transient current data during knotted DNA translocation to molecular conformations and topological states. Using this methodology and a large sampling of single-molecule events, we demonstrate for the first time the co-existence of both loose and tight knots on equilibrium DNA chains. In addition, we are able to sample rare composite knot events, investigate knot localization and probe different modes of translocation.

Keywords: Solid-state nanopores, DNA knots, polymers, DNA sequencing, topology