title: Direct observation of DNA knots using a solid-state nanopore.
abstract: Long DNA molecules can self-entangle into knots. Experimental techniques for observing such DNA knots (primarily gel electrophoresis) are limited to bulk methods and circular molecules below 10 kilobase pairs in length. Here, we show that solid-state nanopores can be used to directly observe individual knots in both linear and circular single DNA molecules of arbitrary length. The DNA knots are observed as short spikes in the nanopore current traces of the traversing DNA molecules and their detection is dependent on a sufficiently high measurement resolution, which can be achieved using high-concentration LiCl buffers. We study the percentage of molecules with knots for DNA molecules of up to 166 kilobase pairs in length and find that the knotting occurrence rises with the length of the DNA molecule, consistent with a constant knotting probability per unit length. Our experimental data compare favourably with previous simulation-based predictions for long polymers. From the translocation time of the knot through the nanopore, we estimate that the majority of the DNA knots are tight, with remarkably small sizes below 100 nm. In the case of linear molecules, we also observe that knots are able to slide out on application of high driving forces (voltage).
authors.affiliation: Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
authors.forename: Calin
authors.identifier: 0000-0002-8121-3344
authors.initials: C
authors.lastname: Plesa
authors.affiliation: Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
authors.forename: Daniel
authors.initials: D
authors.lastname: Verschueren
authors.affiliation: Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
authors.forename: Sergii
authors.initials: S
authors.lastname: Pud
authors.affiliation: Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
authors.forename: Jaco
authors.initials: J
authors.lastname: van der Torre
authors.affiliation: Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
authors.forename: Justus W
authors.initials: JW
authors.lastname: Ruitenberg
authors.affiliation: Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
authors.forename: Menno J
authors.initials: MJ
authors.lastname: Witteveen
authors.affiliation: Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
authors.forename: Magnus P
authors.initials: MP
authors.lastname: Jonsson
authors.affiliation: Department of Physics and Center for Soft Matter Research, New York University, 4 Washington Place, New York, New York 10003, USA.
authors.forename: Alexander Y
authors.initials: AY
authors.lastname: Grosberg
authors.affiliation: Department of Physics and Institute for Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan 52900, Israel.
authors.forename: Yitzhak
authors.initials: Y
authors.lastname: Rabin
authors.affiliation: Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
authors.forename: Cees
authors.initials: C
authors.lastname: Dekker
mesh_terms: D004247:DNA / Q000032:analysis* / Q000737:chemistry*; D027101:DNA Topoisomerase IV / Q000737:chemistry; D058608:Nanopores; D036103:Nanotechnology / Q000379:methods*; D009690:Nucleic Acid Conformation; D010957:Plasmids / Q000235:genetics
chemical_list: D004247:DNA; D027101:DNA Topoisomerase IV