Complex DNA knots detected with a nanopore sensor

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journalNot applicablepeer-review

View graph of relations

Author(s)

  • Rajesh Kumar Sharma
  • Ishita Agrawal
  • Liang Dai
  • Patrick S Doyle
  • Slaven Garaj

Related Research Unit(s)

Detail(s)

Original languageEnglish
Article number4473
Journal / PublicationNature Communications
Volume10
Issue number1
Early online date2 Oct 2019
Publication statusPublished - 2019

Abstract

Equilibrium knots are common in biological polymers-their prevalence, size distribution, structure, and dynamics have been extensively studied, with implications to fundamental biological processes and DNA sequencing technologies. Nanopore microscopy is a high-throughput single-molecule technique capable of detecting the shape of biopolymers, including DNA knots. Here we demonstrate nanopore sensors that map the equilibrium structure of DNA knots, without spurious knot tightening and sliding. We show the occurrence of both tight and loose knots, reconciling previous contradictory results from different experimental techniques. We evidence the occurrence of two quantitatively different modes of knot translocation through the nanopores, involving very different tension forces. With large statistics, we explore the complex knots and, for the first time, reveal the existence of rare composite knots. We use parametrized complexity, in concert with simulations, to test the theoretical assumptions of the models, further asserting the relevance of nanopores in future investigation of knots.

Citation Format(s)

Complex DNA knots detected with a nanopore sensor. / Kumar Sharma, Rajesh; Agrawal, Ishita; Dai, Liang; Doyle, Patrick S; Garaj, Slaven.

In: Nature Communications, Vol. 10, No. 1, 4473, 2019.

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journalNot applicablepeer-review