Complex DNA knots detected with a nanopore sensor

Rajesh Kumar Sharma, Ishita Agrawal, Liang Dai, Patrick S. Doyle () and Slaven Garaj ()
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Rajesh Kumar Sharma: National University of Singapore
Ishita Agrawal: National University of Singapore
Liang Dai: City University of Hong Kong
Patrick S. Doyle: Singapore-MIT Alliance for Research and Technology Centre
Slaven Garaj: National University of Singapore

Nature Communications, 2019, vol. 10, issue 1, 1-9

Abstract: 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.

Date: 2019
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DOI: 10.1038/s41467-019-12358-4

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