Complex DNA knots detected with a nanopore sensor

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.

The Origin of Conductive-Pulse Sensing Inside a Nanopore and the Role of Electro-Hydrodynamics

“…1d). Reports of different DNA con gurations have been witnessed using high ionic strength conditions and with both planar nanopores [34][35][36][37] and nanocapillaries 24 . The ability to discriminate folding states using DNA CEs does not directly help uncover the nature of CEs, but it is important to recognize the existence and understand the effects of having various DNA con gurations upon translocation.…”

Dynamics of DNA Clogging in Hafnium Oxide Nanopores

“…Such specific configurations have been well-characterized using similar-sized pores in previous studies. 52 − 54 The knotting probability of linear dsDNA molecules is experimentally shown to rise with the DNA length, for example, a 13.2% knotting probability is found for 20.7 kbp DNA molecules probed with 20 nm SiN x nanopores. 53 Similarly, for DNA strands of longer length, it is relatively favorable in configurational entropy to translocate with folded configurations because of a higher number of conformation choices compared to shorter DNA.…”

On the Origins of Conductive-Pulse Sensing Inside a Nanopore

“…1d). Reports of different DNA configurations have been witnessed using high ionic strength conditions and with both planar nanopores [34][35][36][37] and nanocapillaries 24 . The ability to discriminate folding states using DNA CEs does not directly help uncover the nature of CEs but it is important to recognize the existence and understand the effects of having various DNA configurations upon translocation.…”