Origins and Consequences of Velocity Fluctuations during DNA Passage through a Nanopore

Abstract

We describe experiments and modeling results that reveal and explain the distribution of times that identical double-stranded DNA (dsDNA) molecules take to pass through a voltage-biased solid-state nanopore. We show that the observed spread in this distribution is caused by viscous-drag-induced velocity fluctuations that are correlated with the initial conformation of nanopore-captured molecules. This contribution exceeds that due to diffusional Brownian motion during the passage. Nevertheless, and somewhat counterintuitively, the diffusional Brownian motion determines the fundamental limitations of rapid DNA strand sequencing with a nanopore. We model both diffusional and conformational fluctuations in a Langevin description. It accounts well for passage time variations for DNA molecules of different lengths, and predicts conditions required for low-error-rate nanopore-strand DNA sequencing with nanopores.

Direct observation of DNA knots using a solid-state nanopore

“…Note that such a small knot size indicates that the DNA knots in these long DNA polymers are remarkably tight. The numbers may underestimate the size of the knots somewhat, especially for those which occur at the end of the translocation process where we know that the velocity is higher than average 41,42 . Measurements on circular versions of the same molecules in the same conditions reveal similar distributions of very tight knots (Supplementary Section 6).…”

Stiff filamentous virus translocations through solid-state nanopores

“…It senses when a single biopolymer threads it by registering a change in its ionic conductance 1,2 . The possibility of applying nanopores to the analysis of nucleic acids, in particular DNA sequencing, has generated interest 3 , and motivated fundamental studies of the physics of nanopore translocations [4][5][6][7][8][9][10][11][12][13][14][15][16][17] . The uses of solid-state nanopores have recently expanded to include detecting single proteins 18 , mapping structural features along RecA-bound DNA-protein complexes 19 and detecting spherical and icosahedral virus strains [20][21][22] .…”

“…According to the conventional theoretical picture, the electrokinetic driving force 10,12,13 and stochastic thermal forces 8,9,15 are balanced by the total viscous drag on the translocating polymer. The translocation is also retarded by electro-osmotic fluid flow through the nanopore 11,31 .…”

“…The translocation is also retarded by electro-osmotic fluid flow through the nanopore 11,31 . The instantaneous drag includes a large contribution from the length of polymer moving towards the nanopore through solution [14][15][16][17] . Consequently, a DNA molecule that first threads the nanopore fully extended will experience more drag and translocate more slowly than if its initial configuration is a tight coil, close to the nanopore.…”

Statistical Inference for Nanopore Sequencing with a Biased Random Walk Model

“…A number of strategies have been proposed, with the common basis of detecting individual nucleotides as they pass through a nanometer-scale aperture in a thin membrane separating two electrolytes (2). To date, a significant obstacle of nanopore approaches has been overcoming the fast stochastic motion of the individual molecules as they are driven through the pore (3,4). Ideally, passage of DNA through the pore would be unidirectional and each base would have a well-resolved signal.…”