DNA conformation and base number simultaneously determined in a nanopore

Abstract

When dsDNA polymers containing the identical number of base pairs were electrophoresed through a nanopore in a voltage biased silicon nitride membrane, the measured time integral of blocked ionic current (the event charge deficit, ecd [1]) for each translocation event was the same regardless of whether the molecules were in a linear, circular relaxed, or supercoiled form. Conversely, when DNA polymers containing different numbers of base pairs were electrophoresed through a nanopore, the ecd depended strongly on, and predicted the value of, the molecule's number of base pairs. Measurements showed that the magnitude of the current blockages was strongly affected by a molecule's form. The current blockages exhibited characteristic differences that distinguished between single stranded linear, double stranded linear, circular relaxed, and supercoiled forms. Because the data that establish ecd are usually determined concomitantly with current blockade measurements, our results show that a single nanopore assay can simultaneously determine both DNA conformation and base number.

Atomically Thin Molybdenum Disulfide Nanopores with High Sensitivity for DNA Translocation

“…As a result, a value of ∼500 ke is obtained, which is at least five times of previously reported data for 3 kbp DNA. 30 This increase is mainly due to the increased blockage amplitude because of the greatly improved sensitivity of MoS 2 nanopores compared to conventional SiN x nanopores. In ref 30, for the circular plasmid DNA, the current drop is ∼100 pA at 100 mV, whereas we got ∼400 pA at 100 mV.…”

“…30 This increase is mainly due to the increased blockage amplitude because of the greatly improved sensitivity of MoS 2 nanopores compared to conventional SiN x nanopores. In ref 30, for the circular plasmid DNA, the current drop is ∼100 pA at 100 mV, whereas we got ∼400 pA at 100 mV. Garaj et al also reported from 2-fold up to 10-fold enhancement in signal for DNA translocation in graphene nanopores.…”

Stiff filamentous virus translocations through solid-state nanopores

“…To avoid these difficulties, we quantify collisions and translocations by their event charge deficit (ECD). ECD is the change in ionic current caused by an event, integrated over the duration of that event 6 . The total ECD of all collisions, P ECD Col , is a useful measure of translocation attempts, and can be compared with the total ECD of all translocations, P ECD Trans .…”

“…Each event was classified as either a collision or a translocation based on its ECD value 6 . ECD is the integrated current change from the local baseline over the duration of the event.…”

“…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] .…”