Interpreting the Conductance Blockades of DNA Translocations through Solid-State Nanopores

Carlsen, Autumn; Zahid, Osama K.; Růžička, Jan; Taylor, Ethan Will; Hall, Adam R.

doi:10.1021/nn501694n

Cited by 80 publications

(118 citation statements)

References 61 publications

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“…19. This effect is due to a slight increase in the current blockade caused by the knot sitting against the pore mouth before being translocated, and is consistent with similar effects reported in literature for DNA docked onto the pore mouth 38,39,40 . These results indicate that knots are able to slip out of linear DNA molecules during their translocation through nanopores.…”

Section: Dna Knot Position Sliding and Slipping Outsupporting

confidence: 91%

Direct observation of DNA knots using a solid-state nanopore

et al. 2016

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Section: Dna Knot Position Sliding and Slipping Outsupporting

confidence: 91%

Direct observation of DNA knots using a solid-state nanopore

et al. 2016

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“…It turns out the resistance between the two 'electrodes' is dominated by the narrow region where the current approaches the electrodes [12]. While the derivation is beyond the scope of this thesis, the result is the generation of the following equation [12,13]:…”

Section: Access Resistancementioning

confidence: 99%

Interfacing solid‐state nanopores with gel media to slow DNA translocations

et al. 2015

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We demonstrate the ability to slow DNA translocations through solid‐state nanopores by interfacing the trans side of the membrane with gel media. In this work, we focus on two reptation regimes: when the DNA molecule is flexible on the length scale of a gel pore, and when the DNA behaves as persistent segments in tight gel pores. The first regime is investigated using agarose gels, which produce a very wide distribution of translocation times for 5 kbp dsDNA fragments, spanning over three orders of magnitude. The second regime is attained with polyacrylamide gels, which can maintain a tight spread and produce a shift in the distribution of the translocation times by an order of magnitude for 100 bp dsDNA fragments, if intermolecular crowding on the trans side is avoided. While previous approaches have proven successful at slowing DNA passage, they have generally been detrimental to the S/N, capture rate, or experimental simplicity. These results establish that by controlling the regime of DNA movement exiting a nanopore interfaced with a gel medium, it is possible to address the issue of rapid biomolecule translocations through nanopores—presently one of the largest hurdles facing nanopore‐based analysis—without affecting the signal quality or capture efficiency.

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“…translocations, fly-by events near a pore, and trapping, [17][18][19][20][21] occurrence of the trapping events is confirmed by current drops alone in almost every nanopore experiment. Therefore, it is of crucial importance to assure the presence of target particles at the pore at the moment when the current drops take place.…”

Section: Introductionmentioning

confidence: 61%

Electrical trapping mechanism of single-microparticles in a pore sensor

Arima

Tsutsui

et al. 2016

AIP Advances

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Nanopore sensing via resistive pulse technique are utilized as a potent tool to characterize physical and chemical property of single –molecules and –particles. In this article, we studied the influence of particle trajectory to the ionic conductance through a pore. We performed the optical/electrical simultaneous sensing of electrophoretic capture dynamics of single-particles at a pore using a microchannel/nanopore system. We detected ionic current drops synchronous to a fluorescently dyed particle being electrophoretically drawn and become immobilized at a pore in the optical imaging. We also identified anomalous trapping events wherein particles were captured at nanoscale pin-holes formed unintentionally in a SiN membrane that gave rise to relatively small current drops. This method is expected to be a useful platform for testing novel nanopore sensor design wherein current behaves in unpredictable manner.

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Interpreting the Conductance Blockades of DNA Translocations through Solid-State Nanopores

Cited by 80 publications

References 61 publications

Direct observation of DNA knots using a solid-state nanopore

Direct observation of DNA knots using a solid-state nanopore

Interfacing solid‐state nanopores with gel media to slow DNA translocations

Electrical trapping mechanism of single-microparticles in a pore sensor

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