Direction- and Salt-Dependent Ionic Current Signatures for DNA Sensing with Asymmetric Nanopores

Chen, Kaikai; Bell, Nicholas A. W.; Kong, Jinglin; Tian, Yu; Keyser, Ulrich F.

doi:10.1016/j.bpj.2016.12.033

Cited by 41 publications

(55 citation statements)

References 44 publications

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“…Figure 1a shows a scanning electron microscope image of a conically shaped nanopore fabricated by laser-assisted capillary pulling. Such conical pores have previously been used to study the transport of ions 30 , 31 and macromolecules 32 – 34 in confinement. The diameter of the nanopores used here was estimated as 14 ± 3 nm (mean ± s.d.)…”

Section: Resultsmentioning

confidence: 99%

Asymmetric dynamics of DNA entering and exiting a strongly confining nanopore

et al. 2017

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In nanopore sensing, changes in ionic current are used to analyse single molecules in solution. The translocation dynamics of polyelectrolytes is of particular interest given potential applications such as DNA sequencing. In this paper, we determine how the dynamics of voltage driven DNA translocation can be affected by the nanopore geometry and hence the available configurational space for the DNA. Using the inherent geometrical asymmetry of a conically shaped nanopore, we examine how DNA dynamics depends on the directionality of transport. The total translocation time of DNA when exiting the extended conical confinement is significantly larger compared to the configuration where the DNA enters the pore from the open reservoir. By using specially designed DNA molecules with positional markers, we demonstrate that the translocation velocity progressively increases as the DNA exits from confinement. We show that a hydrodynamic model can account for these observations.

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Section: Resultsmentioning

confidence: 99%

Asymmetric dynamics of DNA entering and exiting a strongly confining nanopore

et al. 2017

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“…A voltage of À350 mV was applied between the electrode inside the nanopipette and the electrode in the surrounding electrolyte to translocate the origami through the apex of the nanopore. [32] The ion current was sampled at a rate of 100 kHz and low-pass-filtered at 20 kHz. Also, the increase in absolute ion current observed for our DNA origami is in good 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 agreement with previous DNA translocation studies at salt concentrations similar to the one used here.…”

Section: Resultsmentioning

confidence: 99%

Analysis of 2D DNA Origami with Nanopipettes

et al. 2018

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Nanopipettes are a useful tool for the detection and analysis of biological molecules at the single-molecule level. Here, we employ nanopipettes fabricated from glass capillaries to identify differently structured 2D DNA origami through the distinctive amplitude and dwell time of the ion current peak resulting from the translocation of the origami through the nanopipette pore. We demonstrate that the ion current peak originating from frame-like DNA origami comprises two individual peaks in contrast to solid tiles of similar size that only lead to a single peak in the ion current. Interestingly, the fine details of the shape of the double-peak characteristic of the translocation of DNA origami frames are correlated with the structural features of the DNA origami. In particular, the size of the central cavity governs the lag time between the two constituent peaks of the double-peak. This work demonstrates the ability of glass nanopipettes to identify and characterize differently structured DNA origami of similar size, advancing the potential of nanopipettes for high-sensitivity single-molecule studies.

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“… 13 , 29 Four molar LiCl solution was used as the electrolyte as it is known to slow the DNA translocation relative to other commonly used salts such as NaCl and KCl. 13 , 30 , 31 A voltage of 600 mV was chosen to strike a balance between the requirements for high capture rate and slow translocation velocity. 32 When entering the nanopore, DNA molecules cause a lowering of the current and passage of streptavidin bound to the DNA creates additional current drops.…”

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Ionic Current-Based Mapping of Short Sequence Motifs in Single DNA Molecules Using Solid-State Nanopores

et al. 2017

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Nanopore sensors show great potential for rapid, single-molecule determination of DNA sequence information. Here, we develop an ionic current-based method for determining the positions of short sequence motifs in double-stranded DNA molecules with solid-state nanopores. Using the DNA-methyltransferase M.TaqI and a biotinylated S-adenosyl-l-methionine cofactor analogue we create covalently attached biotin labels at 5′-TCGA-3′ sequence motifs. Monovalent streptavidin is then added to bind to the biotinylated sites giving rise to additional current blockade signals when the DNA passes through a conical quartz nanopore. We determine the relationship between translocation time and position along the DNA contour and find a minimum resolvable distance between two labeled sites of ∼200 bp. We then characterize a variety of DNA molecules by determining the positions of bound streptavidin and show that two short genomes can be simultaneously detected in a mixture. Our method provides a simple, generic single-molecule detection platform enabling DNA characterization in an electrical format suited for portable devices for potential diagnostic applications.

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Direction- and Salt-Dependent Ionic Current Signatures for DNA Sensing with Asymmetric Nanopores

Cited by 41 publications

References 44 publications

Asymmetric dynamics of DNA entering and exiting a strongly confining nanopore

Asymmetric dynamics of DNA entering and exiting a strongly confining nanopore

Analysis of 2D DNA Origami with Nanopipettes

Ionic Current-Based Mapping of Short Sequence Motifs in Single DNA Molecules Using Solid-State Nanopores

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