Control of DNA Capture by Nanofluidic Transistors

Paik, Kee-Hyun; Liu, Yang; Tabard‐Cossa, Vincent; Waugh, Matthew; Huber, David; Provine, J.; Howe, Roger T.; Dutton, R.W.; Davis, Ronald W.

doi:10.1021/nn3014917

Cited by 77 publications

(91 citation statements)

References 44 publications

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“…Additional methods have been proposed, including local heating of a gold layer surrounding the nanopore to stretch the DNA [65,66] and ratcheting of nucleotide strands through introduction of a third electrode [67,68]. In fact, researchers have investigated a threeterminal system, or field effect nanofluidic transistor, which would alter the electric field profile in the nanopore [69][70][71] and modulate its surface charge [72][73][74][75]. Base-by-base ratcheting using electrostatic traps in a DNA transistor has yet to be achieved, but nanopore modifications have already reduced translocation speeds by up to an order of magnitude for ssDNA [62,73].…”

Section: The Nanoporementioning

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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Section: The Nanoporementioning

confidence: 99%

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

et al. 2015

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“…Various methods have been suggested in solid-state nanopores to slow DNA translocation speed including the use of stick-slip interactions by using dielectric materials with high surface charge density like Al 2 O 3 and HfO 2 . [28,29] Other proposed techniques include the use of different ionic solutions such as LiCl, [30] increasing solution viscosity with glycerol, [31] optoelectronic control, [32] fluidic gating, [33] reducing nanopore diameter, [34] use of pressure gradients, [35] thicker membranes, [36] and temporary hydrogen bonding. [37] Recently, the potential for DNA–graphene hydrophobic interactions to induce ssDNA translocations in single-nucleotide steps was discussed.…”

Section: Introductionmentioning

confidence: 99%

Slowing DNA Transport Using Graphene–DNA Interactions

Banerjee

Wilson

Shim

et al. 2014

Adv Funct Materials

111

106

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Slowing down DNA translocation speed in a nanopore is essential to ensuring reliable resolution of individual bases. Thin membrane materials enhance spatial resolution but simultaneously reduce the temporal resolution as the molecules translocate far too quickly. In this study, the effect of exposed graphene layers on the transport dynamics of both single (ssDNA) and double-stranded DNA (dsDNA) through nanopores is examined. Nanopore devices with various combinations of graphene and Al2O3 dielectric layers in stacked membrane structures are fabricated. Slow translocations of ssDNA in nanopores drilled in membranes with layers of graphene are reported. The increased hydrophobic interactions between the ssDNA and the graphene layers could explain this phenomenon. Further confirmation of the hydrophobic origins of these interactions is obtained through reporting significantly faster translocations of dsDNA through these graphene layered membranes. Molecular dynamics simulations confirm the preferential interactions of DNA with the graphene layers as compared to the dielectric layer verifying the experimental findings. Based on our findings, we propose that the integration of multiple stacked graphene layers could slow down DNA enough to enable the identification of nucleobases.

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“…Such a device allows for a field effect control of the EDL thickness at the oxide-electrolyte interface by applying an external potential [66]. Potential applications range from biopolymer nanofiltration [18,19,[67][68][69][70][71][72][73][74][75][76] and sensing [29,77] to energy harvesting and fuel cell applications [78][79][80][81]. However, to fabricate these two types of device some challenges must be overcome: Pt must be successfully deposited inside narrow nanopores; a dielectric, e.g.…”

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Pt–Al₂O₃dual layer atomic layer deposition coating in high aspect ratio nanopores

Pardon¹,

Gatty²,

Stemme³

et al. 2012

Nanotechnology

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PostprintThis is the accepted version of a paper published in Nanotechnology. This paper has been peerreviewed but does not include the final publisher proof-corrections or journal pagination. Citation for the original published paper (version of record):Pardon, G., Gatty, H., Stemme, G., van der Wijngaart, W., Roxhed, N. (2013) Pt-Al2O3 dual layer atomic layer deposition coating in high aspect ratio nanopores. Abstract. Functional nanoporous materials are promising for a number of applications ranging from selective biofiltration to fuel cell electrodes. This work reports the functionalization of nanoporous membranes using atomic layer deposition (ALD). ALD is used to conformally deposit platinum (Pt) and aluminium oxide (Al 2 O 3 ) on Pt in nanopores to form a metal-insulator stack inside the nanopore. Deposition of these materials inside nanopores allows adding extra functionalities to nanoporous materials such as anodic aluminium oxide (AAO) membranes. Conformal deposition of Pt on such materials enables increased performances for electrochemical sensing applications or fuel cell electrodes. An additional conformal Al 2 O 3 layer on such Pt film forms a metalinsulator-electrolyte system, enabling field effect control of the nanofluidic properties of the membrane. This opens novel possibilities in electrically controlled biofiltration. In this work, the deposition of these two materials on AAO membrane is investigated theoretically and experimentally. Successful process parameters are proposed for a reliable and cost-effective conformal deposition on high aspect ratio 3D nanostructures. A device consisting of a silicon chip supporting an AAO membrane of 6 mm diameter and 1.3 μm thickness with 80 nm diameter pores is fabricated. The pore diameter is reduced to 40 nm by a conformal deposition of 11 nm Pt and 9 nm Al 2 O 3 using ALD. Nanotechnology IntroductionIn recent years, the interest for novel functional and well-controlled nanoporous materials has grown extensively [1][2][3][4][5]. Nanoporous materials possess a number of interesting features. At the nanoscale, the increased surface-to-volume ratio (~! !! ) enhances the interaction between liquid analytes or electrolyte and the device surface. In addition, the porosity,1 These authors contributed equally to this work.!, increases the effective surface area of the macroscopic material (~!). The porosity also increases the line length of triple phase (solid, liquid, gas) interfaces (~! !! ! ). The increased surface-to-volume is an advantage for surface governed phenomena, such as molecular transport in nanofluidics, largely governed by the surface charges via the electrical double layer (EDL) [6][7][8]. The increased effective surface area improves surface limited phenomena, such as overpotential losses in electrodes [9,10] and the increased line length of the triple phase interface allows increasing the current density in fuel cells [11] or the sensitivity in gas-and biosensors [12][13][14][15][16]. In addition to these intrinsic features, embedding fu...

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Control of DNA Capture by Nanofluidic Transistors

Cited by 77 publications

References 44 publications

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

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

Slowing DNA Transport Using Graphene–DNA Interactions

Pt–Al₂O₃dual layer atomic layer deposition coating in high aspect ratio nanopores

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Control of DNA Capture by Nanofluidic Transistors

Cited by 77 publications

References 44 publications

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

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

Slowing DNA Transport Using Graphene–DNA Interactions

Pt–Al2O3dual layer atomic layer deposition coating in high aspect ratio nanopores

Contact Info

Product

Resources

About

Pt–Al₂O₃dual layer atomic layer deposition coating in high aspect ratio nanopores