Pressure–Voltage Trap for DNA near a Solid-State Nanopore

Hoogerheide, David P.; Lu, Bo; Golovchenko, Jene Andrew

doi:10.1021/nn5025829

Cited by 61 publications

(93 citation statements)

References 31 publications

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“…The red curve is the exact MF result obtained from the numerical solution of the PB Eq. (20). One notes that the Donnan approximation Eq.…”

Section: Drift Velocity Reversalmentioning

confidence: 99%

“…Recent advancements in nanotechnology have significantly improved the reliability of the sequencing techniques. More precisely, the use of solidstate nanopores of various size and charge compositions now offers a wide range of functionalities that can allow to improve the resolution of the method [10][11][12][13][14][15][16][17][18][19][20][21][22][23]. The technological progress requires development of theoretical models that can relate the tunable system parameters to experimentally observable quantities such as polymer capture rates, translocation times, and the ionic current blockade.…”

Section: Introductionmentioning

confidence: 99%

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Controlling polymer capture and translocation by electrostatic polymer-pore interactions

Buyukdagli

Ala-Nissilä

2017

The Journal of Chemical Physics

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Polymer translocation experiments typically involve anionic polyelectrolytes such as DNA molecules driven through negatively charged nanopores. Quantitative modelling of polymer capture to the nanopore followed by translocation therefore necessitates the consideration of the electrostatic barrier resulting from like-charge polymer-pore interactions. To this end, in this work we couple mean-field level electrohydrodynamic equations with the Smoluchowski formalism to characterize the interplay between the electrostatic barrier, the electrophoretic drift, and the electro-osmotic liquid flow. In particular, we find that due to distinct ion density regimes where the salt screening of the drift and barrier effects occur, there exists a characteristic salt concentration maximizing the probability of barrier-limited polymer capture into the pore. We also show that in the barrierdominated regime, the polymer translocation time τ increases exponentially with the membrane charge and decays exponentially fast with the pore radius and the salt concentration. These results suggest that the alteration of these parameters in the barrier-driven regime can be an efficient way to control the duration of the translocation process and facilitate more accurate measurements of the ionic current signal in the pore.

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“…The red curve is the exact MF result obtained from the numerical solution of the PB Eq. (20). One notes that the Donnan approximation Eq.…”

Section: Drift Velocity Reversalmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Controlling polymer capture and translocation by electrostatic polymer-pore interactions

Buyukdagli

Ala-Nissilä

2017

The Journal of Chemical Physics

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“…Polymer confinement occurs in nanotechnology devices, such as nanopore sequencing [3,29], DNA bar coding [5], and polymer separation devices [4].…”

Section: Summary and Discussionmentioning

confidence: 99%

“…This problem has attracted interests due to its applications in the design of nanotechnology devices [3][4][5]. It also helps in obtaining more knowledge of polymers confined in biological environments [6,7].…”

Section: Introductionmentioning

confidence: 99%

Accuracy of the blob model for single flexible polymers inside nanoslits that are a few monomer sizes wide

2014

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The de Gennes' blob model is extensively used in different problems of polymer physics. This model is theoretically applicable when the number of monomers inside each blob is large enough. For confined flexible polymers, this requires the confining geometry to be much larger than the monomer size. In this paper, the opposite limit of polymer in nanoslits with one to several monomers width is studied, using molecular dynamics simulations. Extension of the polymer inside nanoslits, confinement force on the plates, and the effective spring constant of the confined polymer are investigated. Despite the theoretical limitations of the blob model, the simulation results are explained with the blob model very well. The agreement is observed for the static properties and the dynamic spring constant of the polymer. A theoretical description of the conditions under which the dynamic spring constant of the polymer is independent of the small number of monomers inside blobs is given. Our results on the limit of applicability of the blob model can be useful in the design of nanotechnology devices.

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“…The insulating, impermeable SiN x thus acts as a physical barrier and as a support for the channel through which ions and molecules can pass under the influence of an electric field or other suitable driving force. [21][22][23][24][25][26][27][28][29][211][212][213][214][215][216] The most common sensing configuration is the so-called resistive-pulse sensing mode (Fig. 10).…”

Section: Nanofluidic Sample Cellsmentioning

confidence: 99%

Through a Window, Brightly: A Review of Selected Nanofabricated Thin-Film Platforms for Spectroscopy, Imaging, and Detection

Dwyer

Harb

2017

Appl Spectrosc

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We present a review of the use of selected nanofabricated thin films to deliver a host of capabilities and insights spanning bioanalytical and biophysical chemistry, materials science, and fundamental molecular-level research. We discuss approaches where thin films have been vital, enabling experimental studies using a variety of optical spectroscopies across the visible and infrared spectral range, electron microscopies, and related techniques such as electron energy loss spectroscopy, X-ray photoelectron spectroscopy, and single molecule sensing. We anchor this broad discussion by highlighting two particularly exciting exemplars: a thin-walled nanofluidic sample cell concept that has advanced the discovery horizons of ultrafast spectroscopy and of electron microscopy investigations of in-liquid samples; and a unique class of thin-film-based nanofluidic devices, designed around a nanopore, with expansive prospects for single molecule sensing. Free-standing, low-stress silicon nitride membranes are a canonical structural element for these applications, and we elucidate the fabrication and resulting features-including mechanical stability, optical properties, X-ray and electron scattering properties, and chemical natureof this material in this format. We also outline design and performance principles and include a discussion of underlying material preparations and properties suitable for understanding the use of alternative thin-film materials such as graphene.

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Pressure–Voltage Trap for DNA near a Solid-State Nanopore

Cited by 61 publications

References 31 publications

Controlling polymer capture and translocation by electrostatic polymer-pore interactions

Controlling polymer capture and translocation by electrostatic polymer-pore interactions

Accuracy of the blob model for single flexible polymers inside nanoslits that are a few monomer sizes wide

Through a Window, Brightly: A Review of Selected Nanofabricated Thin-Film Platforms for Spectroscopy, Imaging, and Detection

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