Field Effect Regulation of DNA Translocation through a Nanopore

Ai, Ye; Liu, Jing; Zhang, Bingkai; Qian, Shizhi

doi:10.1021/ac101628e

Cited by 110 publications

(175 citation statements)

References 58 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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“…Confinement of the particle in a microchannel, as well as the dielectrophoretic (DEP) effect arising from the interaction between the dielectric particle and the spatially non-uniform electric field, were neglected in the aforementioned study. However, our previous studies clearly revealed the important role played by the DEP effect in the electrokinetic motion of rigid particles in microfluidics [37][38][39][40][41][42].…”

Section: Introductionmentioning

confidence: 88%

Electrokinetic motion of a deformable particle: Dielectrophoretic effect

Mauroy

Sharma

et al. 2011

Electrophoresis

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Electrokinetics-induced motion and deformation of a hyperelastic particle confined in a slit microchannel has been numerically investigated for the first time with a full consideration of the fluid-particle-electric field interactions and the dielectrophoretic (DEP) effect. When the initial orientation of a cylindrical particle with respect to the applied electric field, θ p0 , is 90 o , the particle tends to curl up as a "C" shape when moving from left to right. The electrokineticsinduced particle deformation is due to the joint effects of the shear force arising from the nonuniform Smoluchowski slip velocity on the particle surface, and the asymmetric DEP force with respect to the center of the deformed particle arising from the spatially non-uniform electric field surrounding the particle. The electrokinetics-induced particle deformation is opposite to that of a particle moving in the same direction subjected to a pressure-driven flow. When the initial particle orientation is 0 < θ p0 < 90 o , a net torque arising from the DEP effect progressively rotates and aligns the particle with its longest axis parallel to the applied electric field, thus decreasing the non-uniformity of the electric field and accordingly the particle deformation. The numerical predictions are in qualitative agreement with our previous experimental observation. The results show that the DEP effect is significant and must be taken into account in the modeling of electrokinetic motion of a deformable particle in microfluidics.3

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“…From the viewpoint of the numerical (and analytical) tractability of the problem, two further assumptions are practically unavoidable [6,[23][24][25], see also Sec. III E. First, we restrict our discussion to the axisymmetric case where a particle translocates through the pore along the z-axis (see Fig.…”

Section: Modelmentioning

confidence: 99%

Reluctance of a neutral nanoparticle to enter a charged pore

2013

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We consider the translocation of a neutral (uncharged) nanoparticle through a pore in a thin membrane with constant surface charge density. If the concomitant Debye screening layer is sufficiently thin, the resulting forces experienced by the particle on its way through the pore are negligible. But when the Debye length becomes comparable to the pore diameter, the particle encounters a quite significant potential barrier while approaching and entering the pore, and symmetrically upon exiting the pore. The main reason is an increasing pressure which acts on the particle when it intrudes into the counter ion cloud of the Debye screening layer. In case the polarizability of the particle is different (usually smaller) than that of the ambient fluid, a second, much smaller contribution to the potential barrier is due to self-energy effects. Our numerical treatment of the problem is complemented by analytical approximations for sufficiently long cylindrical particles and pores, which agree very well with the numerics.

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Field Effect Regulation of DNA Translocation through a Nanopore

Cited by 110 publications

References 58 publications

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

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

Electrokinetic motion of a deformable particle: Dielectrophoretic effect

Reluctance of a neutral nanoparticle to enter a charged pore

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