Transverse electric field dragging of DNA in a nanochannel

Tsutsui, Makusu; He, Yuhui; Furuhashi, Masayuki; Rahong, Sakon; Taniguchi, Masateru; Kawai, Tomoji

doi:10.1038/srep00394

Cited by 67 publications

(64 citation statements)

References 34 publications

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“…Various methods have been applied to slow the translocation of biomolecules through nanopores, 7,8 including optical tweezers, 9 magnetic beads, 10 electrostatic 11–14 and steric 15 traps, and modifications to solvent. 16,17 Despite extensive efforts, a general method providing the desired level of control remains a highly researched subject.…”

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confidence: 99%

Stretching and Controlled Motion of Single-Stranded DNA in Locally Heated Solid-State Nanopores

et al. 2013

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Practical applications of solid-state nanopores for DNA detection and sequencing require the electrophoretic motion of DNA through the nanopores to be precisely controlled. Controlling the motion of single-stranded DNA presents a particular challenge, in part because of the multitude of conformations that a DNA strand can adopt in a nanopore. Through continuum, coarse-grained and atomistic modeling, we demonstrate that local heating of the nanopore volume can be used to alter the electrophoretic mobility and conformation of single-stranded DNA. In the nanopore systems considered, the temperature near the nanopore is modulated via a nanometer-size heater element that can be radiatively switched on and off. The local enhancement of temperature produces considerable stretching of the DNA fragment confined within the nanopore. Such stretching is reversible, so that the conformation of DNA can be toggled between compact (local heating is off) and extended (local heating is on) states. The effective thermophoretic force acting on single-stranded DNA in the vicinity of the nanopore is found to be sufficiently large (4–8 pN) to affect such changes in the DNA conformation. The local heating of the nanopore volume is observed to promote single-file translocation of DNA strands at transmembrane biases as low as 10 mV, which opens new avenues for using solid-state nanopores for detection and sequencing of DNA.

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confidence: 99%

Stretching and Controlled Motion of Single-Stranded DNA in Locally Heated Solid-State Nanopores

et al. 2013

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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 three-terminal 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].…”

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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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“…Our data indicate that folded configurations of ssDNA chains in large cross-section pores cause moderate increases in the velocity of the mass center, and this results in high terminal velocities. In other words, our results explain why electrophoretic mobility decreases during transport through a confined space embedded in the fluidic channel [17,26,58]. From the viewpoint of molecular sequencing, increased knowledge of changes in the velocity and suppression of excessive increases in this velocity are desirable when attempting to ascertain details concerning the configuration changes of polymer molecules.…”

Section: Resultsmentioning

confidence: 86%

Theoretical Study of the Transpore Velocity Control of Single-Stranded DNA

Qian

Doi

Uehara

et al. 2014

IJMS

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The electrokinetic transport dynamics of deoxyribonucleic acid (DNA) molecules have recently attracted significant attention in various fields of research. Our group is interested in the detailed examination of the behavior of DNA when confined in micro/nanofluidic channels. In the present study, the translocation mechanism of a DNA-like polymer chain in a nanofluidic channel was investigated using Langevin dynamics simulations. A coarse-grained bead-spring model was developed to simulate the dynamics of a long polymer chain passing through a rectangular cross-section nanopore embedded in a nanochannel, under the influence of a nonuniform electric field. Varying the cross-sectional area of the nanopore was found to allow optimization of the translocation process through modification of the electric field in the flow channel, since a drastic drop in the electric potential at the nanopore was induced by changing the cross-section. Furthermore, the configuration of the polymer chain in the nanopore was observed to determine its translocation velocity. The competition between the strength of the electric field and confinement in the small pore produces various transport mechanisms and the results of this study thus represent a means of optimizing the design of nanofluidic devices for single molecule detection.

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Transverse electric field dragging of DNA in a nanochannel

Cited by 67 publications

References 34 publications

Stretching and Controlled Motion of Single-Stranded DNA in Locally Heated Solid-State Nanopores

Stretching and Controlled Motion of Single-Stranded DNA in Locally Heated Solid-State Nanopores

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

Theoretical Study of the Transpore Velocity Control of Single-Stranded DNA

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