Oxygen bubble mould effect: serrated nanopore formation and porous alumina growth
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Oxygen evolution
Considering emerging modern applications of nanopore-based sensing devices, we model the electrodiffusiophoresis in a charged solid-state nanopore connecting two large reservoirs. Previous analyses are extended for the first time to take account of the effect of ion concentration polarization, an important factor in real sized devices. We show that the relative magnitude of the double layer thickness and the nanopore size plays the key role, yielding profound and interesting results that are important to device design. Both the nanopore radius and its length have an optimum size at which a maximum electrodiffusioosmotic velocity can be achieved. For a fixed nanopore size, an optimum salt concentration is also present. For example, for an aqueous KCl solution if both the radius and the length of a nanopore is smaller than ca. 5 nm, the averaged salt concentration should exceed ca. 0.3 M so that the associated electrodiffusioosmotic velocity is fast enough to decelerate effectively the translocation velocity of an entity (e.g., DNA). Regression relationships correlating the axial liquid velocity at the nanopore center with nanopore radius and length are developed for design purposes.
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The nanopore size effect on translocation of poly(dT)30 through Si3N4 membrane is investigated. In this paper, we report that the speed of the poly(dT)30 transport through Si3N4 nanopores can be slowed down by half through increasing the nanopore diameter from 4.8 nm to 10.8 nm. The results are consistent with our simulation results. Besides, the current blockage induced by DNA passing through the nanopore is less obvious as pore diameter is larger, which is in good agreement with the theoretical prediction. The conclusion about DNA transport through nanopores is beneficial for the design of DNA sequencing devices.
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Nanopore sensor has been identified as a versatile single molecule analytical device for its stability and sensitivity. Modification of solid-state nanopore will optimize the electrical properties when molecules transport through the nanopore after modification. Here, solid-state nanopore, about 50 nm, modified with gold nanoparticles, was fabricated in SiN membrane. λ-DNA was driven to transport through the modified nanopore. The results were shown that the blockage amplitude of the translocation current of λ-DNA significantly increased, while their dwell times were unchanged when the solid-state nanopore was modified with Au nanoparticles.
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Dwell time
Surface Modification
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To slow the translocation of single-stranded DNA (ssDNA) through a solid-state nanopore, a nanopore was narrowed, and the effect of the narrowing on the DNA translocation speed was investigated. In order to accurately measure the speed, long (5.3 kb) ssDNA (namely, ss-poly(dA)) with uniform length (±0.4 kb) was synthesized. The diameters of nanopores fabricated by a transmission electron microscope were controlled by atomic-layer deposition. Reducing the nanopore diameter from 4.5 to 2.3 nm slowed down the translocation of ssDNA by more than 16 times (to 0.18 μs base(-1)) when 300 mV was applied across the nanopore. It is speculated that the interaction between the nanopore and the ssDNA dominates the translocation speed. Unexpectedly, the translocation speed of ssDNA through the 4.5 nm nanopore is more than two orders of magnitude higher than that of double-stranded DNA (dsDNA) through a nanopore of almost the same size. The cause of such a faster translocation of ssDNA can be explained by the weaker drag force inside the nanopore. Moreover, the measured translocation speeds of ssDNA and dsDNA agree well with those calculated by molecular-dynamics (MD) simulation. The MD simulation predicted that reducing the nanopore diameter to almost the same as that of ssDNA (i.e. 1.4 nm) decreases the translocation speed (to 1.4 μs base(-1)). Narrowing the nanopore is thus an effective approach for accomplishing nanopore DNA sequencing.
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Nanopore has the proming to be used as the detection senser for the single molecule at single molecular level or the nanoparticles in different meterials. The diameters of the nanopores can be changed in a large rang with the increasing fabrication technology. For this case, the nanopore could be used as particles‘ sizes senser. We used 15nm gold nanoparticles as exsamples to analyze the effects of nanopore/nanoparticle ratio in deionized water. In the detection experiments, we found that the gold nanoparticles would pass through the nanopore in different behaves. Besides, the diameters of the nanopores might effect the precision accuracy of the translocation events. In view of the former results, we notice that on the basis of nanopore detection technique, nanoparticles translocation share many similarities with DNA.
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Using nanopores for single-molecule sequencing of proteins - similar to nanopore-based sequencing of DNA - faces multiple challenges, including unfolding of the complex tertiary structure of the proteins and enforcing their unidirectional translocation through nanopores. Here, we combine molecular dynamics (MD) simulations with single-molecule experiments to investigate the utility of SDS (Sodium Dodecyl Sulfate) to unfold proteins for solid-state nanopore translocation, while simultaneously endowing them with a stronger electrical charge. Our simulations and experiments prove that SDS-treated proteins show a considerable loss of the protein structure during the nanopore translocation. Moreover, SDS-treated proteins translocate through the nanopore in the direction prescribed by the electrophoretic force due to the negative charge impaired by SDS. In summary, our results suggest that SDS causes protein unfolding while facilitating protein translocation in the direction of the electrophoretic force; both characteristics being advantageous for future protein sequencing applications using solid-state nanopores.
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Transport protein
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Nanopores offer the potential for label-free analysis of individual proteins and low cost DNA sequencing. In order to design and evaluate nanopore devices, an understanding of nanopore electrokinetic transport is crucial. However, most studies of nanopore electrokinetic transport have neglected the effects of concentration polarization (CP) in the bulk fluid surrounding the pore. In this paper, we present a computational model which demonstrates the effects of CP on the background electrolyte in nanopore devices with tip diameters of 40–100 nm. We also present direct experimental observation of the distribution of an anionic dye in the vicinity of a conical nanopore. These results indicate that CP in a nanopore system can affect concentration distributions in the bulk solution tens of microns away from the pore, suggesting that typical boundary conditions used to model nanopore electrokinetic transport are incomplete.
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Nanofluidics
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The control of biomolecule translocation through nanopores is important in nanopore protein detection. Improvement in current nanopore molecule control is desired to enhance capture rates, extend translocation times, and ensure the effective detection of various proteins in the same solutions. We present a method that simultaneously resolves these issues through the use of a gate-modulated conical nanopore coupled with solutions of varying salt concentration. Simulation results show that the presence of an induced reverse electroosmotic flow (IREOF) results in inlet flows from the two ends of the nanopore centerline entering into the nanopore in opposite directions, which simultaneously elevates the capture rate and immobilizes the protein in the nanopore, thus enabling steady current blockage measurements for a range of proteins. In addition, it is shown that proteins with different size/charge ratios can be trapped by a gate modulation intensified flow field at a similar location in the nanopore in the same solution conditions.
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Biomolecule
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Abstract Nanopore is a single‐molecule analysis method which also employed electrophoresis has achieved promising single‐molecule detections. In this study, we designed two kinds of confined spaces by fabricating solid‐state nanopores with desirable diameters to study the structured single‐strand DNA of C‐rich quadruplex. For the nanopore whose diameter is larger than the quadruplex size, the DNA molecule could directly translocate through the nanopore with extremely high speed. For the nanopore whose diameter is smaller than the quadruplex size, DNA molecule which is captured by nanopore could return to the solution without translocation or unzip the quadruplex structure into single‐strand and then pass the nanopore. This study certifies that choosing a suitable sensing interface is the vital importance of observing detailed single‐molecule information. The solid‐state nanopores hold the great potential to study the structural dynamics of quadruplex DNA molecule.
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G-quadruplex
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