101
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Polson JM, Dunn TR. Evaluating the applicability of the Fokker-Planck equation in polymer translocation: a Brownian dynamics study. J Chem Phys 2015; 140:184904. [PMID: 24832303 DOI: 10.1063/1.4874976] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Brownian dynamics (BD) simulations are used to study the translocation dynamics of a coarse-grained polymer through a cylindrical nanopore. We consider the case of short polymers, with a polymer length, N, in the range N = 21-61. The rate of translocation is controlled by a tunable friction coefficient, γ0p, for monomers inside the nanopore. In the case of unforced translocation, the mean translocation time scales with polymer length as <τ1> ∼ (N - Np)(α), where Np is the average number of monomers in the nanopore. The exponent approaches the value α = 2 when the pore friction is sufficiently high, in accord with the prediction for the case of the quasi-static regime where pore friction dominates. In the case of forced translocation, the polymer chain is stretched and compressed on the cis and trans sides, respectively, for low γ0p. However, the chain approaches conformational quasi-equilibrium for sufficiently large γ0p. In this limit the observed scaling of <τ1> with driving force and chain length supports the Fokker-Planck (FP) prediction that <τ> ∝ N/fd for sufficiently strong driving force. Monte Carlo simulations are used to calculate translocation free energy functions for the system. The free energies are used with the FP equation to calculate translocation time distributions. At sufficiently high γ0p, the predicted distributions are in excellent agreement with those calculated from the BD simulations. Thus, the FP equation provides a valid description of translocation dynamics for sufficiently high pore friction for the range of polymer lengths considered here. Increasing N will require a corresponding increase in pore friction to maintain the validity of the FP approach. Outside the regime of low N and high pore friction, the polymer is out of equilibrium, and the FP approach is not valid.
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Affiliation(s)
- James M Polson
- Department of Physics, University of Prince Edward Island, 550 University Ave., Charlottetown,Prince Edward Island C1A 4P3, Canada
| | - Taylor R Dunn
- Department of Physics, University of Prince Edward Island, 550 University Ave., Charlottetown,Prince Edward Island C1A 4P3, Canada
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102
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Cai SL, Cao SH, Zheng YB, Zhao S, Yang JL, Li YQ. Surface charge modulated aptasensor in a single glass conical nanopore. Biosens Bioelectron 2015; 71:37-43. [PMID: 25884732 DOI: 10.1016/j.bios.2015.04.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 03/06/2015] [Accepted: 04/04/2015] [Indexed: 11/17/2022]
Abstract
In this work, we have proposed a label-free nanopore-based biosensing strategy for protein detection by performing the DNA-protein interaction inside a single glass conical nanopore. A lysozyme binding aptamer (LBA) was used to functionalize the walls of glass nanopore via siloxane chemistry and negatively charged recognition sites were thus generated. The covalent modification procedures and their recognition towards lysozyme of the single conical nanopore were characterized via ionic current passing through the nanopore membrane, which was measured by recording the current-voltage (I-V) curves in 1mM KCl electrolyte at pH=7.4. With the occurring of recognition event, the negatively charged wall was partially neutralized by the positively charged lysozyme molecules, leading to a sensitive change of the surface charge-dependent current-voltage (I-V) characteristics. Our results not only demonstrate excellent selectivity and sensitivity towards the target protein, but also suggest a route to extend this nanopore-based sensing strategy to the biosensing platform designs of a wide range of proteins based on a charge modulation.
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Affiliation(s)
- Sheng-Lin Cai
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Shuo-Hui Cao
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yu-Bin Zheng
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Shuang Zhao
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jin-Lei Yang
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yao-Qun Li
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
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103
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Haque F, Wang S, Stites C, Chen L, Wang C, Guo P. Single pore translocation of folded, double-stranded, and tetra-stranded DNA through channel of bacteriophage phi29 DNA packaging motor. Biomaterials 2015; 53:744-52. [PMID: 25890769 DOI: 10.1016/j.biomaterials.2015.02.104] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 02/22/2015] [Accepted: 02/24/2015] [Indexed: 12/11/2022]
Abstract
The elegant architecture of the channel of bacteriophage phi29 DNA packaging motor has inspired the development of biomimetics for biophysical and nanobiomedical applications. The reengineered channel inserted into a lipid membrane exhibits robust electrophysiological properties ideal for precise sensing and fingerprinting of dsDNA at the single-molecule level. Herein, we used single channel conduction assays to quantitatively evaluate the translocation dynamics of dsDNA as a function of the length and conformation of dsDNA. We extracted the speed of dsDNA translocation from the dwell time distribution and estimated the various forces involved in the translocation process. A ∼35-fold slower speed of translocation per base-pair was observed for long dsDNA, a significant contrast to the speed of dsDNA crossing synthetic pores. It was found that the channel could translocate both dsDNA with ∼32% of channel current blockage and with ∼64% for tetra-stranded DNA (two parallel dsDNA). The calculation of both cross-sectional areas of the dsDNA and tetra-stranded DNA suggested that the blockage was purely proportional to the physical space of the channel lumen and the size of the DNA substrate. Folded dsDNA configuration was clearly reflected in their characteristic current signatures. The finding of translocation of tetra-stranded DNA with 64% blockage is in consent with the recently elucidated mechanism of viral DNA packaging via a revolution mode that requires a channel larger than the dsDNA diameter of 2 nm to provide room for viral DNA revolving without rotation. The understanding of the dynamics of dsDNA translocation in the phi29 system will enable us to design more sophisticated single pore DNA translocation devices for future applications in nanotechnology and personal medicine.
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Affiliation(s)
- Farzin Haque
- Nanobiotechnology Center, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA.
| | - Shaoying Wang
- Nanobiotechnology Center, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Chris Stites
- Department of Biomedical Engineering, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Li Chen
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Biostatistics, University of Kentucky, Lexington, KY 40536, USA
| | - Chi Wang
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Biostatistics, University of Kentucky, Lexington, KY 40536, USA
| | - Peixuan Guo
- Nanobiotechnology Center, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA.
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104
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Pitchford WH, Kim HJ, Ivanov AP, Kim HM, Yu JS, Leatherbarrow RJ, Albrecht T, Kim KB, Edel JB. Synchronized optical and electronic detection of biomolecules using a low noise nanopore platform. ACS NANO 2015; 9:1740-8. [PMID: 25635821 DOI: 10.1021/nn506572r] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In the past two decades there has been a tremendous amount of research into the use of nanopores as single molecule sensors, which has been inspired by the Coulter counter and molecular transport across biological pores. Recently, the desire to increase structural resolution and analytical throughput has led to the integration of additional detection methods such as fluorescence spectroscopy. For structural information to be probed electronically high bandwidth measurements are crucial due to the high translocation velocity of molecules. The most commonly used solid-state nanopore sensors consist of a silicon nitride membrane and bulk silicon substrate. Unfortunately, the photoinduced noise associated with illumination of these platforms limits their applicability to high-bandwidth, high-laser-power synchronized optical and electronic measurements. Here we present a unique low-noise nanopore platform, composed of a predominately Pyrex substrate and silicon nitride membrane, for synchronized optical and electronic detection of biomolecules. Proof of principle experiments are conducted showing that the Pyrex substrates have substantially lowers ionic current noise arising from both laser illumination and platform capacitance. Furthermore, using confocal microscopy and a partially metallic pore we demonstrate high signal-to-noise synchronized optical and electronic detection of dsDNA.
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Affiliation(s)
- William H Pitchford
- Department of Chemistry, Imperial College London, South Kensington Campus , London SW7 2AZ, U.K
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105
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Liu X, Skanata MM, Stein D. Entropic cages for trapping DNA near a nanopore. Nat Commun 2015; 6:6222. [DOI: 10.1038/ncomms7222] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 01/07/2015] [Indexed: 12/20/2022] Open
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106
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de Haan HW, Sean D, Slater GW. Using a Péclet number for the translocation of a polymer through a nanopore to tune coarse-grained simulations to experimental conditions. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:022601. [PMID: 25768522 DOI: 10.1103/physreve.91.022601] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Indexed: 06/04/2023]
Abstract
Coarse-grained simulations are often employed to study the translocation of DNA through a nanopore. The majority of these studies investigate the translocation process in a relatively generic sense and do not endeavor to match any particular set of experimental conditions. In this manuscript, we use the concept of a Péclet number for translocation, P(t), to compare the drift-diffusion balance in a typical experiment vs a typical simulation. We find that the standard coarse-grained approach overestimates diffusion effects by anywhere from a factor of 5 to 50 compared to experimental conditions using double stranded DNA (dsDNA). By defining a Péclet control parameter, λ, we are able to correct this and tune the simulations to replicate the experimental P(t) (for dsDNA and other scenarios). To show the effect that a particular P(t) can have on the dynamics of translocation, we perform simulations across a wide range of P(t) values for two different types of driving forces: a force applied in the pore and a pulling force applied to the end of the polymer. As P(t) brings the system from a diffusion dominated to a drift dominated regime, a variety of effects are observed including a non-monotonic dependence of the translocation time τ on P(t) and a steep rise in the probability of translocating. Comparing the two force cases illustrates the impact of the crowding effects that occur on the trans side: a non-monotonic dependence of the width of the τ distributions is obtained for the in-pore force but not for the pulling force.
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Affiliation(s)
- Hendrick W de Haan
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario L1H 7K4, Canada
| | - David Sean
- Physics Department, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Gary W Slater
- Physics Department, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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107
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Rollings R, Graef E, Walsh N, Nandivada S, Benamara M, Li J. The effects of geometry and stability of solid-state nanopores on detecting single DNA molecules. NANOTECHNOLOGY 2015; 26:044001. [PMID: 25556317 PMCID: PMC4288979 DOI: 10.1088/0957-4484/26/4/044001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
In this work we use a combination of 3D-TEM tomography, energy filtered TEM, single molecule DNA translocation experiments, and numerical modeling to show a more precise relationship between nanopore shape and ionic conductance and show that changes in geometry while in solution can account for most deviations between predicted and measured conductance. We compare the structural stability of ion beam sculpted (IBS), IBS-annealed, and TEM drilled nanopores. We demonstrate that annealing can significantly improve the stability of IBS made pores. Furthermore, the methods developed in this work can be used to predict pore conductance and current drop amplitudes of DNA translocation events for a wide variety of pore geometries. We discuss that chemical dissolution is one mechanism of the geometry change for SiNx nanopores and show that small modification in fabrication procedure can significantly increase the stability of IBS nanopores.
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108
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Youn Y, Han S. Investigation of field effects in a solid-state nanopore transistor. Phys Chem Chem Phys 2015; 17:27806-11. [DOI: 10.1039/c5cp03125g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In order to calculate ion currents through solid-state nanopore transistors realistically, we propose a computational model based on the Poisson–Nernst–Plank equation.
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Affiliation(s)
- Yong Youn
- Department of materials Science and Engineering and Research Institute of Advanced Materials
- Seoul National University
- Seoul 151-744
- Korea
| | - Seungwu Han
- Department of materials Science and Engineering and Research Institute of Advanced Materials
- Seoul National University
- Seoul 151-744
- Korea
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109
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Differences in fundamental reaction mechanisms between high and low-LET in recent advancements and applications of ionizing radiation. Radiat Phys Chem Oxf Engl 1993 2014. [DOI: 10.1016/j.radphyschem.2014.05.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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110
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Tang Z, Lu B, Zhao Q, Wang J, Luo K, Yu D. Surface modification of solid-state nanopores for sticky-free translocation of single-stranded DNA. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:4332-9. [PMID: 25044955 DOI: 10.1002/smll.201401091] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 06/15/2014] [Indexed: 05/25/2023]
Abstract
Nanopore technology is one of the most promising approaches for fast and low-cost DNA sequencing application. Single-stranded DNA detection is primary objective in such device, while solid-state nanopores remain less explored than their biological counterparts due to bio-molecule clogging issue caused by surface interaction between DNA and nanopore wall. By surface coating a layer of polyethylene glycol (PEG), solid-state nanopore can achieve long lifetime for single-stranded DNA sticky-free translocation at pH 11.5. Associated with elimination of non-specific binding of molecule, PEG coated nanopore presents new surface characteristic as less hydrophility, lower 1/f noise, and passivated surface charge responsiveness on pH. Meanwhile, conductance blockage of single-stranded DNA is found to be deeper than double-stranded DNA, which can be well described by a string of blobs model for a quasi-equilibrium state polymer in constraint space.
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Affiliation(s)
- Zhipeng Tang
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, P. R. China
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111
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Sun LZ, Luo MB. Langevin dynamics simulation on the translocation of polymer through α-hemolysin pore. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2014; 26:415101. [PMID: 25192215 DOI: 10.1088/0953-8984/26/41/415101] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The forced translocation of a polymer through an α-hemolysin pore under an electrical field is studied using a Langevin dynamics simulation. The α-hemolysin pore is modelled as a connection of a spherical vestibule and a cylindrical β-barrel and polymer-pore attraction is taken into account. The results show that polymer-pore attraction can help the polymer enter the vestibule and the β-barrel as well; however, a strong attraction will slow down the translocation of the polymer through the β-barrel. The mean translocation time for the polymer to thread through the β-barrel increases linearly with the polymer length. By comparing our results with that of a simple pore without a vestibule, we find that the vestibule helps the polymer enter and thread through the β-barrel. Moreover, we find that it is easier for the polymer to thread through the β-barrel if the polymer is located closer to the surface of the vestibule. Some simulation results are explained qualitatively by theoretically analyzing the free-energy landscape of polymer translocation.
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Affiliation(s)
- Li-Zhen Sun
- Department of Physics, Zhejiang University, Hangzhou 310027, People's Republic of China. Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, People's Republic of China
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112
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Buermans H, den Dunnen J. Next generation sequencing technology: Advances and applications. Biochim Biophys Acta Mol Basis Dis 2014; 1842:1932-1941. [DOI: 10.1016/j.bbadis.2014.06.015] [Citation(s) in RCA: 460] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 06/05/2014] [Accepted: 06/15/2014] [Indexed: 12/12/2022]
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113
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Venta KE, Zanjani MB, Ye X, Danda G, Murray CB, Lukes JR, Drndić M. Gold nanorod translocations and charge measurement through solid-state nanopores. NANO LETTERS 2014; 14:5358-64. [PMID: 25093657 DOI: 10.1021/nl502448s] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We study translocations of gold nanoparticles and nanorods through silicon nitride nanopores and present a method for determining the surface charge of nanorods from the magnitude of the ionic current change as nanorods pass through the pore. Positively charged nanorods and spherical nanoparticles with average diameters 10 nm and average nanorod lengths between 44 and 65 nm were translocated through 40 nm thick nanopores with diameters between 19 and 27 nm in 1, 10, or 100 mM KCl solutions. Nanorod passage through the nanopores decreases ion current in larger diameter pores, as in the case of typical Coulter counters, but it increases ion current in smaller diameter nanopores, likely because of the interaction of the nanopore's and nanoparticle's double layers. The presented method predicts a surface charge of 26 mC/m(2) for 44 nm long gold nanorods and 18 mC/m(2) for 65 nm long gold nanorods and facilitates future studies of ligand coverage and surface charge effects in anisotropic particles.
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Affiliation(s)
- Kimberly E Venta
- Department of Physics and Astronomy, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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114
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Balme S, Thiele D, Kraszewski S, Picaud F, Janot J, Déjardin P. Ionic selectivity of nystatin A1 confined in nanoporous track‐etched polymer membrane. IET Nanobiotechnol 2014; 8:138-42. [DOI: 10.1049/iet-nbt.2013.0014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Sébastien Balme
- Institut Européen des MembranesUMR5635 CNRS‐UM2‐ENSCM, Place Eugène Bataillon34095Montpellier cedex 5France
- Institut Charles GerhardtUMR 5253 CNRS‐UM2‐ENSCM‐UM1, Place Eugène Bataillon34095Montpellier cedex 5France
| | - Daniela Thiele
- Institut Européen des MembranesUMR5635 CNRS‐UM2‐ENSCM, Place Eugène Bataillon34095Montpellier cedex 5France
| | - Sebastian Kraszewski
- Laboratoire de NanomédecineImagerie et ThérapeutiqueUniversité de Franche‐ComtéCentre Hospitalier Universitaire de Besançon16 route de Gray25030 Besançon cedexFrance
| | - Fabien Picaud
- Laboratoire de NanomédecineImagerie et ThérapeutiqueUniversité de Franche‐ComtéCentre Hospitalier Universitaire de Besançon16 route de Gray25030 Besançon cedexFrance
| | - Jean‐Marc Janot
- Institut Européen des MembranesUMR5635 CNRS‐UM2‐ENSCM, Place Eugène Bataillon34095Montpellier cedex 5France
| | - Philippe Déjardin
- Institut Européen des MembranesUMR5635 CNRS‐UM2‐ENSCM, Place Eugène Bataillon34095Montpellier cedex 5France
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115
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Liu Z, Liu J, Xiao M, Wang R, Chen YL. Conformation-dependent translocation of a star polymer through a nanochannel. BIOMICROFLUIDICS 2014; 8:054107. [PMID: 25332744 PMCID: PMC4189700 DOI: 10.1063/1.4893637] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 08/11/2014] [Indexed: 06/04/2023]
Abstract
The translocation process of star polymers through a nanochannel is investigated by dissipative particle dynamics simulations. The translocation process is strongly influenced by the star arm arrangement as the polymer enters the channel, and a scaling relation between the translocation time [Formula: see text] and the total number of beads N tot is obtained. Qualitative agreements are found with predictions of the nucleation and growth model for linear block co-polymer translocation. In the intermediate stage where the center of the star polymer is at the channel entrance, the translocation time is found to have power law-dependence on the number of arms outside the channel and very weakly dependent on the number of arms in the channel. Increasing the total number of star arms also increases the star translocation time.
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Affiliation(s)
- Zhu Liu
- Key Laboratory of High Performance Polymer Materials and Technology of Ministry of Education, Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing National Laboratory of Microstructures, Nanjing University , Nanjing 210093, China
| | - Jiannan Liu
- Key Laboratory of High Performance Polymer Materials and Technology of Ministry of Education, Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing National Laboratory of Microstructures, Nanjing University , Nanjing 210093, China
| | - Mengying Xiao
- Key Laboratory of High Performance Polymer Materials and Technology of Ministry of Education, Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing National Laboratory of Microstructures, Nanjing University , Nanjing 210093, China
| | - Rong Wang
- Key Laboratory of High Performance Polymer Materials and Technology of Ministry of Education, Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing National Laboratory of Microstructures, Nanjing University , Nanjing 210093, China
| | - Yeng-Long Chen
- Institute of Physics , Academia Sinica, Taipei 11529, Taiwan
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116
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Abstract
Nanopore-based DNA sequencing has led to fast and high-resolution recognition and detection of DNA bases. Solid-state and biological nanopores have low signal-to-noise ratio (SNR) (< 10) and are generally too thick (> 5 nm) to be able to read at single-base resolution. A nanopore in graphene, a 2-D material with sub-nanometer thickness, has a SNR of ∼3 under DNA ionic current. In this report, using atomistic and quantum simulations, we find that a single-layer MoS2 is an extraordinary material (with a SNR > 15) for DNA sequencing by two competing technologies (i.e., nanopore and nanochannel). A MoS2 nanopore shows four distinct ionic current signals for single-nucleobase detection with low noise. In addition, a single-layer MoS2 shows a characteristic change/response in the total density of states for each base. The band gap of MoS2 is significantly changed compared to other nanomaterials (e.g., graphene, h-BN, and silicon nanowire) when bases are placed on top of the pristine MoS2 and armchair MoS2 nanoribbon, thus making MoS2 a promising material for base detection via transverse current tunneling measurement. MoS2 nanopore benefits from a craftable pore architecture (combination of Mo and S atoms at the edge) which can be engineered to obtain the optimum sequencing signals.
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Affiliation(s)
- Amir Barati Farimani
- Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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117
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Qian W, Doi K, Uehara S, Morita K, Kawano S. Theoretical study of the transpore velocity control of single-stranded DNA. Int J Mol Sci 2014; 15:13817-32. [PMID: 25116683 PMCID: PMC4159826 DOI: 10.3390/ijms150813817] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 07/15/2014] [Accepted: 07/22/2014] [Indexed: 12/17/2022] Open
Abstract
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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Affiliation(s)
- Weixin Qian
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
| | - Kentaro Doi
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
| | - Satoshi Uehara
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
| | - Kaito Morita
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
| | - Satoyuki Kawano
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
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118
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Akahori R, Haga T, Hatano T, Yanagi I, Ohura T, Hamamura H, Iwasaki T, Yokoi T, Anazawa T. Slowing single-stranded DNA translocation through a solid-state nanopore by decreasing the nanopore diameter. NANOTECHNOLOGY 2014; 25:275501. [PMID: 24960034 DOI: 10.1088/0957-4484/25/27/275501] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
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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Affiliation(s)
- Rena Akahori
- Central Research Laboratory, Hitachi, Ltd., 1-280 Higashi-koigakubo, Kokubunji, Tokyo 185-8601, Japan
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119
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Cabello-Aguilar S, Abou Chaaya A, Picaud F, Bechelany M, Pochat-Bohatier C, Yesylevskyy S, Kraszewski S, Bechelany MC, Rossignol F, Balanzat E, Janot JM, Miele P, Dejardin P, Balme S. Experimental and simulation studies of unusual current blockade induced by translocation of small oxidized PEG through a single nanopore. Phys Chem Chem Phys 2014; 16:17883-92. [DOI: 10.1039/c4cp01954g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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120
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Junesch J, Sannomiya T. Ultrathin suspended nanopores with surface plasmon resonance fabricated by combined colloidal lithography and film transfer. ACS APPLIED MATERIALS & INTERFACES 2014; 6:6322-31. [PMID: 24701958 DOI: 10.1021/am405443y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Suspended plasmonic nanopores in ultrathin film layers were fabricated through a simple and widely applicable method combining colloidal lithography and thin film transfer, which allows mass production of short-range ordered nanopore arrays on a large scale. By this combined method, mechanically stable and flexible free-standing nanopore membranes with a thickness down to 15-30 nm were produced. The plasmon resonances of the ultrathin plasmonic nanopores fabricated in AlN/Au/AlN trilayer and single layer Au membranes were tuned to lie in the vis-NIR wavelength range by properly designing their dimensions. The optical responses to the refractive index changes were tested and applied to adlayer sensing. The trilayer nanopore membrane showed a unique property to support water only on one side of the membrane, which was confirmed by the resonance shift and comparison with numerical simulation. Pore size reduction down to 10 nm can be achieved through additional material deposition. The filtering function of such pore-size-reduced conical shaped nanofunnels has also been demonstrated. The presented nanopore fabrication method offers new platforms for ultrathin nanopore sensing or filtering devices with controlled pore-size and optical properties. The film transfer technique employed in this work would enable the transformation of any substrate-based nanostructures to free-standing membrane based devices without complicated multiple etching processes.
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Affiliation(s)
- Juliane Junesch
- Institute of Biomedical Engineering, ETH Zürich , Gloriastrasse 35, 8092, Zürich, Switzerland
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121
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Abstract
Graphene is an ultrathin, impervious membrane. The controlled introduction of nanoscale pores in graphene would lead to applications that involve water purification, chemical separation, and DNA sequencing. However, graphene nanopores are unstable against filling by carbon adatoms. Here, using aberration-corrected scanning transmission electron microscopy and density-functional calculations, we report that Si atoms stabilize graphene nanopores by bridging the dangling bonds around the perimeter of the hole. Si-passivated pores remain intact even under intense electron beam irradiation, and they were observed several months after the sample fabrication, demonstrating that these structures are intrinsically robust and stable against carbon filling. Theoretical calculations reveal the underlying mechanism for this stabilization effect: Si atoms bond strongly to the graphene edge, and their preference for tetrahedral coordination forces C adatoms to form dendrites sticking out of the graphene plane, instead of filling the nanopore. Our results provide a novel way to develop stable nanopores, which is a major step toward reliable graphene-based molecular translocation devices.
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122
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Membrane thickness dependence of nanopore formation with a focused helium ion beam. SENSORS 2014; 14:8150-61. [PMID: 24806739 PMCID: PMC4063082 DOI: 10.3390/s140508150] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 04/11/2014] [Accepted: 04/29/2014] [Indexed: 11/16/2022]
Abstract
Solid-state nanopores are emerging as a valuable tool for the detection and characterization of individual biomolecules. Central to their success is the realization of fabrication strategies that are both rapid and flexible in their ability to achieve diverse device dimensions. In this paper, we demonstrate the membrane thickness dependence of solid-state nanopore formation with a focused helium ion beam. We vary membrane thickness in situ and show that the rate of pore expansion follows a reproducible trend under all investigated membrane conditions. We show that this trend shifts to lower ion dose for thin membranes in a manner that can be described quantitatively, allowing devices of arbitrary dimension to be realized. Finally, we demonstrate that thin, small-diameter nanopores formed with our approach can be utilized for high signal-to-noise ratio resistive pulse sensing of DNA.
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123
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Tailoring the hydrophobicity of graphene for its use as nanopores for DNA translocation. Nat Commun 2014; 4:2619. [PMID: 24126320 DOI: 10.1038/ncomms3619] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 09/15/2013] [Indexed: 01/16/2023] Open
Abstract
Graphene nanopores are potential successors to biological and silicon-based nanopores. For sensing applications, it is however crucial to understand and block the strong nonspecific hydrophobic interactions between DNA and graphene. Here we demonstrate a novel scheme to prevent DNA-graphene interactions, based on a tailored self-assembled monolayer. For bare graphene, we encounter a paradox: whereas contaminated graphene nanopores facilitated DNA translocation well, clean crystalline graphene pores very quickly exhibit clogging of the pore. We attribute this to strong interactions between DNA nucleotides and graphene, yielding sticking and irreversible pore closure. We develop a general strategy to noncovalently tailor the hydrophobic surface of graphene by designing a dedicated self-assembled monolayer of pyrene ethylene glycol, which renders the surface hydrophilic. We demonstrate that this prevents DNA to adsorb on graphene and show that single-stranded DNA can now be detected in graphene nanopores with excellent nanopore durability and reproducibility.
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124
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Liu K, Feng J, Kis A, Radenovic A. Atomically thin molybdenum disulfide nanopores with high sensitivity for DNA translocation. ACS NANO 2014; 8:2504-11. [PMID: 24547924 DOI: 10.1021/nn406102h] [Citation(s) in RCA: 260] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Atomically thin nanopore membranes are considered to be a promising approach to achieve single base resolution with the ultimate aim of rapid and cheap DNA sequencing. Molybdenum disulfide (MoS2) is newly emerging as a material complementary to graphene due to its semiconductive nature and other interesting physical properties that can enable a wide range of potential sensing and nanoelectronics applications. Here, we demonstrate that monolayer or few-layer thick exfoliated MoS2 with subnanometer thickness can be transferred and suspended on a predesigned location on the 20 nm thick SiNx membranes. Nanopores in MoS2 are further sculpted with variable sizes using a transmission electron microscope (TEM) to drill through suspended portions of the MoS2 membrane. Various types of double-stranded (ds) DNA with different lengths and conformations are translocated through such a novel architecture, showing improved sensitivity (signal-to-noise ratio>10) compared to the conventional silicon nitride (SiNx) nanopores with tens of nanometers thickness. Unlike graphene nanopores, no special surface treatment is needed to avoid hydrophobic interaction between DNA and the surface. Our results imply that MoS2 membranes with nanopore can complement graphene nanopore membranes and offer potentially better performance in transverse detection.
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Affiliation(s)
- Ke Liu
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL , 1015 Lausanne, Switzerland
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125
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Liang L, Zhang Z, Shen J, Zhe K, Wang Q, Wu T, Ågren H, Tu Y. Theoretical studies on the dynamics of DNA fragment translocation through multilayer graphene nanopores. RSC Adv 2014. [DOI: 10.1039/c4ra05909c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
DNA translocation through multilayer graphene nanopore with a change of current.
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Affiliation(s)
- Lijun Liang
- Department of Chemistry
- Soft Matter Research Center
- Zhejiang University
- Hangzhou 310027, People's Republic of China
- Division of Theoretical Chemistry and Biology
| | - Zhisen Zhang
- Department of Chemistry
- Soft Matter Research Center
- Zhejiang University
- Hangzhou 310027, People's Republic of China
| | - Jiawei Shen
- School of Medicine
- Hangzhou Normal University
- Hangzhou 310016, People's Republic of China
| | - Kong Zhe
- College of Materials and Environmental Engineering
- Hangzhou Dianzi University
- Hangzhou, People's Republic of China
| | - Qi Wang
- Department of Chemistry
- Soft Matter Research Center
- Zhejiang University
- Hangzhou 310027, People's Republic of China
| | - Tao Wu
- Department of Chemistry
- Soft Matter Research Center
- Zhejiang University
- Hangzhou 310027, People's Republic of China
| | - Hans Ågren
- Division of Theoretical Chemistry and Biology
- School of Biotechnology
- KTH Royal Institute of Technology
- SE-10691 Stockholm, Sweden
| | - Yaoquan Tu
- Division of Theoretical Chemistry and Biology
- School of Biotechnology
- KTH Royal Institute of Technology
- SE-10691 Stockholm, Sweden
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126
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Kumar A, Park KB, Kim HM, Kim KB. Noise and its reduction in graphene based nanopore devices. NANOTECHNOLOGY 2013; 24:495503. [PMID: 24240186 DOI: 10.1088/0957-4484/24/49/495503] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Ionic current fluctuations in graphene nanopore devices are a ubiquitous phenomenon and are responsible for degraded spatial and temporal resolution. Here, we descriptively investigate the impact of different substrate materials (Si and quartz) and membrane thicknesses on noise characteristics of graphene nanopore devices. To mitigate the membrane fluctuations and pin-hole defects, a SiNx membrane is transferred onto the substrate and a pore of approximately 70 nm in diameter is perforated prior to the graphene transfer. Comprehensive noise study reveals that the few layer graphene transferred onto the quartz substrate possesses low noise level and higher signal to noise ratio as compared to single layer graphene, without deteriorating the spatial resolution. The findings here point to improvement of graphene based nanopore devices for exciting opportunities in future single-molecule genomic screening devices.
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Affiliation(s)
- Ashvani Kumar
- Department of Materials Science and Engineering, Seoul National University, Seoul 151-742, Korea
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127
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Traversi F, Raillon C, Benameur SM, Liu K, Khlybov S, Tosun M, Krasnozhon D, Kis A, Radenovic A. Detecting the translocation of DNA through a nanopore using graphene nanoribbons. NATURE NANOTECHNOLOGY 2013; 8:939-45. [PMID: 24240429 DOI: 10.1038/nnano.2013.240] [Citation(s) in RCA: 218] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 10/14/2013] [Indexed: 05/24/2023]
Abstract
Solid-state nanopores can act as single-molecule sensors and could potentially be used to rapidly sequence DNA molecules. However, nanopores are typically fabricated in insulating membranes that are as thick as 15 bases, which makes it difficult for the devices to read individual bases. Graphene is only 0.335 nm thick (equivalent to the spacing between two bases in a DNA chain) and could therefore provide a suitable membrane for sequencing applications. Here, we show that a solid-state nanopore can be integrated with a graphene nanoribbon transistor to create a sensor for DNA translocation. As DNA molecules move through the pore, the device can simultaneously measure drops in ionic current and changes in local voltage in the transistor, which can both be used to detect the molecules. We examine the correlation between these two signals and use the ionic current measurements as a real-time control of the graphene-based sensing device.
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Affiliation(s)
- F Traversi
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, 1015 Lausanne, Switzerland
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128
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Sun LZ, Luo MB. Study on the polymer translocation induced blockade ionic current inside a nanopore by Langevin dynamics simulation. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2013; 25:465101. [PMID: 24099747 DOI: 10.1088/0953-8984/25/46/465101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The blockade ionic current inside a nanopore due to polymer translocation is studied using a three-dimensional Langevin dynamics method. The blockade current IB is dependent on the polymer length N, polymer configuration, polymer-pore interaction, and charge of the polymer. The behavior of IB can be explained using four factors: (1) the volume vacancy fraction fV inside the pore; (2) the conformation of the polymer; (3) the location of the polymer inside the pore; and (4) the total charge Ztot inside the pore. We find that IB increases with fV but decreases with increasing |Ztot|. The influence of the polymer's conformation is complex, dependent on the size of polymer RG and the cross-sectional size of the pore s. A compact conformation can decrease IB when RG > s but increase IB when RG < s. For the latter case, the conformation of the polymer is too small to block the pore, thus providing a broad passage for the ions. At the same fV, monomers will locate close to the surface with a large polymer-pore attraction, which also provides a large IB.
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Affiliation(s)
- Li-Zhen Sun
- Department of Physics, Zhejiang University, Hangzhou 310027, People's Republic of China
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129
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Nosik VL, Rudakova EB. Prospects of biomolecule sequencing with the techniques of translocation through nanopores: A review. CRYSTALLOGR REP+ 2013. [DOI: 10.1134/s1063774513060187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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130
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Polson JM, McCaffrey ACM. Polymer translocation dynamics in the quasi-static limit. J Chem Phys 2013; 138:174902. [PMID: 23656154 DOI: 10.1063/1.4803022] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Monte Carlo (MC) simulations are used to study the dynamics of polymer translocation through a nanopore in the limit where the translocation rate is sufficiently slow that the polymer maintains a state of conformational quasi-equilibrium. The system is modeled as a flexible hard-sphere chain that translocates through a cylindrical hole in a hard flat wall. In some calculations, the nanopore is connected at one end to a spherical cavity. Translocation times are measured directly using MC dynamics simulations. For sufficiently narrow pores, translocation is sufficiently slow that the mean translocation time scales with polymer length N according to <τ> ∝ (N - N(p))(2), where N(p) is the average number of monomers in the nanopore; this scaling is an indication of a quasi-static regime in which polymer-nanopore friction dominates. We use a multiple-histogram method to calculate the variation of the free energy with Q, a coordinate used to quantify the degree of translocation. The free energy functions are used with the Fokker-Planck formalism to calculate translocation time distributions in the quasi-static regime. These calculations also require a friction coefficient, characterized by a quantity N(eff), the effective number of monomers whose dynamics are affected by the confinement of the nanopore. This was determined by fixing the mean of the theoretical distribution to that of the distribution obtained from MC dynamics simulations. The theoretical distributions are in excellent quantitative agreement with the distributions obtained directly by the MC dynamics simulations for physically meaningful values of N(eff). The free energy functions for narrow-pore systems exhibit oscillations with an amplitude that is sensitive to the nanopore length. Generally, larger oscillation amplitudes correspond to longer translocation times.
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Affiliation(s)
- James M Polson
- Department of Physics, University of Prince Edward Island, 550 University Ave., Charlottetown, Prince Edward Island C1A 4P3, Canada
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131
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Edmonds CM, Hesketh PJ, Nair S. Polymer translocation in solid-state nanopores: Dependence on hydrodynamic interactions and polymer configuration. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.07.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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132
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Cecchini MP, Wiener A, Turek VA, Chon H, Lee S, Ivanov AP, McComb DW, Choo J, Albrecht T, Maier SA, Edel JB. Rapid ultrasensitive single particle surface-enhanced Raman spectroscopy using metallic nanopores. NANO LETTERS 2013; 13:4602-9. [PMID: 24021086 DOI: 10.1021/nl402108g] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Nanopore sensors embedded within thin dielectric membranes have been gaining significant interest due to their single molecule sensitivity and compatibility of detecting a large range of analytes, from DNA and proteins, to small molecules and particles. Building on this concept we utilize a metallic Au solid-state membrane to translocate and rapidly detect single Au nanoparticles (NPs) functionalized with 589 dye molecules using surface-enhanced resonance Raman spectroscopy (SERRS). We show that, due to the plasmonic coupling between the Au metallic nanopore surface and the NP, signal intensities are enhanced when probing analyte molecules bound to the NP surface. Although not single molecule, this nanopore sensing scheme benefits from the ability of SERRS to provide rich vibrational information on the analyte, improving on current nanopore-based electrical and optical detection techniques. We show that the full vibrational spectrum of the analyte can be detected with ultrahigh spectral sensitivity and a rapid temporal resolution of 880 μs.
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Affiliation(s)
- Michael P Cecchini
- Department of Chemistry, Imperial College London , South Kensington Campus, London, SW7 2AZ, United Kingdom
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133
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Patel B, Patel M, Bassett M, Landge S, Huang X, Jiang H, Wu J. Ionic Rectification through the Formation of Complexes or Precipitation in Carbon Nanotube Membranes. CHEM LETT 2013. [DOI: 10.1246/cl.130500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Bhavin Patel
- Department of Chemistry, Georgia Southern University
| | - Mayur Patel
- Department of Chemistry, Georgia Southern University
| | | | | | - Xuezhen Huang
- Department of Electrical and Computer Engineering, University of Wisconsin-Madison
| | - Hongrui Jiang
- Department of Electrical and Computer Engineering, University of Wisconsin-Madison
| | - Ji Wu
- Department of Chemistry, Georgia Southern University
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134
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Goyal G, Freedman KJ, Kim MJ. Gold Nanoparticle Translocation Dynamics and Electrical Detection of Single Particle Diffusion Using Solid-State Nanopores. Anal Chem 2013; 85:8180-7. [DOI: 10.1021/ac4012045] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Gaurav Goyal
- School
of Biomedical Engineering, Science and Health Systems, ‡Department of Chemical
and Biological Engineering, and §Department of Mechanical Engineering and Mechanics, Drexel University, 3141 Chestnut Street,
Philadelphia, Pennsylvania 19104, United States
| | - Kevin J. Freedman
- School
of Biomedical Engineering, Science and Health Systems, ‡Department of Chemical
and Biological Engineering, and §Department of Mechanical Engineering and Mechanics, Drexel University, 3141 Chestnut Street,
Philadelphia, Pennsylvania 19104, United States
| | - Min Jun Kim
- School
of Biomedical Engineering, Science and Health Systems, ‡Department of Chemical
and Biological Engineering, and §Department of Mechanical Engineering and Mechanics, Drexel University, 3141 Chestnut Street,
Philadelphia, Pennsylvania 19104, United States
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135
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Hyun C, Kaur H, Rollings R, Xiao M, Li J. Threading immobilized DNA molecules through a solid-state nanopore at >100 μs per base rate. ACS NANO 2013; 7:5892-900. [PMID: 23758046 PMCID: PMC3782089 DOI: 10.1021/nn4012434] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
In pursuit of developing solid-state nanopore-based DNA sequencing technology, we have designed and constructed an apparatus that can place a DNA-tethered probe tip near a solid-state nanopore, control the DNA moving speed, and measure the ionic current change when a DNA molecule is captured and released from a nanopore. The probe tip's position is sensed and controlled by a tuning fork based feedback force sensor and a nanopositioning system. Using this newly constructed apparatus, a DNA strand moving rate of >100 μs/base or <1 nm/ms in silicon nitride nanopores has been accomplished. This rate is 10 times slower than by manipulating DNA-tethered beads using optical tweezers and 1000 times slower than free DNA translocation through solid-state nanopores reported previously, which provides enough temporal resolution to read each base on a tethered DNA molecule using available single-channel recording electronics on the market today. This apparatus can measure three signals simultaneously: ionic current through a nanopore, tip position, and tip vibrational amplitude during the process of a DNA molecule's capture and release by a nanopore. We show results of this apparatus for measuring λ DNA's capture and release distances and for current blockage signals of λ DNA molecules biotinylated with one end and with both ends tethered to a tip.
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Affiliation(s)
- Changbae Hyun
- Department of Physics, University of Arkansas, Fayetteville AR 72701
| | - Harpreet Kaur
- Department of Physics, University of Arkansas, Fayetteville AR 72701
| | - Ryan Rollings
- Department of Physics, University of Arkansas, Fayetteville AR 72701
| | - Min Xiao
- Department of Physics, University of Arkansas, Fayetteville AR 72701
| | - Jiali Li
- Department of Physics, University of Arkansas, Fayetteville AR 72701
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136
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Abstract
It has recently been recognized that solid-state nanopores in single-atomic-layer graphene membranes can be used to electronically detect and characterize single long charged polymer molecules. We have now fabricated nanopores in single-layer graphene that are closely matched to the diameter of a double-stranded DNA molecule. Ionic current signals during electrophoretically driven translocation of DNA through these nanopores were experimentally explored and theoretically modeled. Our experiments show that these nanopores have unusually high sensitivity (0.65 nA/Å) to extremely small changes in the translocating molecule's outer diameter. Such atomically short graphene nanopores can also resolve nanoscale-spaced molecular structures along the length of a polymer, but do so with greatest sensitivity only when the pore and molecule diameters are closely matched. Modeling confirms that our most closely matched pores have an inherent resolution of ≤ 0.6 nm along the length of the molecule.
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137
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Adela Booth M, Vogel R, Curran JM, Harbison S, Travas-Sejdic J. Detection of target-probe oligonucleotide hybridization using synthetic nanopore resistive pulse sensing. Biosens Bioelectron 2013; 45:136-40. [DOI: 10.1016/j.bios.2013.01.044] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 01/08/2013] [Accepted: 01/24/2013] [Indexed: 01/23/2023]
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138
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Venta K, Shemer G, Puster M, Rodríguez-Manzo JA, Balan A, Rosenstein JK, Shepard K, Drndić M. Differentiation of short, single-stranded DNA homopolymers in solid-state nanopores. ACS NANO 2013; 7:4629-36. [PMID: 23621759 PMCID: PMC3724363 DOI: 10.1021/nn4014388] [Citation(s) in RCA: 165] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
In the last two decades, new techniques that monitor ionic current modulations as single molecules pass through a nanoscale pore have enabled numerous single-molecule studies. While biological nanopores have recently shown the ability to resolve single nucleotides within individual DNA molecules, similar developments with solid-state nanopores have lagged, due to challenges both in fabricating stable nanopores of similar dimensions as biological nanopores and in achieving sufficiently low-noise and high-bandwidth recordings. Here we show that small silicon nitride nanopores (0.8- to 2-nm diameter in 5- to 8-nm-thick membranes) can resolve differences between ionic current signals produced by short (30 base) ssDNA homopolymers (poly(dA), poly(dC), poly(dT)), when combined with measurement electronics that allow a signal-to-noise ratio of better than 10 to be achieved at 1-MHz bandwidth. While identifying intramolecular DNA sequences with silicon nitride nanopores will require further improvements in nanopore sensitivity and noise levels, homopolymer differentiation represents an important milestone in the development of solid-state nanopores.
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Affiliation(s)
- Kimberly Venta
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania, 19104
| | - Gabriel Shemer
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania, 19104
| | - Matthew Puster
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania, 19104
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, 19104
| | - Julio A. Rodríguez-Manzo
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania, 19104
| | - Adrian Balan
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania, 19104
| | - Jacob K. Rosenstein
- Department of Electrical Engineering, Columbia University, New York, New York, 10027
- School of Engineering, Brown University, Providence, Rhode Island, 02912
| | - Ken Shepard
- Department of Electrical Engineering, Columbia University, New York, New York, 10027
| | - Marija Drndić
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania, 19104
- Correspondence to Marija Drndić
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139
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Liu L, Wang B, Sha J, Yang Y, Hou Y, Ni Z, Chen Y. Voltage-driven translocation behaviors of IgG molecule through nanopore arrays. NANOSCALE RESEARCH LETTERS 2013; 8:229. [PMID: 23676116 PMCID: PMC3664219 DOI: 10.1186/1556-276x-8-229] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Accepted: 01/12/2013] [Indexed: 06/01/2023]
Abstract
Nanopore-based biosensing has attracted more and more interests in the past years, which is also regarded as an emerging field with major impact on bio-analysis and fundamental understanding of nanoscale interactions down to single-molecule level. In this work, the voltage-driven translocation properties of goat antibody to human immunoglobulin G (IgG) are investigated using nanopore arrays in polycarbonate membranes. Obviously, the background ionic currents are modulated by IgG molecules for their physical place-holding effect. However, the detected ionic currents do 'not' continuously decrease as conceived; the currents first decrease, then increase, and finally stabilize with increasing IgG concentration. To understand this phenomenon, a simplified model is suggested, and the calculated results contribute to the understanding of the abnormal phenomenon in the actual ionic current changing tendency.
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Affiliation(s)
- Lei Liu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanics, Southeast University, Nanjing 210096, People's Republic of China
| | - Bing Wang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanics, Southeast University, Nanjing 210096, People's Republic of China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanics, Southeast University, Nanjing 210096, People's Republic of China
| | - Yue Yang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanics, Southeast University, Nanjing 210096, People's Republic of China
| | - Yaozong Hou
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanics, Southeast University, Nanjing 210096, People's Republic of China
| | - Zhonghua Ni
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanics, Southeast University, Nanjing 210096, People's Republic of China
| | - Yunfei Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanics, Southeast University, Nanjing 210096, People's Republic of China
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140
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Avdoshenko SM, Nozaki D, Gomes da Rocha C, González JW, Lee MH, Gutierrez R, Cuniberti G. Dynamic and electronic transport properties of DNA translocation through graphene nanopores. NANO LETTERS 2013; 13:1969-1976. [PMID: 23586585 DOI: 10.1021/nl304735k] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Graphene layers have been targeted in the last years as excellent host materials for sensing a remarkable variety of gases and molecules. Such sensing abilities can also benefit other important scientific fields such as medicine and biology. This has automatically led scientists to probe graphene as a potential platform for sequencing DNA strands. In this work, we use robust numerical tools to model the dynamic and electronic properties of molecular sensor devices composed of a graphene nanopore through which DNA molecules are driven by external electric fields. We performed molecular dynamic simulations to determine the relation between the intensity of the electric field and the translocation time spent by the DNA to pass through the pore. Our results reveal that one can have extra control on the DNA passage when four additional graphene layers are deposited on the top of the main graphene platform containing the pore in a 2 × 2 grid arrangement. In addition to the dynamic analysis, we carried electronic transport calculations on realistic pore structures with diameters reaching nanometer scales. The transmission obtained along the graphene sensor at the Fermi level is affected by the presence of the DNA. However, it is rather hard to distinguish the respective nucleobases. This scenario can be significantly altered when the transport is conducted away from the Fermi level of the graphene platform. Under an energy shift, we observed that the graphene pore manifests selectiveness toward DNA nucleobases.
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141
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Tahir MN, Ali M, Andre R, Müller WEG, Schröder HC, Tremel W, Ensinger W. Silicatein conjugation inside nanoconfined geometries through immobilized NTA–Ni(ii) chelates. Chem Commun (Camb) 2013; 49:2210-2. [DOI: 10.1039/c3cc38605h] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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142
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Jou IA, Melnikov DV, McKinney CR, Gracheva ME. DNA translocation through a nanopore in a single-layered doped semiconductor membrane. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:061906. [PMID: 23367975 DOI: 10.1103/physreve.86.061906] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Indexed: 06/01/2023]
Abstract
Recently, we developed a computational model that allowed us to study the influence a semiconductor membrane has on a DNA molecule translocating through a nanopore in this membrane. Our model incorporated both the self-consistent Poisson-Nernst-Planck simulations for the electric potential of a solid state membrane immersed in an electrolyte solution together with the Brownian dynamics of the biomolecule. In this paper, we study how the applied electrolyte bias, the semiconductor membrane bias, and the semiconductor material type (n-Si or p-Si) affect the translocation dynamics of a single-stranded DNA moving through a nanopore in a single-layered semiconductor membrane. We show that the type of semiconductor material used for the membrane has a prominent effect on the biomolecule's translocation time, with DNA exhibiting much longer translocation times through the p-type membrane than through the n type at the same electrolyte and membrane potentials, while the extension of the biomolecule remains practically unchanged. In addition, we find the optimal combination for the membrane-electrolyte system's parameters to achieve the longest translocation time and largest DNA extension. With our single-layered electrically tunable membranes, the DNA translocation time can be manipulated to have an order of magnitude increase.
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Affiliation(s)
- Ining A Jou
- Department of Physics, Clarkson University, Potsdam, New York 13699, USA
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143
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Uplinger J, Thomas B, Rollings R, Fologea D, McNabb D, Li J. K(+) , Na(+) , and Mg(2+) on DNA translocation in silicon nitride nanopores. Electrophoresis 2012; 33:3448-57. [PMID: 23147752 PMCID: PMC3514626 DOI: 10.1002/elps.201200165] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 06/19/2012] [Accepted: 06/20/2012] [Indexed: 11/06/2022]
Abstract
In this work, we report on how salt concentration and cation species affect DNA translocation in voltage-biased silicon nitride nanopores. The translocation of dsDNA in linear, circular, and supercoiled forms was measured in salt solutions containing KCl, NaCl, and MgCl(2) . As the KCl concentrations were decreased from 1 to 0.1 M, the time taken by a DNA molecule to pass through a nanopore was shorter and the frequency of the translocation in a folded configuration was reduced, suggesting an increase in DNA electrophoretic mobility and DNA persistence length. When the salt concentration was kept at 1 M, but replacing K(+) with Na(+) , longer DNA translocation times (t(d) ) were observed. The addition of low concentrations of MgCl(2) with 1.6 M KCl resulted in longer t(d) and an increased frequency of supercoiled DNA molecules in a branched form. These observations were consistent with the greater counterion charge screening ability of Na(+) and Mg(2+) as compared to K(+) . In addition, we demonstrated that dsDNA molecules indeed translocated through a ∼10 nm nanopore by PCR amplification and gel electrophoresis. We also compared the dependence of DNA mobility and conformation on KCl concentration and cation species measured at single molecule level by silicon nitride nanopores with existing bulk-based experimental results and theoretical predictions.
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Affiliation(s)
| | | | | | | | - David McNabb
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701
| | - Jiali Li
- Corresponding Author: Jiali Li, Department of Physics, Room 226, University of Arkansas, 825 w Dickson Street, Fayetteville, AR 72701, , Phone: (479) 575-7593. Fax: (479) 575-4580
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144
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Ando G, Hyun C, Li J, Mitsui T. Directly observing the motion of DNA molecules near solid-state nanopores. ACS NANO 2012; 6:10090-7. [PMID: 23046052 PMCID: PMC3508321 DOI: 10.1021/nn303816w] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We investigate the diffusion and the drift motion of λ DNA molecules near solid-state nanopores prior to their translocation through the nanopores using fluorescence microscopy. The radial dependence of the electric field near a nanopore generated by an applied voltage in ionic solution can be estimated quantitatively in 3D by analyzing the motion of negatively charged DNA molecules. We find that the electric field is approximately spherically symmetric around the nanopore under the conditions investigated. In addition, DNA clogging at the nanopore was directly observed. Surprisingly, the probability of the clogging event increases with increasing external bias voltage. We also find that DNA molecules clogging the nanopore reduce the electric field amplitude at the nanopore membrane surface. To better understand these experimental results, analytical method with Ohm's law and computer simulation with Poisson and Nernst-Planck (PNP) equations are used to calculate the electric field near the nanopore. These results are of great interest in both experimental and theoretical considerations of the motion of DNA molecules near voltage-biased nanopores. These findings will also contribute to the development of solid-state nanopore-based DNA sensing devices.
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Affiliation(s)
- Genki Ando
- Aoyama-Gakuin University. Sagamihara Campus L617, 5-10-1 Fuchinobe, Chuo, Sagamihara, Kanagawa, 252-5258, Japan
| | - Changbae Hyun
- Physics Department, University of Arkansas, Fayetteville, AR 72701, USA
| | - Jiali Li
- Physics Department, University of Arkansas, Fayetteville, AR 72701, USA
| | - Toshiyuki Mitsui
- Aoyama-Gakuin University. Sagamihara Campus L617, 5-10-1 Fuchinobe, Chuo, Sagamihara, Kanagawa, 252-5258, Japan
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145
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Reiner JE, Balijepalli A, Robertson JWF, Campbell J, Suehle J, Kasianowicz JJ. Disease Detection and Management via Single Nanopore-Based Sensors. Chem Rev 2012; 112:6431-51. [DOI: 10.1021/cr300381m] [Citation(s) in RCA: 195] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Joseph E. Reiner
- Department of Physics, Virginia
Commonwealth University, 701 W. Grace Street, Richmond, Virginia 23284,
United States
| | - Arvind Balijepalli
- Physical
Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899-8120, United States
- Laboratory of Computational Biology,
National Heart Lung and Blood Institute, Rockville, Maryland 20852,
United States
| | - Joseph W. F. Robertson
- Physical
Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899-8120, United States
| | - Jason Campbell
- Physical
Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899-8120, United States
| | - John Suehle
- Physical
Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899-8120, United States
| | - John J. Kasianowicz
- Physical
Measurement Laboratory,
National Institute of Standards and Technology, Gaithersburg, Maryland
20899-8120, United States
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146
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Modulating DNA translocation by a controlled deformation of a PDMS nanochannel device. Sci Rep 2012; 2:791. [PMID: 23145315 PMCID: PMC3494361 DOI: 10.1038/srep00791] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 09/28/2012] [Indexed: 11/21/2022] Open
Abstract
Several strategies have been developed for the control of DNA translocation in nanopores and nanochannels. However, the possibility to reduce the molecule speed is still challenging for applications in the field of single molecule analysis, such as ultra-rapid sequencing. This paper demonstrates the possibility to alter the DNA translocation process through an elastomeric nanochannel device by dynamically changing its cross section. More in detail, nanochannel deformation is induced by a macroscopic mechanical compression of the polymeric device. This nanochannel squeezing allows slowing down the DNA molecule passage inside it. This simple and low cost method is based on the exploitation of the elastomeric nature of the device, can be coupled with different sensing techniques, is applicable in many research fields, such as DNA detection and manipulation, and is promising for further development in sequencing technology.
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147
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Abstract
Lipid bilayers are natural barriers of biological cells and cellular compartments. Membrane proteins integrated in biological membranes enable vital cell functions such as signal transduction and the transport of ions or small molecules. In order to determine the activity of a protein of interest at defined conditions, the membrane protein has to be integrated into artificial lipid bilayers immobilized on a surface. For the fabrication of such biosensors expertise is required in material science, surface and analytical chemistry, molecular biology and biotechnology. Specifically, techniques are needed for structuring surfaces in the micro- and nanometer scale, chemical modification and analysis, lipid bilayer formation, protein expression, purification and solubilization, and most importantly, protein integration into engineered lipid bilayers. Electrochemical and optical methods are suitable to detect membrane activity-related signals. The importance of structural knowledge to understand membrane protein function is obvious. Presently only a few structures of membrane proteins are solved at atomic resolution. Functional assays together with known structures of individual membrane proteins will contribute to a better understanding of vital biological processes occurring at biological membranes. Such assays will be utilized in the discovery of drugs, since membrane proteins are major drug targets.
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148
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Yeh LH, Zhang M, Joo SW, Qian S, Hsu JP. Controlling pH-Regulated Bionanoparticles Translocation through Nanopores with Polyelectrolyte Brushes. Anal Chem 2012; 84:9615-22. [DOI: 10.1021/ac302429d] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Li-Hsien Yeh
- Department of Chemical and Materials Engineering, National Yunlin University of Science and Technology, Yunlin 64002, Taiwan
| | - Mingkan Zhang
- Institute of Micro/Nanotechnology, Old Dominion University, Norfolk, Virginia 23529, United
States
| | - Sang W. Joo
- School
of Mechanical Engineering, Yeungnam University, Gyongsan 712-719, South Korea
| | - Shizhi Qian
- Institute of Micro/Nanotechnology, Old Dominion University, Norfolk, Virginia 23529, United
States
- School
of Mechanical Engineering, Yeungnam University, Gyongsan 712-719, South Korea
| | - Jyh-Ping Hsu
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
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149
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Liu Q, Wu H, Wu L, Xie X, Kong J, Ye X, Liu L. Voltage-driven translocation of DNA through a high throughput conical solid-state nanopore. PLoS One 2012; 7:e46014. [PMID: 23029365 PMCID: PMC3454345 DOI: 10.1371/journal.pone.0046014] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 08/27/2012] [Indexed: 11/18/2022] Open
Abstract
Nanopores have become an important tool for molecule detection at single molecular level. With the development of fabrication technology, synthesized solid-state membranes are promising candidate substrates in respect of their exceptional robustness and controllable size and shape. Here, a 30-60 (tip-base) nm conical nanopore fabricated in 100 nm thick silicon nitride (Si(3)N(4)) membrane by focused ion beam (FIB) has been employed for the analysis of λ-DNA translocations at different voltage biases from 200 to 450 mV. The distributions of translocation time and current blockage, as well as the events frequencies as a function of voltage are investigated. Similar to previously published work, the presence and configurations of λ-DNA molecules are characterized, also, we find that greater applied voltages markedly increase the events rate, and stretch the coiled λ-DNA molecules into linear form. However, compared to 6-30 nm ultrathin solid-state nanopores, a threshold voltage of 181 mV is found to be necessary to drive DNA molecules through the nanopore due to conical shape and length of the pore. The speed is slowed down ∼5 times, while the capture radius is ∼2 fold larger. The results show that the large nanopore in thick membrane with an improved stability and throughput also has the ability to detect the molecules at a single molecular level, as well as slows down the velocity of molecules passing through the pore. This work will provide more motivations for the development of nanopores as a Multi-functional sensor for a wide range of biopolymers and nano materials.
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Affiliation(s)
- Quanjun Liu
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, China.
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150
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Mirigian S, Wang Y, Muthukumar M. Translocation of a heterogeneous polymer. J Chem Phys 2012; 137:064904. [PMID: 22897308 PMCID: PMC3738248 DOI: 10.1063/1.4742970] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 07/25/2012] [Indexed: 12/11/2022] Open
Abstract
We present results on the sequence dependence of translocation kinetics for a partially charged heteropolymer moving through a very thin pore using theoretical tools and Langevin dynamics simulational techniques. The chain is composed of two types of monomers of differing frictional interaction with the pore and charge. We present exact analytical expressions for passage probability, mean first passage time, and mean successful passage times for both reflecting/absorbing and absorbing/absorbing boundary conditions, showing rich and unexpected dependence of translocation behavior on charge fraction, distribution along the chain, and electric field configuration. We find excellent qualitative and good quantitative agreement between theoretical and simulation results. Surprisingly, there emerges a threshold charge fraction of a diblock copolymer beyond which the success rate of translocation is independent of charge fraction. Also, the mean successful translocation time of a diblock copolymer displays non-monotonic behavior with increasing length of the charged block; there is an optimum length of the charged block where the mean translocation rate is the slowest; and there can be a substantial range of higher charge fractions which make the translocation slower than even a minimally charged chain. Additionally, we find for a fixed total charge on the chain, finer distribution along the backbone significantly decreases mean translocation time.
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Affiliation(s)
- Stephen Mirigian
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, USA
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