151
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Kang Y, Zhang Z, Shi H, Zhang J, Liang L, Wang Q, Ågren H, Tu Y. Na⁺ and K⁺ ion selectivity by size-controlled biomimetic graphene nanopores. NANOSCALE 2014; 6:10666-10672. [PMID: 25089590 DOI: 10.1039/c4nr01383b] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Because biological ionic channels play a key role in cellular transport phenomena, they have attracted extensive research interest for the design of biomimetic nanopores with high permeability and selectivity in a variety of technical applications. Inspired by the structure of K(+) channel proteins, we designed a series of oxygen doped graphene nanopores of different sizes by molecular dynamics simulations to discriminate between K(+) and Na(+) channel transport. The results from free energy calculations indicate that the ion selectivity of such biomimetic graphene nanopores can be simply controlled by the size of the nanopore; compared to K(+), the smaller radius of Na(+) leads to a significantly higher free energy barrier in the nanopore of a certain size. Our results suggest that graphene nanopores with a distance of about 3.9 Å between two neighboring oxygen atoms could constitute a promising candidate to obtain excellent ion selectivity for Na(+) and K(+) ions.
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Affiliation(s)
- Yu Kang
- Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou 310027, People's Republic of China.
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152
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Iliafar S, Mittal J, Vezenov D, Jagota A. Interaction of single-stranded DNA with curved carbon nanotube is much stronger than with flat graphite. J Am Chem Soc 2014; 136:12947-57. [PMID: 25162693 DOI: 10.1021/ja5055498] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We used single molecule force spectroscopy to measure the force required to remove single-stranded DNA (ssDNA) homopolymers from single-walled carbon nanotubes (SWCNTs) deposited on methyl-terminated self-assembled monolayers (SAMs). The peeling forces obtained from these experiments are bimodal in distribution. The cluster of low forces corresponds to peeling from the SAM surface, while the cluster of high forces corresponds to peeling from the SWCNTs. Using a simple equilibrium model of the single molecule peeling process, we calculated the free energy of binding per nucleotide. We found that the free energy of ssDNA binding to hydrophobic SAMs decreases as poly(A) > poly(G) ≈ poly(T) > poly(C) (16.9 ± 0.1; 9.7 ± 0.1; 9.5 ± 0.1; 8.7 ± 0.1 kBT, per nucleotide). The free energy of ssDNA binding to SWCNT adsorbed on this SAM also decreases in the same order poly(A) > poly(G) > poly(T) > poly(C), but its magnitude is significantly greater than that of DNA-SAM binding energy (38.1 ± 0.2; 33.9 ± 0.1; 23.3 ± 0.1; 17.1 ± 0.1 kBT, per nucleotide). An unexpected finding is that binding strength of ssDNA to the curved SWCNTs is much greater than to flat graphite, which also has a different ranking (poly(T) > poly(A) > poly(G) ≥ poly(C); 11.3 ± 0.8, 9.9 ± 0.5, 8.3 ± 0.2, and 7.5 ± 0.8 kBT, respectively, per nucleotide). Replica-exchange molecular dynamics simulations show that ssDNA binds preferentially to the curved SWCNT surface, leading us to conclude that the differences in ssDNA binding between graphite and nanotubes arise from the spontaneous curvature of ssDNA.
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Affiliation(s)
- Sara Iliafar
- Department of Chemical and Biomolecular Engineering and ‡Bioengineering Program, Lehigh University , Bethlehem, Pennsylvania 18015, United States
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153
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Chen H, Ruckenstein E. Nanomembrane Containing a Nanopore in an Electrolyte Solution: A Molecular Dynamics Approach. J Phys Chem Lett 2014; 5:2979-2982. [PMID: 26278246 DOI: 10.1021/jz501502y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Molecular dynamics simulation is used to acquire information about the characteristics of a nanographene membrane immersed in an electrolyte solution of KCl and subjected to an electric field. The membrane possesses one nanopore. It is shown that the solution contains in addition to hydrated ions, hydrated ion pairs, and hydrated clusters with more than two ions. The fractions of hydrated ions, hydrated ion pairs and hydrated clusters as well as their hydration numbers were also calculated. It was found that the hydration numbers remain constant at low electric fields but decrease at high electric fields. Under the action of an electric field, the K(+) and Cl(-) ions separate on the two sides of graphene, thus generating hydrated ion polarization layers, which result in negative charge density layers and positive ones on the left and right interfaces of the water/graphene. Thus, the neutral graphene becomes asymmetrically charged.
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Affiliation(s)
- Houyang Chen
- †Department of Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- ‡Department of Chemical and Biological Engineering, State University of New York at Buffalo, Buffalo, New York 14260-4200, United States
| | - Eli Ruckenstein
- ‡Department of Chemical and Biological Engineering, State University of New York at Buffalo, Buffalo, New York 14260-4200, United States
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154
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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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155
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Ahmed T, Haraldsen JT, Zhu JX, Balatsky AV. Next-Generation Epigenetic Detection Technique: Identifying Methylated Cytosine Using Graphene Nanopore. J Phys Chem Lett 2014; 5:2601-2607. [PMID: 26277950 DOI: 10.1021/jz501085e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
DNA methylation plays a pivotal role in the genetic evolution of both embryonic and adult cells. For adult somatic cells, the location and dynamics of methylation have been very precisely pinned down with the 5-cytosine markers on cytosine-phosphate-guanine (CpG) units. Unusual methylation on CpG islands is identified as one of the prime causes for silencing the tumor suppressant genes. Early detection of methylation changes can diagnose the potentially harmful oncogenic evolution of cells and provide promising guideline for cancer prevention. With this motivation, we propose a cytosine methylation detection technique. Our hypothesis is that electronic signatures of DNA acquired as a molecule translocates through a nanopore would be significantly different for methylated and nonmethylated bases. This difference in electronic fingerprints would allow for reliable real-time differentiation of methylated DNA. We calculate transport currents through a punctured graphene membrane while the cytosine and methylated cytosine translocate through the nanopore. We also calculate the transport properties for uracil and cyanocytosine for comparison. Our calculations of transmission, current, and tunneling conductance show distinct signatures in their spectrum for each molecular type. Thus, in this work, we provide a theoretical analysis that points to a viability of our hypothesis.
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Affiliation(s)
| | - Jason T Haraldsen
- ‡Department of Physics and Astronomy, James Madison University, Harrisonburg, Virginia 22807, United States
| | | | - Alexander V Balatsky
- ¶Nordic Institute for Theoretical Physics, KTH Royal Institute of Technology and Stockholm University, Roslagstullsbacken 23, 106 91 Stockholm, Sweden
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156
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Xie G, Yang R, Chen P, Zhang J, Tian X, Wu S, Zhao J, Cheng M, Yang W, Wang D, He C, Bai X, Shi D, Zhang G. A general route towards defect and pore engineering in graphene. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:2280-2284. [PMID: 24610779 DOI: 10.1002/smll.201303671] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 02/12/2014] [Indexed: 06/03/2023]
Abstract
Defect engineering in graphene is important for tailoring graphene's properties thus applicable in various applications such as porous membranes and ultra-capacitors. In this paper, we report a general route towards defect- and pore- engineering in graphene through remote plasma treatments. Oxygen plasma irradiation was employed to create homogenous defects in graphene with controllable density from a few to ≈10(3) (μm(-2)). The created defects can be further enlarged into nanopores by hydrogen plasma anisotropic etching with well-defined pore size of a few nm or above. The achieved smallest nanopores are ≈2 nm in size, showing the potential for ultra-small graphene nanopores fabrication.
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Affiliation(s)
- Guibai Xie
- Beijing National Laboratory for Condensed Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
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157
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Sadeghi H, Algaragholy L, Pope T, Bailey S, Visontai D, Manrique D, Ferrer J, Garcia-Suarez V, Sangtarash S, Lambert CJ. Graphene Sculpturene Nanopores for DNA Nucleobase Sensing. J Phys Chem B 2014; 118:6908-14. [DOI: 10.1021/jp5034917] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Hatef Sadeghi
- Physics
Department, Lancaster University, Lancaster LA1 4YB, U.K
| | - L. Algaragholy
- Physics
Department, Lancaster University, Lancaster LA1 4YB, U.K
| | - T. Pope
- Physics
Department, Lancaster University, Lancaster LA1 4YB, U.K
| | - S. Bailey
- Physics
Department, Lancaster University, Lancaster LA1 4YB, U.K
| | - D. Visontai
- Physics
Department, Lancaster University, Lancaster LA1 4YB, U.K
| | - D. Manrique
- Physics
Department, Lancaster University, Lancaster LA1 4YB, U.K
| | - J. Ferrer
- Physics
Department, Lancaster University, Lancaster LA1 4YB, U.K
| | - V. Garcia-Suarez
- Physics
Department, Lancaster University, Lancaster LA1 4YB, U.K
| | - Sara Sangtarash
- Physics
Department, Lancaster University, Lancaster LA1 4YB, U.K
| | - Colin J. Lambert
- Physics
Department, Lancaster University, Lancaster LA1 4YB, U.K
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158
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Yanagi I, Akahori R, Hatano T, Takeda KI. Fabricating nanopores with diameters of sub-1 nm to 3 nm using multilevel pulse-voltage injection. Sci Rep 2014; 4:5000. [PMID: 24847795 PMCID: PMC4028839 DOI: 10.1038/srep05000] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 04/14/2014] [Indexed: 12/22/2022] Open
Abstract
To date, solid-state nanopores have been fabricated primarily through a focused-electronic beam via TEM. For mass production, however, a TEM beam is not suitable and an alternative fabrication method is required. Recently, a simple method for fabricating solid-state nanopores was reported by Kwok, H. et al. and used to fabricate a nanopore (down to 2 nm in size) in a membrane via dielectric breakdown. In the present study, to fabricate smaller nanopores stably--specifically with a diameter of 1 to 2 nm (which is an essential size for identifying each nucleotide)--via dielectric breakdown, a technique called "multilevel pulse-voltage injection" (MPVI) is proposed and evaluated. MPVI can generate nanopores with diameters of sub-1 nm in a 10-nm-thick Si3N4 membrane with a probability of 90%. The generated nanopores can be widened to the desired size (as high as 3 nm in diameter) with sub-nanometre precision, and the mean effective thickness of the fabricated nanopores was 3.7 nm.
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Affiliation(s)
- Itaru Yanagi
- Hitachi Ltd., Central Research Laboratory, 1-280 Higashi-koigakubo, Kokubunji, Tokyo, 185-8603
| | - Rena Akahori
- Hitachi Ltd., Central Research Laboratory, 1-280 Higashi-koigakubo, Kokubunji, Tokyo, 185-8603
| | - Toshiyuki Hatano
- Hitachi Ltd., Central Research Laboratory, 1-280 Higashi-koigakubo, Kokubunji, Tokyo, 185-8603
| | - Ken-ichi Takeda
- Hitachi Ltd., Central Research Laboratory, 1-280 Higashi-koigakubo, Kokubunji, Tokyo, 185-8603
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159
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Zhang Z, Shen J, Wang H, Wang Q, Zhang J, Liang L, Ågren H, Tu Y. Effects of Graphene Nanopore Geometry on DNA Sequencing. J Phys Chem Lett 2014; 5:1602-1607. [PMID: 26270103 DOI: 10.1021/jz500498c] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In this Letter we assess the effect of graphene nanopore geometries on DNA sequencing by considering DNA fragments including A, T, C, G, and 5-methylcytosine (MC) pulled out of graphene nanopores of different geometries with diameters down to ∼1 nm. Using steered molecular dynamics simulations it is demonstrated that the bases (A, T, C, G, and MC) can be indentified at single-base resolution through the characteristic peaks on the force profile in a circular graphene nanopore but not in nanopores with other asymmetric geometries. Our study suggests that the graphene nanopore surface should be modified as symmetrically as possible in order to sequence DNA by atomic force microscopy or optical tweezers.
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Affiliation(s)
- Zhisen Zhang
- †Department of Chemistry and 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
| | - Hongbo Wang
- §College of Automation, Hangzhou Dianzi University, Hangzhou 310018, People's Republic of China
| | - Qi Wang
- †Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou 310027, People's Republic of China
| | - Junqiao Zhang
- †Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou 310027, People's Republic of China
| | - Lijun Liang
- †Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou 310027, People's Republic of China
- ∥Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - 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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160
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Connelly LS, Meckes B, Larkin J, Gillman AL, Wanunu M, Lal R. Graphene nanopore support system for simultaneous high-resolution AFM imaging and conductance measurements. ACS APPLIED MATERIALS & INTERFACES 2014; 6:5290-6. [PMID: 24581087 PMCID: PMC4232248 DOI: 10.1021/am500639q] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 02/28/2014] [Indexed: 05/24/2023]
Abstract
Accurately defining the nanoporous structure and sensing the ionic flow across nanoscale pores in thin films and membranes has a wide range of applications, including characterization of biological ion channels and receptors, DNA sequencing, molecule separation by nanoparticle films, sensing by block co-polymers films, and catalysis through metal-organic frameworks. Ionic conductance through nanopores is often regulated by their 3D structures, a relationship that can be accurately determined only by their simultaneous measurements. However, defining their structure-function relationships directly by any existing techniques is still not possible. Atomic force microscopy (AFM) can image the structures of these pores at high resolution in an aqueous environment, and electrophysiological techniques can measure ion flow through individual nanoscale pores. Combining these techniques is limited by the lack of nanoscale interfaces. We have designed a graphene-based single-nanopore support (∼5 nm thick with ∼20 nm pore diameter) and have integrated AFM imaging and ionic conductance recording using our newly designed double-chamber recording system to study an overlaid thin film. The functionality of this integrated system is demonstrated by electrical recording (<10 pS conductance) of suspended lipid bilayers spanning a nanopore and simultaneous AFM imaging of the bilayer.
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Affiliation(s)
- Laura S. Connelly
- Materials Science and Engineering
Program, Department of Bioengineering, and Department of Mechanical and Aerospace Engineering, University of California−San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Brian Meckes
- Materials Science and Engineering
Program, Department of Bioengineering, and Department of Mechanical and Aerospace Engineering, University of California−San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Joseph Larkin
- Department of Physics, Northeastern University, 110 Forsyth Street, Boston, Massachusetts 02115, United States
| | - Alan L. Gillman
- Materials Science and Engineering
Program, Department of Bioengineering, and Department of Mechanical and Aerospace Engineering, University of California−San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Meni Wanunu
- Department of Physics, Northeastern University, 110 Forsyth Street, Boston, Massachusetts 02115, United States
| | - Ratnesh Lal
- Materials Science and Engineering
Program, Department of Bioengineering, and Department of Mechanical and Aerospace Engineering, University of California−San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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161
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Rezzonico F. Nanopore-based instruments as biosensors for future planetary missions. ASTROBIOLOGY 2014; 14:344-351. [PMID: 24684166 DOI: 10.1089/ast.2013.1120] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Data from automated orbiters and landers have dashed humankind's hopes of finding complex life-forms elsewhere in the Solar System. The focus of exobiological research was thus forced to shift from the detection of life through simple visual imaging to complex biochemical experiments aimed at the detection of microbial activity. Searching for biosignatures over interplanetary distances is a formidable task and poses the dilemma of what are the proper experiments that can be performed on-site to maximize the chances of success if extraterrestrial life is present but not evident. Despite their astonishing morphological diversity, all known organisms on Earth share the same basic molecular architecture; thus the vast majority of our detection and identification techniques are b(i)ased on Terran biochemistry. There is, however, a distinct possibility that life may have emerged elsewhere by using other molecular building blocks, a fact that is likely to make the outcome of most of the current molecular biological and biochemical life-detection protocols difficult to interpret if not completely ineffective. Nanopore-based sensing devices allow the analysis of single molecules, including the sequence of informational biopolymers such as DNA or RNA, by measuring current changes across an electrically resistant membrane when the analyte flows through an embedded transmembrane protein or a solid-state nanopore. Under certain basic assumptions about their physical properties, this technology has the potential to discriminate and possibly analyze biopolymers, in particular genetic information carriers, without prior detailed knowledge of their fundamental chemistry and is sufficiently portable to be used for automated analysis in planetary exploration, all of which makes it the ideal candidate for the search for life signatures in remote watery environments such as Mars, Europa, or Enceladus.
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Affiliation(s)
- Fabio Rezzonico
- Research group Environmental Genomics and Systems Biology, Zurich University for Applied Sciences (ZHAW) , Wädenswil, Switzerland
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162
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Lv W, Liu S, Li X, Wu R. Spatial blockage of ionic current for electrophoretic translocation of DNA through a graphene nanopore. Electrophoresis 2014; 35:1144-51. [PMID: 24459097 DOI: 10.1002/elps.201300501] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Revised: 01/10/2014] [Accepted: 01/10/2014] [Indexed: 11/11/2022]
Abstract
Graphene nanopore has been promising the ultra-high resolution for DNA sequencing due to the atomic thickness and excellent electronic properties of the graphene monolayer. The dynamical translocation phenomena and/or behaviors underneath the blocked ionic current, however, have not been well unveiled to date for the translocation of DNA electrophoretically through a graphene nanopore. In this report, the assessment on the sensitivity of ionic current to instantaneous statuses of DNA in a 2.4 nm graphene nanopore was carried out based on the all-atom molecular dynamics simulations. By filtering out the thermal noise of ionic current, the instantaneous conformational variations of DNA in a graphene nanopore have been unveiled from the fluctuations of ionic current, because of the spatial blockage effect of DNA against ionic current. Interestingly, the neighborhood effect of DNA against ionic current was also observed within a distance of 1.5 nm nearby the graphene nanopore, suggesting the further precise control for DNA translocation through a graphene nanopore in gene sequencing. Moreover, the sensitivity of the blocked ionic current toward the instantaneous conformations of DNA in a graphene nanopore demonstrates the great potential of graphene nanopores in the dynamics analysis of single molecules.
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Affiliation(s)
- Wenping Lv
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, P. R. China
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163
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Liang L, Wang Q, Agren H, Tu Y. Computational studies of DNA sequencing with solid-state nanopores: key issues and future prospects. Front Chem 2014; 2:5. [PMID: 24790974 PMCID: PMC3982512 DOI: 10.3389/fchem.2014.00005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 02/05/2014] [Indexed: 01/25/2023] Open
Abstract
Owing to the potential use for real personalized genome sequencing, DNA sequencing with solid-state nanopores has been investigated intensively in recent time. However, the area still confronts problems and challenges. In this work, we present a brief overview of computational studies of key issues in DNA sequencing with solid-state nanopores by addressing the progress made in the last few years. We also highlight future challenges and prospects for DNA sequencing using this technology.
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Affiliation(s)
- Lijun Liang
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology Stockholm, Sweden ; Department of Chemistry and Soft Matter Research Center, Zhejiang University Hangzhou, China
| | - Qi Wang
- Department of Chemistry and Soft Matter Research Center, Zhejiang University Hangzhou, China
| | - Hans Agren
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology Stockholm, Sweden
| | - Yaoquan Tu
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology Stockholm, Sweden
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164
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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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165
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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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166
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Shan YP, Tiwari PB, Krishnakumar P, Vlassiouk I, Li W, Wang X, Darici Y, Lindsay S, Wang HD, Smirnov S, He J. Surface modification of graphene nanopores for protein translocation. NANOTECHNOLOGY 2013; 24:495102. [PMID: 24231385 PMCID: PMC3925770 DOI: 10.1088/0957-4484/24/49/495102] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Studies of DNA translocation through graphene nanopores have revealed their potential for DNA sequencing. Here we report a study of protein translocation through chemically modified graphene nanopores. A transmission electron microscope (TEM) was used to cut nanopores with diameters between 5 and 20 nm in multilayer graphene prepared by chemical vapor deposition (CVD). After oxygen plasma treatment, the dependence of the measured ionic current on salt concentration and pH was consistent with a small surface charge induced by the formation of carboxyl groups. While translocation of gold nanoparticles (10 nm) was readily detected through such treated pores of a larger diameter, translocation of the protein ferritin was not observed either for oxygen plasma treated pores, or for pores modified with mercaptohexadecanoic acid. Ferritin translocation events were reliably observed after the pores were modified with the phospholipid-PEG (DPPE-PEG750) amphiphile. The ion current signature of translocation events was complex, suggesting that a series of interactions between the protein and pores occurs during the process.
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Affiliation(s)
- Y. P. Shan
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - P. B. Tiwari
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - P. Krishnakumar
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - I. Vlassiouk
- Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - W.Z. Li
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - X.W. Wang
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - Y. Darici
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - S.M. Lindsay
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - H. D. Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China
| | - S. Smirnov
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM 88003, USA
- Corresponding Author: Sergei, Smirnov, ; He, Jin,
| | - J. He
- Department of Physics, Florida International University, Miami, FL 33199, USA
- Corresponding Author: Sergei, Smirnov, ; He, Jin,
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167
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He Z, Zhou J, Lu X, Corry B. Bioinspired graphene nanopores with voltage-tunable ion selectivity for Na(+) and K(+). ACS NANO 2013; 7:10148-10157. [PMID: 24151957 DOI: 10.1021/nn4043628] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Biological protein channels have many remarkable properties such as gating, high permeability, and selectivity, which have motivated researchers to mimic their functions for practical applications. Herein, using molecular dynamics simulations, we design bioinspired nanopores in graphene sheets that can discriminate between Na(+) and K(+), two ions with very similar properties. The simulation results show that, under transmembrane voltage bias, a nanopore containing four carbonyl groups to mimic the selectivity filter of the KcsA K(+) channel preferentially conducts K(+) over Na(+). A nanopore functionalized by four negatively charged carboxylate groups to mimic the selectivity filter of the NavAb Na(+) channel selectively binds Na(+) but transports K(+) over Na(+). Surprisingly, the ion selectivity of the smaller diameter pore containing three carboxylate groups can be tuned by changing the magnitude of the applied voltage bias. Under lower voltage bias, it transports ions in a single-file manner and exhibits Na(+) selectivity, dictated by the knock-on ion conduction and selective blockage by Na(+). Under higher voltage bias, the nanopore is K(+)-selective, as the blockage by Na(+) is destabilized and the stronger affinity for carboxylate groups slows the passage of Na(+) compared with K(+). The computational design of biomimetic ion-selective nanopores helps to understand the mechanisms of selectivity in biological ion channels and may also lead to a wide range of potential applications such as sensitive ion sensors, nanofiltration membranes for Na(+)/K(+) separation, and voltage-tunable nanofluidic devices.
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Affiliation(s)
- Zhongjin He
- School of Chemistry and Chemical Engineering, South China University of Technology , Guangzhou, Guangdong 510640, China
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168
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Abstract
By using the nonequilibrium Green's function technique, we show that the shape of the edge, the carrier concentration, and the position and size of a nanopore in graphene nanoribbons can strongly affect its electronic conductance as well as its sensitivity to external charges. This technique, combined with a self-consistent Poisson-Boltzmann formalism to account for ion charge screening in solution, is able to detect the rotational and positional conformation of a DNA strand inside the nanopore. In particular, we show that a graphene membrane with quantum point contact geometry exhibits greater electrical sensitivity than a uniform armchair geometry provided that the carrier concentration is tuned to enhance charge detection. We propose a membrane design that contains an electrical gate in a configuration similar to a field-effect transistor for a graphene-based DNA sensing device.
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169
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Zhao S, Xue J, Kang W. Ion selection of charge-modified large nanopores in a graphene sheet. J Chem Phys 2013; 139:114702. [DOI: 10.1063/1.4821161] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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170
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Wang M, Tian Y, Cui S, Qian L. Effect of salt concentration on the conformation and friction behaviour of DNA. Colloids Surf A Physicochem Eng Asp 2013. [DOI: 10.1016/j.colsurfa.2013.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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171
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Freedman KJ, Ahn CW, Kim MJ. Detection of long and short DNA using nanopores with graphitic polyhedral edges. ACS NANO 2013; 7:5008-16. [PMID: 23713602 DOI: 10.1021/nn4003665] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Graphene is a unique material with a thickness as low as a single atom, high in-plane conductivity and a robust lattice that is self-supporting over large length scales. Schematically, graphene is an ideal solid-state material for tuning the properties of a nanopore because self-supported sheets, ranging from single to multiple atomic layers, can create pores with near-arbitrary dimensions which can provide exquisite control of the electric field drop within the pore. In this study, we characterize the drilling kinetics of nanopores using a thermionic electron source and various electron beam fluxes to minimize secondary hole formation. Once established, we investigated the use of multilayer graphene to create highly tailored nanostructures including nanopores with graphite polyhedral crystals formed around the nanopore edge. Finally, we report on the translocation of double stranded and single stranded DNA through such graphene pores and show that the single stranded DNA translocates much slower allowing detection of extremely short fragments (25 nucleotides in length). Our findings suggest that the kinetic and controllable properties of graphene nanopores under sculpting conditions can be used to further enhance the detection of DNA analytes.
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Affiliation(s)
- Kevin J Freedman
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, USA
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172
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Luan B, Stolovitzky G. An electro-hydrodynamics-based model for the ionic conductivity of solid-state nanopores during DNA translocation. NANOTECHNOLOGY 2013; 24:195702. [PMID: 23579206 PMCID: PMC3681960 DOI: 10.1088/0957-4484/24/19/195702] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A solid-state nanopore can be used to sense DNA (or other macromolecules) by monitoring ion-current changes that result from translocation of the molecule through the pore. When transiting a nanopore, the highly negatively charged DNA interacts with a nanopore both electrically and hydrodynamically, causing a current blockage or a current enhancement at different ion concentrations. This effect was previously characterized using a phenomenological model that can be considered as the limit of the electro-hydrodynamics model presented here. We show theoretically that the effect of surface charge of a nanopore (or electro-osmotic effect) can be equivalently treated as modifications of electrophoretic mobilities of ions in the pore, providing an improved physical understanding of the current blockage (or enhancement).
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173
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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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174
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Novak BR, Moldovan D, Nikitopoulos DE, Soper SA. Distinguishing single DNA nucleotides based on their times of flight through nanoslits: a molecular dynamics simulation study. J Phys Chem B 2013; 117:3271-9. [PMID: 23461845 DOI: 10.1021/jp309486c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Transport of single molecules in nanochannels or nanoslits might be used to identify them via their transit (flight) times. In this paper, we present molecular dynamics simulations of transport of single deoxynucleotide 5'-monophoshates (dNMP) in aqueous solution under pressure-driven flow, to average velocities between 0.4 and 1.0 m/s, in 3 nm wide slits with hydrophobic walls. The simulation results show that, while moving along the slit, the mononucleotides are adsorbed and desorbed from the walls multiple times. For the simulations, the estimated minimum slit length required for separation of the dNMP flight time distributions is about 5.9 μm, and the minimum analysis time per dNMP is about 10 μs. These are determined by the nature of the nucleotide-wall interactions, channel width, and by the flow characteristics. A simple analysis using realistic dNMP velocities shows that, in order to reduce the effects of diffusional broadening and keep the analysis time per dNMP reasonably small, the nucleotide velocity should be relatively high. Tailored surface chemistry could lead to further reduction of the analysis time toward its minimum value for a given driving force.
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Affiliation(s)
- Brian R Novak
- Department of Mechanical and Industrial Engineering, and Center for Computation and Technology, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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175
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Haque F, Li J, Wu HC, Liang XJ, Guo P. Solid-State and Biological Nanopore for Real-Time Sensing of Single Chemical and Sequencing of DNA. NANO TODAY 2013; 8:56-74. [PMID: 23504223 PMCID: PMC3596169 DOI: 10.1016/j.nantod.2012.12.008] [Citation(s) in RCA: 227] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Sensitivity and specificity are two most important factors to take into account for molecule sensing, chemical detection and disease diagnosis. A perfect sensitivity is to reach the level where a single molecule can be detected. An ideal specificity is to reach the level where the substance can be detected in the presence of many contaminants. The rapidly progressing nanopore technology is approaching this threshold. A wide assortment of biomotors and cellular pores in living organisms perform diverse biological functions. The elegant design of these transportation machineries has inspired the development of single molecule detection based on modulations of the individual current blockage events. The dynamic growth of nanotechnology and nanobiotechnology has stimulated rapid advances in the study of nanopore based instrumentation over the last decade, and inspired great interest in sensing of single molecules including ions, nucleotides, enantiomers, drugs, and polymers such as PEG, RNA, DNA, and polypeptides. This sensing technology has been extended to medical diagnostics and third generation high throughput DNA sequencing. This review covers current nanopore detection platforms including both biological pores and solid state counterparts. Several biological nanopores have been studied over the years, but this review will focus on the three best characterized systems including α-hemolysin and MspA, both containing a smaller channel for the detection of single-strand DNA, as well as bacteriophage phi29 DNA packaging motor connector that contains a larger channel for the passing of double stranded DNA. The advantage and disadvantage of each system are compared; their current and potential applications in nanomedicine, biotechnology, and nanotechnology are discussed.
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Affiliation(s)
- Farzin Haque
- Nanobiotechnology Center, Markey Cancer Center and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Jinghong Li
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Beijing 100084, China
| | - Hai-Chen Wu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Xing-Jie Liang
- Laboratory of Nanomedicine and Nanosafety, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Peixuan Guo
- Nanobiotechnology Center, Markey Cancer Center and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
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176
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Stoloff DH, Wanunu M. Recent trends in nanopores for biotechnology. Curr Opin Biotechnol 2012; 24:699-704. [PMID: 23266100 DOI: 10.1016/j.copbio.2012.11.008] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 11/20/2012] [Indexed: 10/27/2022]
Abstract
Nanopore technology employs a nanoscale hole in an insulating membrane to stochastically sense with high throughput individual biomolecules in solution. The generality of the nanopore detection principle and the ease of single-molecule detection suggest many potential applications of nanopores in biotechnology. Recent progress has been made with nanopore fabrication and sophistication, as well as with applications in DNA/protein mapping, biomolecular structure analysis, protein detection, and DNA sequencing. In addition, concepts for DNA sequencing devices have been suggested, and computational efforts have been made. The state of the nanopore field is maturing and given the right type of nanopore and operating conditions, nearly every application could revolutionize medicine in terms of speed, cost, and quality. In this review, we summarize progress in nanopores for biotechnological applications over the past 2-3 years.
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Affiliation(s)
- Daniel H Stoloff
- Department of Physics, Northeastern University, Boston, MA, United States
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177
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Maffeo C, Bhattacharya S, Yoo J, Wells D, Aksimentiev A. Modeling and simulation of ion channels. Chem Rev 2012; 112:6250-84. [PMID: 23035940 PMCID: PMC3633640 DOI: 10.1021/cr3002609] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Christopher Maffeo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Swati Bhattacharya
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Jejoong Yoo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - David Wells
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
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178
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Affiliation(s)
- Stephen M. Oja
- Department of Chemistry, University of Washington, Seattle, Washington 98195,
United States
| | - Marissa Wood
- Department of Chemistry, University of Washington, Seattle, Washington 98195,
United States
| | - Bo Zhang
- Department of Chemistry, University of Washington, Seattle, Washington 98195,
United States
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