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Fotouhi B, Faramarzi V, Ahmadi V. DNA sequencing by Förster resonant energy transfer. OPTICS EXPRESS 2022; 30:21854-21865. [PMID: 36224897 DOI: 10.1364/oe.454459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/19/2022] [Indexed: 06/16/2023]
Abstract
We propose a new DNA sequencing concept based on nonradiative Förster resonant energy transfer (FRET) from a donor quantum dot (QD) to an acceptor molecule. The FRET mechanism combined with the nanopore-based DNA translocation is suggested as a novel concept for sequencing DNA molecules. A recently-developed hybrid quantum/classical method is employed, which uses time-dependent density functional theory and quasistatic finite difference time domain calculations. Due to the significant absorbance of DNA bases for photon energies higher than 4 eV, biocompatibility, and stability, we use Zinc-Oxide (ZnO) QD as a donor in the FRET mechanism. The most sensitivity for the proposed method to DNA is achieved for the Hoechst fluorescent-dye acceptor and 1 nm ZnO-QD. Results show that the insertion of each type of DNA nucleobases between the donor and acceptor changes the frequency of the emitted light from the acceptor molecule between 0.25 to 1.6 eV. The noise analysis shows that the method can determine any unknown DNA nucleobases if the signal-to-noise ratio is larger than 5 dB. The proposed concept and excellent results shed light on a new promising class of DNA sequencers.
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2
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Zhou Y, Ren M, Zhang P, Jiang D, Yao X, Luo Y, Yang Z, Wang Y. Application of Nanopore Sequencing in the Detection of Foodborne Microorganisms. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:1534. [PMID: 35564242 PMCID: PMC9100974 DOI: 10.3390/nano12091534] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 12/21/2022]
Abstract
Foodborne pathogens have become the subject of intense interest because of their high incidence and mortality worldwide. In the past few decades, people have developed many methods to solve this challenge. At present, methods such as traditional microbial culture methods, nucleic acid or protein-based pathogen detection methods, and whole-genome analysis are widely used in the detection of pathogenic microorganisms in food. However, these methods are limited by time-consuming, cumbersome operations or high costs. The development of nanopore sequencing technology offers the possibility to address these shortcomings. Nanopore sequencing, a third-generation technology, has the advantages of simple operation, high sensitivity, real-time sequencing, and low turnaround time. It can be widely used in the rapid detection and serotyping of foodborne pathogens. This review article discusses foodborne diseases, the principle of nanopore sequencing technology, the application of nanopore sequencing technology in foodborne pathogens detection, as well as its development prospects.
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Affiliation(s)
| | | | | | | | | | | | | | - Yin Wang
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; (Y.Z.); (M.R.); (P.Z.); (D.J.); (X.Y.); (Y.L.); (Z.Y.)
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3
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Dematties D, Wen C, Pérez MD, Zhou D, Zhang SL. Deep Learning of Nanopore Sensing Signals Using a Bi-Path Network. ACS NANO 2021; 15:14419-14429. [PMID: 34583465 PMCID: PMC8482760 DOI: 10.1021/acsnano.1c03842] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Temporal changes in electrical resistance of a nanopore sensor caused by translocating target analytes are recorded as a sequence of pulses on current traces. Prevalent algorithms for feature extraction in pulse-like signals lack objectivity because empirical amplitude thresholds are user-defined to single out the pulses from the noisy background. Here, we use deep learning for feature extraction based on a bi-path network (B-Net). After training, the B-Net acquires the prototypical pulses and the ability of both pulse recognition and feature extraction without a priori assigned parameters. The B-Net is evaluated on simulated data sets and further applied to experimental data of DNA and protein translocation. The B-Net results are characterized by small relative errors and stable trends. The B-Net is further shown capable of processing data with a signal-to-noise ratio equal to 1, an impossibility for threshold-based algorithms. The B-Net presents a generic architecture applicable to pulse-like signals beyond nanopore currents.
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Affiliation(s)
- Dario Dematties
- Instituto
de Ciencias Humanas, Sociales y Ambientales CONICET Mendoza Technological
Scientific Center, Mendoza M5500, Argentina
| | - Chenyu Wen
- Division
of Solid-State Electronics, Department of Electrical Engineering, Uppsala University, SE-751 03 Uppsala, Sweden
| | - Mauricio David Pérez
- Division
of Solid-State Electronics, Department of Electrical Engineering, Uppsala University, SE-751 03 Uppsala, Sweden
| | - Dian Zhou
- Department
of Electrical and Computer Engineering, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Shi-Li Zhang
- Division
of Solid-State Electronics, Department of Electrical Engineering, Uppsala University, SE-751 03 Uppsala, Sweden
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4
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Saharia J, Bandara YMNDY, Karawdeniya BI, Alexandrakis G, Kim MJ. Assessment of 1/f noise associated with nanopores fabricated through chemically tuned controlled dielectric breakdown. Electrophoresis 2021; 42:899-909. [PMID: 33340118 DOI: 10.1002/elps.202000285] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/21/2020] [Accepted: 12/14/2020] [Indexed: 02/01/2023]
Abstract
Recently, we developed a fabrication method-chemically-tuned controlled dielectric breakdown (CT-CDB)-that produces nanopores (through thin silicon nitride membranes) surpassing legacy drawbacks associated with solid-state nanopores (SSNs). However, the noise characteristics of CT-CDB nanopores are largely unexplored. In this work, we investigated the 1/f noise of CT-CDB nanopores of varying solution pH, electrolyte type, electrolyte concentration, applied voltage, and pore diameter. Our findings indicate that the bulk Hooge parameter (αb ) is about an order of magnitude greater than SSNs fabricated by transmission electron microscopy (TEM) while the surface Hooge parameter (αs ) is ∼3 order magnitude greater. Theαs of CT-CDB nanopores was ∼5 orders of magnitude greater than theirαb , which suggests that the surface contribution plays a dominant role in 1/f noise. Experiments with DNA exhibited increasing capture rates with pH up to pH ∼8 followed by a drop at pH ∼9 perhaps due to the onset of electroosmotic force acting against the electrophoretic force. The1/f noise was also measured for several electrolytes and LiCl was found to outperform NaCl, KCl, RbCl, and CsCl. The 1/f noise was found to increase with the increasing electrolyte concentration and pore diameter. Taken together, the findings of this work suggest the pH approximate 7-8 range to be optimal for DNA sensing with CT-CDB nanopores.
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Affiliation(s)
- Jugal Saharia
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX, USA
| | - Y M Nuwan D Y Bandara
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX, USA
| | - Buddini I Karawdeniya
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX, USA
| | | | - Min Jun Kim
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX, USA
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5
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Su S, Guo X, Fu Y, Xie Y, Wang X, Xue J. Origin of nonequilibrium 1/f noise in solid-state nanopores. NANOSCALE 2020; 12:8975-8981. [PMID: 32270161 DOI: 10.1039/c9nr09829a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Nanopore devices are applied in many fields such as molecular sensing and DNA sequencing, and the detection precision is primarily determined by 1/f noise. The mechanism of 1/f noise in nanopores is still not clearly understood, especially the nonequilibrium 1/f noise in rectifying nanopores. Hereby, we propose that 1/f noise in solid-state nanopores originates from the electrolyte ion trapping-detrapping process occurring on the inner surface of the nanopores, which can nonlinearly affect the ion number inside the rectifying nanopores due to the specific ion enrichment/depletion effect. Our model can not only quantitatively explain the nonlinear dependence of 1/f noise on the applied voltage, i.e., the nonequilibrium 1/f noise, for current rectifying nanopores, but also provide a unified explanation on the influence of the electrolyte concentration, pH value, and geometry of the nanopores. From our model, we observe a new flattening phenomenon of 1/f noise in conical nanopores, and this is further confirmed by our experimental results. Our research can be helpful in understanding and reducing 1/f noise in other nanopore devices, especially where the enrichment or depletion of ions exists.
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Affiliation(s)
- Shihao Su
- State Key Laboratory of Nuclear Physics and Technology, School of Physics, Peking University, Beijing 100871, P. R. China.
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Chandiramouli R, Nagarajan V. Silicene nanosheet device with nanopore to identify the nucleobases – A first-principles perspective. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.05.038] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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7
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Nie XL, Liu HL, Pan ZQ, Ahmed SA, Shen Q, Yang JM, Pan JB, Pang J, Li CY, Xia XH, Wang K. Recognition of plastic nanoparticles using a single gold nanopore fabricated at the tip of a glass nanopipette. Chem Commun (Camb) 2019; 55:6397-6400. [DOI: 10.1039/c9cc01358j] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A single gold nanopore with high surface enhanced Raman spectroscopy (SERS) activity is fabricated on the tip of a glass nanopipette.
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8
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Wen C, Zeng S, Zhang Z, Zhang SL. Group Behavior of Nanoparticles Translocating Multiple Nanopores. Anal Chem 2018; 90:13483-13490. [PMID: 30372031 DOI: 10.1021/acs.analchem.8b03408] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nanopores have been implemented as nanosensors for DNA sequencing, biomolecule inspection, chemical analysis, nanoparticle detection, etc. For high-throughput and parallelized measurement using nanopore arrays, individual addressability has been a crucial technological solution in order to enable scrutiny of signals generated at each and every nanopore. Here, an alternative pathway of employing arrayed nanopores to perform sensor functions is investigated by examining the group behavior of nanoparticles translocating multiple nanopores. As no individual addressability is required, fabrication of nanopore devices along with microfluidic cells and readout circuits can be greatly simplified. Experimentally, arrays of less than 10 pores are shown to be capable of analyzing translocating nanoparticles with a good signal-to-noise margin. According to theoretical predictions, more pores (than 10) per array can perform high-fidelity analysis if the noise level of the measurement system can be better controlled. More pores per array would also allow for faster measurement at lower concentration because of larger capture cross sections for target nanoparticles. By experimentally varying the number of pores, the concentration of nanoparticles, or the applied bias voltage across the nanopores, we have identified the basic characteristics of this multievent process. By characterizing average pore current and associated standard deviation during translocation and by performing physical modeling and extensive numerical simulations, we have shown the possibility of determining the size and concentration of two kinds of translocating nanoparticles over 4 orders of magnitude in concentration. Hence, we have demonstrated the potential and versatility of the multiple-nanopore approach for high-throughput nanoparticle detection.
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Affiliation(s)
- Chenyu Wen
- Division of Solid-State Electronics, The Ångström Laboratory , Uppsala University , SE-751 21 Uppsala , Sweden
| | - Shuangshuang Zeng
- Division of Solid-State Electronics, The Ångström Laboratory , Uppsala University , SE-751 21 Uppsala , Sweden
| | - Zhen Zhang
- Division of Solid-State Electronics, The Ångström Laboratory , Uppsala University , SE-751 21 Uppsala , Sweden
| | - Shi-Li Zhang
- Division of Solid-State Electronics, The Ångström Laboratory , Uppsala University , SE-751 21 Uppsala , Sweden
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Gilpin C, Darmon D, Siwy Z, Martens C. Information Dynamics of a Nonlinear Stochastic Nanopore System. ENTROPY 2018; 20:e20040221. [PMID: 33265312 PMCID: PMC7512734 DOI: 10.3390/e20040221] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 03/19/2018] [Accepted: 03/21/2018] [Indexed: 12/22/2022]
Abstract
Nanopores have become a subject of interest in the scientific community due to their potential uses in nanometer-scale laboratory and research applications, including infectious disease diagnostics and DNA sequencing. Additionally, they display behavioral similarity to molecular and cellular scale physiological processes. Recent advances in information theory have made it possible to probe the information dynamics of nonlinear stochastic dynamical systems, such as autonomously fluctuating nanopore systems, which has enhanced our understanding of the physical systems they model. We present the results of local (LER) and specific entropy rate (SER) computations from a simulation study of an autonomously fluctuating nanopore system. We learn that both metrics show increases that correspond to fluctuations in the nanopore current, indicating fundamental changes in information generation surrounding these fluctuations.
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Affiliation(s)
- Claire Gilpin
- Department of Physics and Astronomy, University of California-Irvine, Irvine, CA 92697-4575, USA
- Correspondence:
| | - David Darmon
- Department of Military and Emergency Medicine, Uniformed Services University, Bethesda, MD 20814, USA
| | - Zuzanna Siwy
- Department of Physics and Astronomy, University of California-Irvine, Irvine, CA 92697-4575, USA
| | - Craig Martens
- Department of Chemistry, University of California-Irvine, Irvine, CA 92697-2025, USA
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Wen C, Zhang Z, Zhang SL. Physical Model for Rapid and Accurate Determination of Nanopore Size via Conductance Measurement. ACS Sens 2017; 2:1523-1530. [PMID: 28974095 DOI: 10.1021/acssensors.7b00576] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nanopores have been explored for various biochemical and nanoparticle analyses, primarily via characterizing the ionic current through the pores. At present, however, size determination for solid-state nanopores is experimentally tedious and theoretically unaccountable. Here, we establish a physical model by introducing an effective transport length, Leff, that measures, for a symmetric nanopore, twice the distance from the center of the nanopore where the electric field is the highest to the point along the nanopore axis where the electric field falls to e-1 of this maximum. By [Formula: see text], a simple expression S0 = f (G, σ, h, β) is derived to algebraically correlate minimum nanopore cross-section area S0 to nanopore conductance G, electrolyte conductivity σ, and membrane thickness h with β to denote pore shape that is determined by the pore fabrication technique. The model agrees excellently with experimental results for nanopores in graphene, single-layer MoS2, and ultrathin SiNx films. The generality of the model is verified by applying it to micrometer-size pores.
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Affiliation(s)
- Chenyu Wen
- Solid-State
Electronics, The Ångström Laboratory, Uppsala University, SE-751 21 Uppsala, Sweden
| | - Zhen Zhang
- Solid-State
Electronics, The Ångström Laboratory, Uppsala University, SE-751 21 Uppsala, Sweden
| | - Shi-Li Zhang
- Solid-State
Electronics, The Ångström Laboratory, Uppsala University, SE-751 21 Uppsala, Sweden
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11
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12
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Wen C, Zeng S, Arstila K, Sajavaara T, Zhu Y, Zhang Z, Zhang SL. Generalized Noise Study of Solid-State Nanopores at Low Frequencies. ACS Sens 2017; 2:300-307. [PMID: 28723146 DOI: 10.1021/acssensors.6b00826] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nanopore technology has been extensively investigated for analysis of biomolecules, and a success story in this field concerns DNA sequencing using a nanopore chip featuring an array of hundreds of biological nanopores (BioNs). Solid-state nanopores (SSNs) have been explored to attain longer lifetime and higher integration density than what BioNs can offer, but SSNs are generally considered to generate higher noise whose origin remains to be confirmed. Here, we systematically study low-frequency (including thermal and flicker) noise characteristics of SSNs measuring 7 to 200 nm in diameter drilled through a 20-nm-thick SiNx membrane by focused ion milling. Both bulk and surface ionic currents in the nanopore are found to contribute to the flicker noise, with their respective contributions determined by salt concentration and pH in electrolytes as well as bias conditions. Increasing salt concentration at constant pH and voltage bias leads to increase in the bulk ionic current and noise therefrom. Changing pH at constant salt concentration and current bias results in variation of surface charge density, and hence alteration of surface ionic current and noise. In addition, the noise from Ag/AgCl electrodes can become predominant when the pore size is large and/or the salt concentration is high. Analysis of our comprehensive experimental results leads to the establishment of a generalized nanopore noise model. The model not only gives an excellent account of the experimental observations, but can also be used for evaluation of various noise components in much smaller nanopores currently not experimentally available.
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Affiliation(s)
- Chenyu Wen
- Division
of Solid-State Electronics, Department of Engineering Sciences, Uppsala University, SE-751 21 Uppsala, Sweden
| | - Shuangshuang Zeng
- Division
of Solid-State Electronics, Department of Engineering Sciences, Uppsala University, SE-751 21 Uppsala, Sweden
| | - Kai Arstila
- Department
of Physics, University of Jyväskylä, P.O. Box 35, FI-40014, Jyvaskylä, Finland
| | - Timo Sajavaara
- Department
of Physics, University of Jyväskylä, P.O. Box 35, FI-40014, Jyvaskylä, Finland
| | - Yu Zhu
- IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10598, United States
| | - Zhen Zhang
- Division
of Solid-State Electronics, Department of Engineering Sciences, Uppsala University, SE-751 21 Uppsala, Sweden
| | - Shi-Li Zhang
- Division
of Solid-State Electronics, Department of Engineering Sciences, Uppsala University, SE-751 21 Uppsala, Sweden
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13
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Qiu H, Sarathy A, Schulten K, Leburton JP. Detection and Mapping of DNA Methylation with 2D Material Nanopores. NPJ 2D MATERIALS AND APPLICATIONS 2017; 1:3. [PMID: 29399640 PMCID: PMC5794036 DOI: 10.1038/s41699-017-0005-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/24/2016] [Accepted: 01/10/2017] [Indexed: 05/21/2023]
Abstract
DNA methylation is an epigenetic modification involving the addition of a methyl group to DNA, which is heavily involved in gene expression and regulation, thereby critical to the progression of diseases such as cancer. In this work we show that detection and localization of DNA methylation can be achieved with nanopore sensors made of two-dimensional (2D) materials such as graphene and molybdenum di-sulphide (MoS2). We label each DNA methylation site with a methyl-CpG binding domain protein (MBD1), and combine molecular dynamics simulations with electronic transport calculations to investigate the translocation of the methylated DNA-MBD1 complex through 2D material nanopores under external voltage biases. The passage of the MBD1-labeled methylation site through the pore is identified by dips in the current blockade induced by the DNA strand, as well as by peaks in the transverse electronic sheet current across the 2D layer. The position of the methylation sites can be clearly recognized by the relative positions of the dips in the recorded ionic current blockade with an estimated error ranging from 0% to 16%. Finally, we define the spatial resolution of the 2D material nanopore device as the minimal distance between two methylation sites identified within a single measurement, which is 15 base pairs by ionic current recognition, but as low as 10 base pairs by transverse electronic conductance detection, indicating better resolution with this latter technique. The present approach opens a new route for precise and efficient profiling of DNA methylation.
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Affiliation(s)
- Hu Qiu
- Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, Illinois 61801, United States
| | - Aditya Sarathy
- Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, Illinois 61801, United States
- Department of Electrical and Computer Engineering, University of Illinois, Urbana, Illinois 61801, United States
| | - Klaus Schulten
- Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, Illinois 61801, United States
- Department of Physics, University of Illinois, Urbana, Illinois 61801, United States
| | - Jean-Pierre Leburton
- Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, Illinois 61801, United States
- Department of Electrical and Computer Engineering, University of Illinois, Urbana, Illinois 61801, United States
- Department of Physics, University of Illinois, Urbana, Illinois 61801, United States
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