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Fang S, Zeng D, He S, Li Y, Pang Z, Wang Y, Liang L, Weng T, Xie W, Wang D. Fast Fabrication Nanopores on a PMMA Membrane by a Local High Electric Field Controlled Breakdown. SENSORS (BASEL, SWITZERLAND) 2024; 24:2109. [PMID: 38610321 PMCID: PMC11013984 DOI: 10.3390/s24072109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/18/2024] [Accepted: 03/24/2024] [Indexed: 04/14/2024]
Abstract
The sensitivity and accuracy of nanopore sensors are severely hindered by the high noise associated with solid-state nanopores. To mitigate this issue, the deposition of organic polymer materials onto silicon nitride (SiNx) membranes has been effective in obtaining low-noise measurements. Nonetheless, the fabrication of nanopores sub-10 nm on thin polymer membranes remains a significant challenge. This work proposes a method for fabricating nanopores on polymethyl methacrylate (PMMA) membrane by the local high electrical field controlled breakdown, exploring the impact of voltage and current on the breakdown of PMMA membranes and discussing the mechanism underlying the breakdown voltage and current during the formation of nanopores. By improving the electric field application method, transient high electric fields that are one-seven times higher than the breakdown electric field can be utilized to fabricate nanopores. A comparative analysis was performed on the current noise levels of nanopores in PMMA-SiNx composite membranes and SiNx nanopores with a 5 nm diameter. The results demonstrated that the fast fabrication of nanopores on PMMA-SiNx membranes exhibited reduced current noise compared to SiNx nanopores. This finding provides evidence supporting the feasibility of utilizing this technology for efficiently fabricating low-noise nanopores on polymer composite membranes.
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Affiliation(s)
- Shaoxi Fang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (S.F.); (S.H.); (Y.W.); (L.L.); (T.W.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Delin Zeng
- School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing 400065, China; (D.Z.); (Y.L.); (Z.P.)
| | - Shixuan He
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (S.F.); (S.H.); (Y.W.); (L.L.); (T.W.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Yadong Li
- School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing 400065, China; (D.Z.); (Y.L.); (Z.P.)
| | - Zichen Pang
- School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing 400065, China; (D.Z.); (Y.L.); (Z.P.)
| | - Yunjiao Wang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (S.F.); (S.H.); (Y.W.); (L.L.); (T.W.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Liyuan Liang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (S.F.); (S.H.); (Y.W.); (L.L.); (T.W.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Ting Weng
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (S.F.); (S.H.); (Y.W.); (L.L.); (T.W.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Wanyi Xie
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (S.F.); (S.H.); (Y.W.); (L.L.); (T.W.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Deqiang Wang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (S.F.); (S.H.); (Y.W.); (L.L.); (T.W.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing 400065, China; (D.Z.); (Y.L.); (Z.P.)
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Nguyen SH, Vu PKT, Tran MT. Absorbance biosensors-based hybrid [Formula: see text] nanosheets for Escherichia coli detection. Sci Rep 2023; 13:10235. [PMID: 37353545 PMCID: PMC10290106 DOI: 10.1038/s41598-023-37395-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/21/2023] [Indexed: 06/25/2023] Open
Abstract
Detecting Escherichia coli is essential in biomedical, environmental, and food safety applications. In this paper, we have developed a simple, rapid, sensitive, and selective E. coli DNA sensor based on the novel hybrid-type [Formula: see text] and [Formula: see text] nanosheets. The sensor uses the absorbance measurement to distinguish among the DNA of E. coli, Vibrio proteolyticus, and Bacillus subtilis when implemented in conjunction with [Formula: see text]-probes. Our experiments showed that the absorbance increased when sensors detected E. coli DNA, whereas it decreased when sensors detected V. proteolyticus and B. subtilis DNA. To the best of authors' knowledge, there are no reports using the novel hybrid-[Formula: see text] and [Formula: see text] materials for differentiating three types of DNA using cost-effective and rapid absorbance measurements. In addition, the label-free E. coli DNA biosensor exhibited a linear response in the range of 0 fM to 11.65 fM with a limit of detection of 2 fM. The effect of [Formula: see text]-probes on our sensors' working performance is also investigated. Our results will facilitate further research in pathogen detection applications, which have not been fully developed yet.
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Affiliation(s)
- Son Hai Nguyen
- School of Mechanical Engineering, Hanoi University of Science and Technology, Hanoi, 100000 Vietnam
| | - Phan Kim Thi Vu
- College of Engineering and Computer Science, VinUniversity, Hanoi, 100000 Vietnam
| | - Mai Thi Tran
- College of Engineering and Computer Science, VinUniversity, Hanoi, 100000 Vietnam
- VinUni-Illinois Smart Health Center, VinUniversity, Hanoi, 100000 Vietnam
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Huang C, Li Z, Zhu X, Ma X, Li N, Fan J. Two Detection Modes of Nanoslit Sensing Based on Planar Heterostructure of Graphene/Hexagonal Boron Nitride. ACS NANO 2023; 17:3301-3312. [PMID: 36638059 DOI: 10.1021/acsnano.2c05002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Solid-state nanopore sequencing is now confronted with problems of stochastic pore clogging and too fast speed during the DNA permeation through a nanopore, although this technique is revolutionary with long readability and high efficiency. These two problems are related to controlling molecular transportation during sequencing. To control the DNA motion and identify the four bases, we propose nanoslit sensing based on the planar heterostructure of two-dimensional graphene and hexagonal boron nitride. Molecular dynamics simulations are performed on investigating the motion of DNA molecules on the heterostructure with a nanoslit sensor. Results show that the DNA molecules are confined within the hexagonal boron nitride (HBN) domain of the heterostructure. And the confinement effects of the heterostructure can be optimized by tailoring the stripe length. Besides, there are two ways of DNA permeation through nanoslits: the DNA can cross or translocate the nanoslit under applied voltages along the y and z directions. The two detection modes are named cross-slit and trans-slit, respectively. In both modes, the ionic current drops can be observed when the nanoslit is occupied by the DNA. And the ionic currents and dwell times can be simultaneously detected to identify the four different DNA bases. This study can shed light on the sensing mechanism based on the nanoslit sensor of a planar heterostructure and provide theoretical guidance on designing devices controlling molecular transportation during nanopore sequencing.
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Affiliation(s)
- Changxiong Huang
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong, 999077, China
| | - Zhen Li
- School of Materials Science and Engineering, China University of Petroleum (East China), Qingdao266580, China
| | - Xiaohong Zhu
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong, 999077, China
| | - Xinyao Ma
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong, 999077, China
| | - Na Li
- School of Chemistry and Materials Science, Key Laboratory of Magnetic Molecules and Magnetic Information Materials of Ministry of Education, Shanxi Normal University, Taiyuan030000, China
| | - Jun Fan
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong, 999077, China
- Center for Advanced Nuclear Safety and Sustainable Development, City University of Hong Kong, Kowloon, Hong Kong, 999077, China
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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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Faramarzi V, Ahmadi V, Heidari M, Fotouhi B, Hwang MT. Interband plasmon-enhanced optical absorption of DNA nucleobases through the graphene nanopore. OPTICS LETTERS 2022; 47:194-197. [PMID: 34951915 DOI: 10.1364/ol.443993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/29/2021] [Indexed: 06/14/2023]
Abstract
We propose a novel, to the best of our knowledge, plasmonic-based methodology for the purpose of fast DNA sequencing. The interband surface plasmon resonance and field-enhancement properties of graphene nanopore in the presence of the DNA nucleobases are investigated using a hybrid quantum/classical method (HQCM), which employs time-dependent density functional theory and a quasistatic finite difference time domain approach. In the strong plasmonic-molecular coupling regime where the plasmon and DNA absorption frequencies are degenerated, the optical response of DNA molecule in the vicinity of the nanopore is enhanced. In contrast, when the plasmon and nucleobases resonances are detuned the distinct peaks and broadening of the molecular resonances represent the inherent properties of the nucleobase. Due to the different optical properties of DNA nucleobases in the ultraviolet (UV) region of light, the signal corresponding to the replacement of nucleobases in a DNA block can be determined by considering the differential absorbance. Results show the promising capability of the present mechanism for practical DNA sequencing.
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Faramarzi V, Ahmadi V, Hwang MT, Snapp P. Highly sensitive crumpled 2D material-based plasmonic biosensors. BIOMEDICAL OPTICS EXPRESS 2021; 12:4544-4559. [PMID: 34457431 PMCID: PMC8367231 DOI: 10.1364/boe.428537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 05/04/2023]
Abstract
We propose surface plasmon resonance biosensors based on crumpled graphene and molybdenum disulphide (MoS2) flakes supported on stretchable polydimethylsiloxane (PDMS) or silicon substrates. Accumulation of specific biomarkers resulting in measurable shifts in the resonance wavelength of the plasmon modes of two-dimensional (2D) material structures, with crumpled structures demonstrating large refractive index shifts. Using theoretical calculations based on the semiclassical Drude model, combined with the finite element method, we demonstrate that the interaction between the surface plasmons of crumpled graphene/MoS2 layers and the surrounding analyte results in high sensitivity to biomarker driven refractive index shifts, up to 7499 nm/RIU for structures supported on silicon substrates. We can achieve a high figure of merit (FOM), defined as the ratio of the refractive index sensitivity to the full width at half maximum of the resonant peak, of approximately 62.5 RIU-1. Furthermore, the sensing properties of the device can be tuned by varying crumple period and aspect ratio through simple stretching and integrating material interlayers. By stacking multiple 2D materials in heterostructures supported on the PDMS layer, we produced hybrid plasmon resonances detuned from the PDMS absorbance region allowing higher sensitivity and FOM compared to pure crumpled graphene structures on the PDMS substrates. The high sensitivity and broad mechanical tunability of these crumpled 2D material biosensors considerable advantages over traditional refractive index sensors, providing a new platform for ultrasensitive biosensing.
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Affiliation(s)
- Vahid Faramarzi
- Department of Electrical and Computer Engineering, Tarbiat Modares University, 14115-194, Tehran, Iran
| | - Vahid Ahmadi
- Department of Electrical and Computer Engineering, Tarbiat Modares University, 14115-194, Tehran, Iran
| | - Michael T. Hwang
- Department of BioNano Technology, Gachon University, 1342 Seongnamdae-ro, Sujeong-gu, Seongnam, Gyeonggi, 13120, Republic of Korea
| | - Peter Snapp
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, IL 61801, USA
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Abstract
Molybdenum disulfide (MoS2) is one of the compounds discussed nowadays due to its outstanding properties that allowed its usage in different applications. Its band gap and its distinctive structure make it a promising material to substitute graphene and other semiconductor devices. It has different applications in electronics especially sensors like optical sensors, biosensors, electrochemical biosensors that play an important role in the detection of various diseases’ like cancer and Alzheimer. It has a wide range of energy applications in batteries, solar cells, microwave, and Terahertz applications. It is a promising material on a nanoscale level, with favorable characteristics in spintronics and magnetoresistance. In this review, we will discuss MoS2 properties, structure and synthesis techniques with a focus on its applications and future challenges.
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Yin B, Fang S, Zhou D, Liang L, Wang L, Wang Z, Wang D, Yuan J. Nanopore Fabrication via Transient High Electric Field Controlled Breakdown and Detection of Single RNA Molecules. ACS APPLIED BIO MATERIALS 2020; 3:6368-6375. [DOI: 10.1021/acsabm.0c00812] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Bohua Yin
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun, Jilin Province 130022, PR China
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Shaoxi Fang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Daming Zhou
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Liyuan Liang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Liang Wang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Zuobin Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun, Jilin Province 130022, PR China
| | - Deqiang Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun, Jilin Province 130022, PR China
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Jiahu Yuan
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, PR China
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A novel shaped-controlled fabrication of nanopore and its applications in quantum electronics. Sci Rep 2019; 9:18663. [PMID: 31819125 PMCID: PMC6901593 DOI: 10.1038/s41598-019-55190-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 11/25/2019] [Indexed: 02/05/2023] Open
Abstract
High-intensity (107–108 A m−2) electron beams can be used to fabricate nanoscale pores. This approach enables real-time observation of nanopore drilling and precise control of the diameter of the nanopore. Nevertheless, it is not suitable for tuning the nanopore’s sidewall shape. In this study, we demonstrate the use of low-intensity electron beams to fabricate nanopores on a silicon nitride (SiNx) membrane. This technique allows the precise adjustment of the nanopore dimension and the shaping of its three-dimensional (3D) nanostructure. The 3D structures of the nanopore were evaluated by electron tomography, and series of oblique images were used in reconstructing the 3D images of nanopores using a weighted back-projection method. The sidewall shape of the nanopore was observed at different electron-beam conditions, and the formation mechanism was elucidated based on these results. The nanopore fabricated with this technique can be used as a template to develop electronics at the nanoscale based on which a quantum-dot device can be prepared with a simple evaporation process. The measured results show that the device can resolve well-defined electronic states that are characteristic for the behaviors of the quantum-dot device.
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