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Rahman M, Sampad MJN, Hawkins A, Schmidt H. Recent advances in integrated solid-state nanopore sensors. LAB ON A CHIP 2021; 21:3030-3052. [PMID: 34137407 PMCID: PMC8372664 DOI: 10.1039/d1lc00294e] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The advent of single-molecule probing techniques has revolutionized the biomedical and life science fields and has spurred the development of a new class of labs-on-chip based on powerful biosensors. Nanopores represent one of the most recent and most promising single molecule sensing paradigms that is seeing increased chip-scale integration for improved convenience and performance. Due to their physical structure, nanopores are highly sensitive, require low sample volume, and offer label-free, amplification-free, high-throughput real-time detection and identification of biomolecules. Over the last 25 years, nanopores have been extensively employed to detect a variety of biomolecules with a growing range of applicatons ranging from nucleic acid sequencing to ultrasensitive diagnostics to single-molecule biophysics. Nanopores, in particular those in solid-state membranes, also have the potential for integration with other technologies such as optics, plasmonics, microfluidics, and optofluidics to perform more complex tasks for an ever-expanding demand. A number of breakthrough results using integrated nanopore platforms have already been reported, and more can be expected as nanopores remain the focus of innovative research and are finding their way into commercial instruments. This review provides an overview of different aspects and challenges of nanopore technology with a focus on chip-scale integration of solid-state nanopores for biosensing and bioanalytical applications.
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Affiliation(s)
- Mahmudur Rahman
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064 USA. and Dhaka University of Engineering & Technology, Gazipur, Bangladesh
| | | | - Aaron Hawkins
- ECEn Department, Brigham Young University, 459 Clyde Building, Provo, UT, 84602 USA
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064 USA.
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Perotto S, Biagini C, Hubarevich A, Tantussi F, De Angelis F. Toward all on chip optical detection in the few molecule regime. Biosens Bioelectron 2020; 169:112600. [PMID: 32971342 DOI: 10.1016/j.bios.2020.112600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/04/2020] [Accepted: 09/06/2020] [Indexed: 10/23/2022]
Abstract
Integrated optics devices are one of the most promising technologies in many fields such as biosensing, optical monitoring, and portable devices. They provide several advantages such as unique sensitivity and the possibility of the well-established and developed silicon photonics technology. However some challenges still remain open, as the implementation of multiplex assay able to reach the single particle sensitivity. In this context, we propose a new design for a Si-based photonic structure that enables the realization of on chip sub-wavelength optical sources. The idea is based on the insertion of opportunely designed nanometric holes in the photonic circuit, which are available for analyte detection with high efficiency. We propose three different configurations in which both excitation and detection are obtained through the same waveguide thus simplifying the detection scheme and potentially enabling multiplexed detection. We proved the high confinement of the electromagnetic field in the holes both by theoretical modelling and spectroscopic measurements. We investigate the possibility of inserting an arbitrary number of optical sources by using a resonator and evaluate advantages and drawbacks of resonating and non-resonating solutions. Finally, we report the proof-of-concept experiment, where detection sensitivity down to single Quantum Dots is obtained by combining the novel design with fluorescence-based techniques. Importantly, the presented results are achieved by a simple modification of photonic sensing chips which are already on the market thus having an excellent translational perspective.
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Affiliation(s)
- Sara Perotto
- Istituto Italiano di Tecnologia, via Morego 30, I-16159 Genova, Italy; Department of Physics, Politecnico di Milano, Milan, Italy
| | - Claudio Biagini
- Istituto Italiano di Tecnologia, via Morego 30, I-16159 Genova, Italy; Università degli Studi di Genova, via Balbi 5, I-16126 Genova, Italy
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Si W, Sha J, Sun Q, He Z, Wu L, Chen C, Yu S, Chen Y. Shape characterization and discrimination of single nanoparticles using solid-state nanopores. Analyst 2020; 145:1657-1666. [PMID: 31922169 DOI: 10.1039/c9an01889a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Resistive pulse sensing with nanopores is expected to enable identification and analysis of nanoscale objects in ionic solutions. However, there is currently no remarkable method to characterize the three-dimensional shape of charged biomolecules or nanoparticles with low-cost and high-throughput. Here we demonstrate the sensing capability of solid-state nanopores for shape characterization of single nanoparticles by monitoring the ionic current blockades during their electrophoretic translocation through nanopores. By using nanopores that are a bit larger than the particles, shape characterization of both spherical and cubic silver nanoparticles is successfully realized due to their rapid rotation with respect to the pore axis, which is further validated by our all-atom molecular dynamics simulations. The single-molecule approach based on nanopores will allow people to measure the dimension and to characterize the shape of single nanoparticles or proteins simultaneously in real time, which is significant for its potential application in investigation of structural biology and proteomics in the near future.
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Affiliation(s)
- Wei Si
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China.
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Li Q, Ying YL, Liu SC, Lin Y, Long YT. Detection of Single Proteins with a General Nanopore Sensor. ACS Sens 2019; 4:1185-1189. [PMID: 30860364 DOI: 10.1021/acssensors.9b00228] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Single protein sensing based on solid-state nanopores is promising but challenging, because the fast translocation velocity of a protein is beyond the bandwidth of nanopore instruments. To decelerate the translocation speed, here, we employed a common protein cross-link interaction to achieve a general and robust nanopore sensing platform for single-molecule detection of protein. Benefiting from the EDC/NHS coupling interaction between nanopore and proteins, a 10-fold decrease in speed has been achieved. The clearly distinguishable current signatures further reveal that the anisotropic translocation of a protein, which are horizontal, vertical, and flipping transit inside nanopore confinement. This strategy provides a general platform for rapid detection of proteins as well as exploring fundamental protein dynamics at the single-molecule level.
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Affiliation(s)
- Qiao Li
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Shao-Chuang Liu
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yao Lin
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
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Huang JA, Caprettini V, Zhao Y, Melle G, Maccaferri N, Deleye L, Zambrana-Puyalto X, Ardini M, Tantussi F, Dipalo M, De Angelis F. On-Demand Intracellular Delivery of Single Particles in Single Cells by 3D Hollow Nanoelectrodes. NANO LETTERS 2019; 19:722-731. [PMID: 30673248 PMCID: PMC6378653 DOI: 10.1021/acs.nanolett.8b03764] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Delivery of molecules into intracellular compartments is one of the fundamental requirements in molecular biology. However, the possibility of delivering a precise number of nano-objects with single-particle resolution is still an open challenge. Here we present an electrophoretic platform based on 3D hollow nanoelectrodes to enable delivery of single nanoparticles into single selected cells and monitoring of the single-particle delivery by surface-enhanced Raman scattering (SERS). The gold-coated hollow nanoelectrode capable of confinement and enhancement of electromagnetic fields upon laser illumination can distinguish the SERS signals of a single nanoparticle flowing through the nanoelectrode. Tight wrapping of cell membranes around the nanoelectrodes allows effective membrane electroporation such that single gold nanorods are delivered on demand into a living cell by electrophoresis. The capability of the 3D hollow nanoelectrodes to porate cells and reveal single emitters from the background in continuous flow is promising for the analysis of both intracellular delivery and sampling.
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Affiliation(s)
- Jian-An Huang
- Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Valeria Caprettini
- Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
- DIBRIS, University of Genoa, Via all’Opera Pia 13, 16145 Genova, Italy
| | - Yingqi Zhao
- Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Giovanni Melle
- Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
- DIBRIS, University of Genoa, Via all’Opera Pia 13, 16145 Genova, Italy
| | | | - Lieselot Deleye
- Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | | | - Matteo Ardini
- Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | | | - Michele Dipalo
- Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
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Lin Y, Shi X, Liu SC, Ying YL, Li Q, Gao R, Fathi F, Long YT, Tian H. Characterization of DNA duplex unzipping through a sub-2 nm solid-state nanopore. Chem Commun (Camb) 2017; 53:3539-3542. [DOI: 10.1039/c7cc00060j] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The unzipping and translocation of DNA duplexes through a sub-2 nm SiNx solid-state nanopore have been demonstrated by well-resolved three-level blockades.
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Affiliation(s)
- Yao Lin
- School of Chemistry & Molecular Engineering
- East China University of Science and Technology
- Shanghai
- P. R. China
| | - Xin Shi
- School of Chemistry & Molecular Engineering
- East China University of Science and Technology
- Shanghai
- P. R. China
| | - Shao-Chuang Liu
- School of Chemistry & Molecular Engineering
- East China University of Science and Technology
- Shanghai
- P. R. China
| | - Yi-Lun Ying
- School of Chemistry & Molecular Engineering
- East China University of Science and Technology
- Shanghai
- P. R. China
| | - Qiao Li
- School of Chemistry & Molecular Engineering
- East China University of Science and Technology
- Shanghai
- P. R. China
| | - Rui Gao
- School of Chemistry & Molecular Engineering
- East China University of Science and Technology
- Shanghai
- P. R. China
| | - Farkhondeh Fathi
- Department of Chemistry and Biochemistry
- Mount Allison University
- Sackville
- Canada
| | - Yi-Tao Long
- School of Chemistry & Molecular Engineering
- East China University of Science and Technology
- Shanghai
- P. R. China
| | - He Tian
- School of Chemistry & Molecular Engineering
- East China University of Science and Technology
- Shanghai
- P. R. China
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