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Zhou J, Zhou PL, Shen Q, Ahmed SA, Pan XT, Liu HL, Ding XL, Li J, Wang K, Xia XH. Probing Multidimensional Structural Information of Single Molecules Transporting through a Sub-10 nm Conical Plasmonic Nanopore by SERS. Anal Chem 2021; 93:11679-11685. [PMID: 34415740 DOI: 10.1021/acs.analchem.1c00875] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Probing the orientation and oxygenation state of single molecules (SMs) is of great importance for understanding the advanced structure of individual molecules. Here, we manipulate molecules transporting through the hot spot of a sub-10 nm conical gold nanopore and acquire the multidimensional structural information of the SMs by surface enhanced Raman scattering (SERS) detection. The sub-10 nm size and conical shape of the plasmonic nanopore guarantee its high detection sensitivity. SERS spectra show a high correlation with the orientations of small-sized single rhodamine 6G (R6G) during transport. Meanwhile, SERS spectra of a single hemoglobin (Hb) reveal both the vertical/parallel orientations of the porphyrin ring and oxygenated/deoxygenated states of Hb. The present study provides a new strategy for bridging the primary sequence and the advanced structure of SMs.
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Affiliation(s)
- Juan Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Pan-Ling Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Qi Shen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Saud Asif Ahmed
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xiao-Tong Pan
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hai-Ling Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xin-Lei Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jian Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Kang Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xing-Hua Xia
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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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: 20] [Impact Index Per Article: 6.7] [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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53
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Shen Q, Zhou PL, Huang BT, Zhou J, Liu HL, Ahmed SA, Ding XL, Li J, Zhai YM, Wang K. Mass transport through a sub-10 nm single gold nanopore: SERS and ionic current measurement. J Electroanal Chem (Lausanne) 2021. [DOI: 10.1016/j.jelechem.2021.115373] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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54
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Deng Y, Zhuang X, Wang W, Gu R, He D, Wang L, Cheng X. Direct visualization of beam-resist interaction volume for sub-nanometer helium ion beam-lithography. NANOTECHNOLOGY 2021; 32:415302. [PMID: 34198269 DOI: 10.1088/1361-6528/ac1099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/01/2021] [Indexed: 06/13/2023]
Abstract
Interaction volume of beam-resist is a basis unit of beam-lithography, directly determines the critical parameters of beam-lithography. We have visualized the interaction volume at the state-of-the-art sub-10 nm scale by a spot irradiation of sub-nanometer helium ion beam into an approximately free-standing resist. The visualized interaction volume suggests helium ion beam has an excellent capability in nanofabrication. Specifically, helium ion beam-lithography is 1000 times more efficient than electron beam-lithography (EBL), owns a sub-4 nm resolution, can achieve a large pattern aspect ratio (greater than 8), and does not suffer from backscattering effect at a normal exposure dose. Furthermore, the interaction volume has been theoretically studied by considering the spatial distribution of energy deposited in the resist, and eventually lead to a model for pattern prediction and proximity effect corrections. We expect that, our approach to visualize the interaction volume may be applied to study other high resolution lithographic techniques such as x-ray lithography and EBL, and it may open new possibilities in other applications, like beam-imaging, beam-milling, and beam-modification.
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Affiliation(s)
- Yunsheng Deng
- Pico Center and SUSTech Core Research Facilities, Southern University of Science and Technology, Shenzhen, 518055, People's Republic of China
| | - Xin Zhuang
- Shenzhen Key Laboratory for Nanoimprint Technology, Department of Materials Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, People's Republic of China
- Department of Mechanical Engineering, the University of Hong Kong, Hong Kong
- HKU-Zhejiang Institute of Research and Innovation (HKU-ZIRI), Hangzhou, Zhejiang 311300, People's Republic of China
| | - Wu Wang
- Department of Physics, Southern University of Science and Technology, Shenzhen 518055, People's Republic of China
| | - Rui Gu
- Pico Center and SUSTech Core Research Facilities, Southern University of Science and Technology, Shenzhen, 518055, People's Republic of China
| | - Dongsheng He
- Pico Center and SUSTech Core Research Facilities, Southern University of Science and Technology, Shenzhen, 518055, People's Republic of China
| | - Liqiu Wang
- Department of Mechanical Engineering, the University of Hong Kong, Hong Kong
- HKU-Zhejiang Institute of Research and Innovation (HKU-ZIRI), Hangzhou, Zhejiang 311300, People's Republic of China
| | - Xing Cheng
- Pico Center and SUSTech Core Research Facilities, Southern University of Science and Technology, Shenzhen, 518055, People's Republic of China
- Shenzhen Key Laboratory for Nanoimprint Technology, Department of Materials Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, People's Republic of China
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55
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SERS and DFT investigations of methyl 4‑bromo-1H-pyrrole-2-carboxylate adsorbed on silver and gold substrates: In perspective of biosensor applications. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130272] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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56
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Rapid single-molecule detection of COVID-19 and MERS antigens via nanobody-functionalized organic electrochemical transistors. Nat Biomed Eng 2021; 5:666-677. [PMID: 34031558 DOI: 10.1038/s41551-021-00734-9] [Citation(s) in RCA: 167] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/16/2021] [Indexed: 02/07/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has highlighted the need for rapid and sensitive protein detection and quantification in simple and robust formats for widespread point-of-care applications. Here, we report on nanobody-functionalized organic electrochemical transistors with a modular architecture for the rapid quantification of single-molecule-to-nanomolar levels of specific antigens in complex bodily fluids. The sensors combine a solution-processable conjugated polymer in the transistor channel and high-density and orientation-controlled bioconjugation of nanobody-SpyCatcher fusion proteins on disposable gate electrodes. The devices provide results after 10 min of exposure to 5 μl of unprocessed samples, maintain high specificity and single-molecule sensitivity in human saliva and serum, and can be reprogrammed to detect any protein antigen if a corresponding specific nanobody is available. We used the sensors to detect green fluorescent protein, and severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and Middle East respiratory syndrome coronavirus (MERS-CoV) spike proteins, and for the COVID-19 screening of unprocessed clinical nasopharyngeal swab and saliva samples with a wide range of viral loads.
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57
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Wu LZ, Ye Y, Wang ZX, Ma D, Li L, Xi GH, Bao BQ, Weng LX. Sensitive Detection of Single-Nucleotide Polymorphisms by Solid Nanopores Integrated With DNA Probed Nanoparticles. Front Bioeng Biotechnol 2021; 9:690747. [PMID: 34277589 PMCID: PMC8279778 DOI: 10.3389/fbioe.2021.690747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/21/2021] [Indexed: 12/01/2022] Open
Abstract
Single-nucleotide polymorphisms (SNPs) are the abundant forms of genetic variations, which are closely associated with serious genetic and inherited diseases, even cancers. Here, a novel SNP detection assay has been developed for single-nucleotide discrimination by nanopore sensing platform with DNA probed Au nanoparticles as transport carriers. The SNP of p53 gene mutation in gastric cancer has been successfully detected in the femtomolar concentration by nanopore sensing. The robust biosensing strategy offers a way for solid nanopore sensors integrated with varied nanoparticles to achieve single-nucleotide distinction with high sensitivity and spatial resolution, which promises tremendous potential applications of nanopore sensing for early diagnosis and disease prevention in the near future.
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Affiliation(s)
- Ling Zhi Wu
- Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, National Synergetic Innovation Center for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, China.,College of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Yuan Ye
- Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, National Synergetic Innovation Center for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Zhi Xuan Wang
- College of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Die Ma
- Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, National Synergetic Innovation Center for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Li Li
- Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, National Synergetic Innovation Center for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Guo Hao Xi
- Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, National Synergetic Innovation Center for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Bi Qing Bao
- Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, National Synergetic Innovation Center for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Li Xing Weng
- College of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing, China
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58
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Diederichs T, Tampé R. Membrane-Suspended Nanopores in Microchip Arrays for Stochastic Transport Recording and Sensing. FRONTIERS IN NANOTECHNOLOGY 2021. [DOI: 10.3389/fnano.2021.703673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The transport of nutrients, xenobiotics, and signaling molecules across biological membranes is essential for life. As gatekeepers of cells, membrane proteins and nanopores are key targets in pharmaceutical research and industry. Multiple techniques help in elucidating, utilizing, or mimicking the function of biological membrane-embedded nanodevices. In particular, the use of DNA origami to construct simple nanopores based on the predictable folding of nucleotides provides a promising direction for innovative sensing and sequencing approaches. Knowledge of translocation characteristics is crucial to link structural design with function. Here, we summarize recent developments and compare features of membrane-embedded nanopores with solid-state analogues. We also describe how their translocation properties are characterized by microchip systems. The recently developed silicon chips, comprising solid-state nanopores of 80 nm connecting femtoliter cavities in combination with vesicle spreading and formation of nanopore-suspended membranes, will pave the way to characterize translocation properties of nanopores and membrane proteins in high-throughput and at single-transporter resolution.
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59
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Alfaro JA, Bohländer P, Dai M, Filius M, Howard CJ, van Kooten XF, Ohayon S, Pomorski A, Schmid S, Aksimentiev A, Anslyn EV, Bedran G, Cao C, Chinappi M, Coyaud E, Dekker C, Dittmar G, Drachman N, Eelkema R, Goodlett D, Hentz S, Kalathiya U, Kelleher NL, Kelly RT, Kelman Z, Kim SH, Kuster B, Rodriguez-Larrea D, Lindsay S, Maglia G, Marcotte EM, Marino JP, Masselon C, Mayer M, Samaras P, Sarthak K, Sepiashvili L, Stein D, Wanunu M, Wilhelm M, Yin P, Meller A, Joo C. The emerging landscape of single-molecule protein sequencing technologies. Nat Methods 2021; 18:604-617. [PMID: 34099939 PMCID: PMC8223677 DOI: 10.1038/s41592-021-01143-1] [Citation(s) in RCA: 163] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 04/02/2021] [Indexed: 02/04/2023]
Abstract
Single-cell profiling methods have had a profound impact on the understanding of cellular heterogeneity. While genomes and transcriptomes can be explored at the single-cell level, single-cell profiling of proteomes is not yet established. Here we describe new single-molecule protein sequencing and identification technologies alongside innovations in mass spectrometry that will eventually enable broad sequence coverage in single-cell profiling. These technologies will in turn facilitate biological discovery and open new avenues for ultrasensitive disease diagnostics.
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Affiliation(s)
- Javier Antonio Alfaro
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland.
| | - Peggy Bohländer
- Faculty of Applied Sciences, Delft University of Technology, Delft, the Netherlands
| | - Mingjie Dai
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Mike Filius
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Cecil J Howard
- Department of Chemistry, University of Texas at Austin, Austin, TX, USA
| | - Xander F van Kooten
- Department of Biomedical Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Shilo Ohayon
- Department of Biomedical Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Adam Pomorski
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Sonja Schmid
- NanoDynamicsLab, Laboratory of Biophysics, Wageningen University, Wageningen, the Netherlands
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Eric V Anslyn
- Department of Chemistry, University of Texas at Austin, Austin, TX, USA
| | - Georges Bedran
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland
| | - Chan Cao
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Mauro Chinappi
- Dipartimento di Ingegneria Industriale, Università di Roma Tor Vergata, Rome, Italy
| | - Etienne Coyaud
- Univ. Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France
| | - Cees Dekker
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Gunnar Dittmar
- Department of Infection and Immunity, Luxembourg Institute of Health, Strassen, Luxembourg
- Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | - Rienk Eelkema
- Faculty of Applied Sciences, Delft University of Technology, Delft, the Netherlands
| | - David Goodlett
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland
- Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada
| | | | - Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Zvi Kelman
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, University of Maryland, Rockville, MD, USA
- Biomolecular Labeling Laboratory, Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
| | - Sung Hyun Kim
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
- Bavarian Center for Biomolecular Mass Spectrometry, Freising, Germany
| | - David Rodriguez-Larrea
- Department of Biochemistry and Molecular Biology, Biofisika Institute (CSIC, UPV/EHU), Leioa, Spain
| | - Stuart Lindsay
- Biodesign Institute, School of Molecular Sciences, Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Edward M Marcotte
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA
| | - John P Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, University of Maryland, Rockville, MD, USA
| | | | - Michael Mayer
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
| | - Patroklos Samaras
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
| | - Kumar Sarthak
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Lusia Sepiashvili
- University of Toronto, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Derek Stein
- Department of Physics, Brown University, Providence, RI, USA
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, MA, USA
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technische Universität München, Freising, Germany
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Amit Meller
- Department of Biomedical Engineering, Technion-Israel Institute of Technology, Haifa, Israel.
- Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa, Israel.
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
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60
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Versatile approach to nanoporous polymers with bicontinuous morphology using metal templated synthesis. Eur Polym J 2021. [DOI: 10.1016/j.eurpolymj.2021.110509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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61
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Yang H, Saqib M, Hao R. Single-Entity Detection With TEM-Fabricated Nanopores. Front Chem 2021; 9:664820. [PMID: 34026729 PMCID: PMC8138203 DOI: 10.3389/fchem.2021.664820] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 04/13/2021] [Indexed: 12/04/2022] Open
Abstract
Nanopore-based single-entity detection shows immense potential in sensing and sequencing technologies. Solid-state nanopores permit unprecedented detail while preserving mechanical robustness, reusability, adjustable pore size, and stability in different physical and chemical environments. The transmission electron microscope (TEM) has evolved into a powerful tool for fabricating and characterizing nanometer-sized pores within a solid-state ultrathin membrane. By detecting differences in the ionic current signals due to single-entity translocation through the nanopore, solid-state nanopores can enable gene sequencing and single molecule/nanoparticle detection with high sensitivity, improved acquisition speed, and low cost. Here we briefly discuss the recent progress in the modification and characterization of TEM-fabricated nanopores. Moreover, we highlight some key applications of these nanopores in nucleic acids, protein, and nanoparticle detection. Additionally, we discuss the future of computer simulations in DNA and protein sequencing strategies. We also attempt to identify the challenges and discuss the future development of nanopore-detection technology aiming to promote the next-generation sequencing technology.
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Affiliation(s)
| | | | - Rui Hao
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, China
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62
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Fried JP, Swett JL, Nadappuram BP, Mol JA, Edel JB, Ivanov AP, Yates JR. In situ solid-state nanopore fabrication. Chem Soc Rev 2021; 50:4974-4992. [PMID: 33623941 DOI: 10.1039/d0cs00924e] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nanopores in solid-state membranes are promising for a wide range of applications including DNA sequencing, ultra-dilute analyte detection, protein analysis, and polymer data storage. Techniques to fabricate solid-state nanopores have typically been time consuming or lacked the resolution to create pores with diameters down to a few nanometres, as required for the above applications. In recent years, several methods to fabricate nanopores in electrolyte environments have been demonstrated. These in situ methods include controlled breakdown (CBD), electrochemical reactions (ECR), laser etching and laser-assisted controlled breakdown (la-CBD). These techniques are democratising solid-state nanopores by providing the ability to fabricate pores with diameters down to a few nanometres (i.e. comparable to the size of many analytes) in a matter of minutes using relatively simple equipment. Here we review these in situ solid-state nanopore fabrication techniques and highlight the challenges and advantages of each method. Furthermore we compare these techniques by their desired application and provide insights into future research directions for in situ nanopore fabrication methods.
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Affiliation(s)
- Jasper P Fried
- Department of Materials, University of Oxford, Oxford, OX1 3PH, UK
| | - Jacob L Swett
- Department of Materials, University of Oxford, Oxford, OX1 3PH, UK
| | - Binoy Paulose Nadappuram
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, W12 0BZ, UK
| | - Jan A Mol
- School of Physics and Astronomy, Queen Mary University of London, Mile End Road, E1 4NS, UK
| | - Joshua B Edel
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, W12 0BZ, UK
| | - Aleksandar P Ivanov
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, W12 0BZ, UK
| | - James R Yates
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.
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63
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Plasmonic Biosensors for Single-Molecule Biomedical Analysis. BIOSENSORS-BASEL 2021; 11:bios11040123. [PMID: 33921010 PMCID: PMC8071374 DOI: 10.3390/bios11040123] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/18/2021] [Accepted: 04/13/2021] [Indexed: 11/16/2022]
Abstract
The rapid spread of epidemic diseases (i.e., coronavirus disease 2019 (COVID-19)) has contributed to focus global attention on the diagnosis of medical conditions by ultrasensitive detection methods. To overcome this challenge, increasing efforts have been driven towards the development of single-molecule analytical platforms. In this context, recent progress in plasmonic biosensing has enabled the design of novel detection strategies capable of targeting individual molecules while evaluating their binding affinity and biological interactions. This review compiles the latest advances in plasmonic technologies for monitoring clinically relevant biomarkers at the single-molecule level. Functional applications are discussed according to plasmonic sensing modes based on either nanoapertures or nanoparticle approaches. A special focus was devoted to new analytical developments involving a wide variety of analytes (e.g., proteins, living cells, nucleic acids and viruses). The utility of plasmonic-based single-molecule analysis for personalized medicine, considering technological limitations and future prospects, is also overviewed.
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Abstract
The field of single nanoparticle plasmonics has grown enormously. There is no doubt that a wide diversity of the nanoplasmonic techniques and nanostructures represents a tremendous opportunity for fundamental biomedical studies as well as sensing and imaging applications. Single nanoparticle plasmonic biosensors are efficient in label-free single-molecule detection, as well as in monitoring real-time binding events of even several biomolecules. In the present review, we have discussed the prominent advantages and advances in single particle characterization and synthesis as well as new insight into and information on biomedical diagnosis uniquely obtained using single particle approaches. The approaches include the fundamental studies of nanoplasmonic behavior, two typical methods based on refractive index change and characteristic light intensity change, exciting innovations of synthetic strategies for new plasmonic nanostructures, and practical applications using single particle sensing, imaging, and tracking. The basic sphere and rod nanostructures are the focus of extensive investigations in biomedicine, while they can be programmed into algorithmic assemblies for novel plasmonic diagnosis. Design of single nanoparticles for the detection of single biomolecules will have far-reaching consequences in biomedical diagnosis.
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Affiliation(s)
- Xingyi Ma
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Korea.
| | - Sang Jun Sim
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Korea.
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65
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Yadav P, Cao Z, Barati Farimani A. DNA Detection with Single-Layer Ti 3C 2 MXene Nanopore. ACS NANO 2021; 15:4861-4869. [PMID: 33660990 DOI: 10.1021/acsnano.0c09595] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Nanopore based sequencing is an exciting alternative to the conventional sequencing methods as it allows for high-throughput sequencing with lower reagent costs and time requirements. Biological nanopores, such as α-hemolysin, are subject to breakdown under thermal, electrical, and mechanical stress after being used millions of times. On the contrary, two-dimensional (2D) nanomaterials have been explored as a solid-state platform for the sequencing of DNA. Their subnanometer thickness and outstanding mechanical properties have made possible the high-resolution and high-signal-to-noise ratio detection of DNA, but such a performance is dependent on the type of nanomaterial selected. Solid-state nanopores of graphene, Si3N4, and MoS2 have been studied as potential candidates for DNA detection. However, it is important to understand the sensitivity and characterization of these solid-state materials for nanopore based detection. Recent developments in the synthesis of MXene have inspired our interest in its application as a nanopore based DNA detection membrane. Here, we simulate the metal carbide, MXene (Ti3C2), with single stranded DNA to understand its interactions and the efficiency of MXene as a putative material for the development of a nanopore based detection platform. Using molecular dynamics (MD) simulations, we present evidence that a MXene based nanopore is able to detect the different types of DNA bases. We have successfully identified features to differentiate the translocation of different types of DNA bases across the nanopore.
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66
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Farshad M, Rasaiah JC. Light-Nucleotide versus Ion-Nucleotide Interactions for Single-Nucleotide Resolution. J Phys Chem B 2021; 125:2863-2870. [PMID: 33688740 DOI: 10.1021/acs.jpcb.0c10759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Several parallel reads of ionic currents through multiple CsgG nanopores provide information about ion-nucleotide interactions for sequencing single-stranded DNA (ss-DNA) using base-calling algorithms. However, the information in ion-nucleotide interactions seems insufficient for single-read nanopore DNA sequencing. Here we report discriminative light-nucleotide interactions calculated from density functional theory (DFT), which are compared with ionic currents obtained from molecular dynamics (MD) simulations. The MD simulations were performed on a system containing a transverse nanochannel and a longitudinal solid state nanopore. We show that both of the transverse and longitudinal ionic currents during the translocation of A16, G16, T16, and C16 through the nanopore, overlapped widely. On the other hand, the UV-vis and Raman spectra of different types of single nucleotides, nucleosides, and nucleobases show relatively higher resolution than the ionic currents. Light-nucleotide interactions provide better information for characterizing the nucleotides in comparison to ion-nucleotide interactions for nanopore DNA sequencing. This can be realized by using optical techniques including surface-enhanced Raman spectroscopy (SERS) or tip-enhanced Raman spectroscopy (TERS), while plasmon excitation can be used to localize light and control the rate of nucleotide flow.
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Affiliation(s)
- Mohsen Farshad
- Department of Chemistry, University of Maine, Orono, Maine 04469, United States
| | - Jayendran C Rasaiah
- Department of Chemistry, University of Maine, Orono, Maine 04469, United States
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Ahmed R, Butt H. Strain-Multiplex Metalens Array for Tunable Focusing and Imaging. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2003394. [PMID: 33643805 PMCID: PMC7887606 DOI: 10.1002/advs.202003394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/01/2020] [Indexed: 05/08/2023]
Abstract
Metalenses on a flexible template are engineered metal-dielectric interfaces that improve conventional imaging system and offer dynamic focusing and zooming capabilities by controlling the focal length and bandwidth through a mechanical or external stretch. However, realizing large-scale and cost-effective flexible metalenses with high yields in a strain-multiplex fashion remains as a great challenge. Here, single-pulsed, maskless light interference and imprinting technique is utilized to fabricate reconfigurable, flexible metalenses on a large-scale and demonstrate its strain-multiplex tunable focusing. Experiments, in accordance with the theory, show that applied stretch on the flexible-template reconfigurable diffractive metalenses (FDMLs) accurately mapped focused wavefront, bandwidth, and focal length. The surface relief metastructures consisted of metal-coated hemispherical cavities in a hexagonal close-packed arrangement to enhance tunable focal length, numerical aperture, and fill factor, FF ≈ 100% through normal and angular light illumination with external stretch. The strain-multiplex of FDMLs approach lays the foundation of a new class of large-scale, cost-effective metalens offering tunable light focusing and imaging.
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Affiliation(s)
- Rajib Ahmed
- School of EngineeringUniversity of BirminghamBirminghamB15 2TTUK
- Stanford School of MedicinePalo AltoCA94304United States
| | - Haider Butt
- Department of Mechanical EngineeringKhalifa UniversityAbu DhabiP.O. 127788UAE
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68
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Li P, Chen S, Dai H, Yang Z, Chen Z, Wang Y, Chen Y, Peng W, Shan W, Duan H. Recent advances in focused ion beam nanofabrication for nanostructures and devices: fundamentals and applications. NANOSCALE 2021; 13:1529-1565. [PMID: 33432962 DOI: 10.1039/d0nr07539f] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The past few decades have witnessed growing research interest in developing powerful nanofabrication technologies for three-dimensional (3D) structures and devices to achieve nano-scale and nano-precision manufacturing. Among the various fabrication techniques, focused ion beam (FIB) nanofabrication has been established as a well-suited and promising technique in nearly all fields of nanotechnology for the fabrication of 3D nanostructures and devices because of increasing demands from industry and research. In this article, a series of FIB nanofabrication factors related to the fabrication of 3D nanostructures and devices, including mechanisms, instruments, processes, and typical applications of FIB nanofabrication, are systematically summarized and analyzed in detail. Additionally, current challenges and future development trends of FIB nanofabrication in this field are also given. This work intends to provide guidance for practitioners, researchers, or engineers who wish to learn more about the FIB nanofabrication technology that is driving the revolution in 3D nanostructures and devices.
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Affiliation(s)
- Ping Li
- National Engineering Research Centre for High Efficiency Grinding, College of Mechanical and Vehicle Engineering, Hunan University, Changsha 410082, P. R. China.
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Peri SSS, Sabnani MK, Raza MU, Urquhart EL, Ghaffari S, Lee JS, Kim MJ, Weidanz J, Alexandrakis G. Quantification of low affinity binding interactions between natural killer cell inhibitory receptors and targeting ligands with a self-induced back-action actuated nanopore electrophoresis (SANE) sensor. NANOTECHNOLOGY 2021; 32:045501. [PMID: 33027774 PMCID: PMC8346883 DOI: 10.1088/1361-6528/abbf26] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A plasmonic nanopore sensor enabling detection of bimodal optical and electrical molecular signatures was fabricated and tested for its ability to characterize low affinity ligand-receptor interactions. This plasmonic nanosensor uses self-induced back-action (SIBA) for optical trapping to enable SIBA-actuated nanopore electrophoresis (SANE) through a nanopore located immediately below the optical trap volume. A natural killer (NK) cell inhibitory receptor heterodimer molecule CD94/NKG2A was synthesized to target a specific peptide-presenting Qa-1b Qdm ligand as a simplified model of low-affinity interactions between immune cells and peptide-presenting cancer cells that occurs during cancer immunotherapy. A cancer-irrelevant Qa-1b GroEL ligand was also targeted by the same receptor as a control experiment to test for non-specific binding. The analysis of different pairs of bimodal SANE sensor signatures enabled discrimination of ligand, receptor and their complexes and enabled differentiating between specific and non-specific ligand interactions. We were able to detect ligand-receptor complex binding at concentrations over 500 times lower than the free solution equilibrium binding constant (K D ). Additionally, SANE sensor measurements enabled estimation of the fast dissociation rate (k off) for this low-affinity specific ligand-receptor system, previously shown to be challenging to quantify with commercial technologies. The k off value of targeted peptide-presenting ligands is known to correlate with the subsequent activation of immune cells in vivo, suggesting the potential utility of the SANE senor as a screening tool in cancer immunotherapy.
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Affiliation(s)
- Sai Santosh Sasank Peri
- Department of Electrical Engineering, University of Texas at Arlington, Arlington, TX, United States of America
| | - Manoj Kumar Sabnani
- Department of Biology, University of Texas at Arlington, Arlington, TX, United States of America
| | - Muhammad Usman Raza
- Department of Electrical Engineering, University of Texas at Arlington, Arlington, TX, United States of America
| | - Elizabeth L Urquhart
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX, United States of America
| | - Soroush Ghaffari
- Department of Biology, University of Texas at Arlington, Arlington, TX, United States of America
| | - Jung Soo Lee
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX, United States of America
| | - Min Jun Kim
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX, United States of America
| | - Jon Weidanz
- Department of Biology, University of Texas at Arlington, Arlington, TX, United States of America
| | - George Alexandrakis
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX, United States of America
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Yilmaz D, Kaya D, Kececi K, Dinler A. Role of Nanopore Geometry in Particle Resolution by Resistive‐Pulse Sensing. ChemistrySelect 2021. [DOI: 10.1002/slct.202004425] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Durdane Yilmaz
- Nanoscience and Nanoengineering Program Istanbul Medeniyet University İstanbul Turkey
| | - Dila Kaya
- Department of Chemistry Istanbul Medeniyet University İstanbul Turkey
| | - Kaan Kececi
- Department of Chemistry Istanbul Medeniyet University İstanbul Turkey
| | - Ali Dinler
- Department of Mathematics Istanbul Medeniyet University İstanbul Turkey
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Chircov C, Bîrcă AC, Grumezescu AM, Andronescu E. Biosensors-on-Chip: An Up-to-Date Review. Molecules 2020; 25:E6013. [PMID: 33353220 PMCID: PMC7765790 DOI: 10.3390/molecules25246013] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 12/13/2022] Open
Abstract
Generally, biosensors are designed to translate physical, chemical, or biological events into measurable signals, thus offering qualitative and/or quantitative information regarding the target analytes. While the biosensor field has received considerable scientific interest, integrating this technology with microfluidics could further bring significant improvements in terms of sensitivity and specificity, resolution, automation, throughput, reproducibility, reliability, and accuracy. In this manner, biosensors-on-chip (BoC) could represent the bridging gap between diagnostics in central laboratories and diagnostics at the patient bedside, bringing substantial advancements in point-of-care (PoC) diagnostic applications. In this context, the aim of this manuscript is to provide an up-to-date overview of BoC system development and their most recent application towards the diagnosis of cancer, infectious diseases, and neurodegenerative disorders.
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Affiliation(s)
- Cristina Chircov
- Department of Science and Engineering of Oxide Materials and Nanomaterials, University Politehnica of Bucharest, 011061 Bucharest, Romania; (C.C.); (A.C.B.); (E.A.)
| | - Alexandra Cătălina Bîrcă
- Department of Science and Engineering of Oxide Materials and Nanomaterials, University Politehnica of Bucharest, 011061 Bucharest, Romania; (C.C.); (A.C.B.); (E.A.)
| | - Alexandru Mihai Grumezescu
- Department of Science and Engineering of Oxide Materials and Nanomaterials, University Politehnica of Bucharest, 011061 Bucharest, Romania; (C.C.); (A.C.B.); (E.A.)
- Research Institute of the University of Bucharest—ICUB, University of Bucharest, 050657 Bucharest, Romania
| | - Ecaterina Andronescu
- Department of Science and Engineering of Oxide Materials and Nanomaterials, University Politehnica of Bucharest, 011061 Bucharest, Romania; (C.C.); (A.C.B.); (E.A.)
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Shepherd BA, Tanjil MRE, Jeong Y, Baloğlu B, Liao J, Wang MC. Ångström- and Nano-scale Pore-Based Nucleic Acid Sequencing of Current and Emergent Pathogens. MRS ADVANCES 2020; 5:2889-2906. [PMID: 33437534 PMCID: PMC7790041 DOI: 10.1557/adv.2020.402] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
State-of-the-art nanopore sequencing enables rapid and real-time identification of novel pathogens, which has wide application in various research areas and is an emerging diagnostic tool for infectious diseases including COVID-19. Nanopore translocation enables de novo sequencing with long reads (> 10 kb) of novel genomes, which has advantages over existing short-read sequencing technologies. Biological nanopore sequencing has already achieved success as a technology platform but it is sensitive to empirical factors such as pH and temperature. Alternatively, ångström- and nano-scale solid-state nanopores, especially those based on two-dimensional (2D) membranes, are promising next-generation technologies as they can surpass biological nanopores in the variety of membrane materials, ease of defining pore morphology, higher nucleotide detection sensitivity, and facilitation of novel and hybrid sequencing modalities. Since the discovery of graphene, atomically-thin 2D materials have shown immense potential for the fabrication of nanopores with well-defined geometry, rendering them viable candidates for nanopore sequencing membranes. Here, we review recent progress and future development trends of 2D materials and their ångström- and nano-scale pore-based nucleic acid (NA) sequencing including fabrication techniques and current and emerging sequencing modalities. In addition, we discuss the current challenges of translocation-based nanopore sequencing and provide an outlook on promising future research directions.
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Affiliation(s)
- Britney A. Shepherd
- Department of Medical Engineering, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620 USA
| | - Md Rubayat-E Tanjil
- Department of Mechanical Engineering, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620 USA
| | - Yunjo Jeong
- Department of Mechanical Engineering, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620 USA
| | - Bilgenur Baloğlu
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G2W1 Canada
| | - Jingqiu Liao
- Department of Systems Biology, Columbia University, 1130 St. Nicholas Avenue, New York, New York 10032 USA
| | - Michael Cai Wang
- Department of Medical Engineering, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620 USA
- Department of Mechanical Engineering, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620 USA
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TANG J, WANG S, WU J, LIANG LY, WANG L, WANG DQ. Applications of Photo-Responsive Molecules in Nanopore-based Devices. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(20)60058-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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74
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ABC Spotlight on single-molecule detection. Anal Bioanal Chem 2020; 412:7043-7045. [PMID: 32856109 PMCID: PMC7497507 DOI: 10.1007/s00216-020-02838-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 12/27/2022]
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Huang Q, Li N, Zhang H, Che C, Sun F, Xiong Y, Canady TD, Cunningham BT. Critical Review: digital resolution biomolecular sensing for diagnostics and life science research. LAB ON A CHIP 2020; 20:2816-2840. [PMID: 32700698 PMCID: PMC7485136 DOI: 10.1039/d0lc00506a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
One of the frontiers in the field of biosensors is the ability to quantify specific target molecules with enough precision to count individual units in a test sample, and to observe the characteristics of individual biomolecular interactions. Technologies that enable observation of molecules with "digital precision" have applications for in vitro diagnostics with ultra-sensitive limits of detection, characterization of biomolecular binding kinetics with a greater degree of precision, and gaining deeper insights into biological processes through quantification of molecules in complex specimens that would otherwise be unobservable. In this review, we seek to capture the current state-of-the-art in the field of digital resolution biosensing. We describe the capabilities of commercially available technology platforms, as well as capabilities that have been described in published literature. We highlight approaches that utilize enzymatic amplification, nanoparticle tags, chemical tags, as well as label-free biosensing methods.
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Affiliation(s)
- Qinglan Huang
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Nantao Li
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Hanyuan Zhang
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Congnyu Che
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Department of Bioengineering, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Fu Sun
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Yanyu Xiong
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Taylor D. Canady
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Brian T. Cunningham
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Department of Bioengineering, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Illinois Cancer Center, University of Illinois at Urbana-Champaign Urbana, IL 61801
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76
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Huang J, Mousavi MZ, Giovannini G, Zhao Y, Hubarevich A, Soler MA, Rocchia W, Garoli D, De Angelis F. Multiplexed Discrimination of Single Amino Acid Residues in Polypeptides in a Single SERS Hot Spot. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jian‐An Huang
- Plasmon Nanotechology Unit Istituto Italiano di Tecnologia Via Morego 30 16163 Genova Italy
| | - Mansoureh Z. Mousavi
- Plasmon Nanotechology Unit Istituto Italiano di Tecnologia Via Morego 30 16163 Genova Italy
| | - Giorgia Giovannini
- Plasmon Nanotechology Unit Istituto Italiano di Tecnologia Via Morego 30 16163 Genova Italy
- Present address: EMPA Federal Swiss research Institute 9014 St. Gallen Switzerland
| | - Yingqi Zhao
- Plasmon Nanotechology Unit Istituto Italiano di Tecnologia Via Morego 30 16163 Genova Italy
| | - Aliaksandr Hubarevich
- Plasmon Nanotechology Unit Istituto Italiano di Tecnologia Via Morego 30 16163 Genova Italy
| | - Miguel A. Soler
- CONCEPT Lab Istituto Italiano di Tecnologia Via Melen 83 16152 Genova Italy
| | - Walter Rocchia
- CONCEPT Lab Istituto Italiano di Tecnologia Via Melen 83 16152 Genova Italy
| | - Denis Garoli
- Plasmon Nanotechology Unit Istituto Italiano di Tecnologia Via Morego 30 16163 Genova Italy
- AB ANALITICA s.r.l. Via Svizzera 16 35127 Padova Italy
| | - Francesco De Angelis
- Plasmon Nanotechology Unit Istituto Italiano di Tecnologia Via Morego 30 16163 Genova Italy
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77
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Huang JA, Mousavi MZ, Giovannini G, Zhao Y, Hubarevich A, Soler MA, Rocchia W, Garoli D, De Angelis F. Multiplexed Discrimination of Single Amino Acid Residues in Polypeptides in a Single SERS Hot Spot. Angew Chem Int Ed Engl 2020; 59:11423-11431. [PMID: 32250516 DOI: 10.1002/anie.202000489] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 04/03/2020] [Indexed: 01/19/2023]
Abstract
The SERS-based detection of protein sequences with single-residue sensitivity suffers from signal dominance of aromatic amino acid residues and backbones, impeding detection of non-aromatic amino acid residues. Herein, we trap a gold nanoparticle in a plasmonic nanohole to generate a single SERS hot spot for single-molecule detection of 2 similar polypeptides (vasopressin and oxytocin) and 10 distinct amino acids that constitute the 2 polypeptides. Significantly, both aromatic and non-aromatic amino acids are detected and discriminated at the single-molecule level either at individual amino acid molecules or within the polypeptide chains. Correlated with molecular dynamics simulations, our results suggest that the signal dominance due to large spatial occupancy of aromatic rings of the polypeptide sidechains on gold surfaces can be overcome by the high localization of the single hot spot. The superior spectral and spatial discriminative power of our approach can be applied to single-protein analysis, fingerprinting, and sequencing.
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Affiliation(s)
- Jian-An Huang
- Plasmon Nanotechology Unit, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
| | - Mansoureh Z Mousavi
- Plasmon Nanotechology Unit, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
| | - Giorgia Giovannini
- Plasmon Nanotechology Unit, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy.,Present address: EMPA Federal Swiss research Institute, 9014, St. Gallen, Switzerland
| | - Yingqi Zhao
- Plasmon Nanotechology Unit, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
| | - Aliaksandr Hubarevich
- Plasmon Nanotechology Unit, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
| | - Miguel A Soler
- CONCEPT Lab, Istituto Italiano di Tecnologia, Via Melen 83, 16152, Genova, Italy
| | - Walter Rocchia
- CONCEPT Lab, Istituto Italiano di Tecnologia, Via Melen 83, 16152, Genova, Italy
| | - Denis Garoli
- Plasmon Nanotechology Unit, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy.,AB ANALITICA s.r.l., Via Svizzera 16, 35127, Padova, Italy
| | - Francesco De Angelis
- Plasmon Nanotechology Unit, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
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Melnychuk N, Egloff S, Runser A, Reisch A, Klymchenko AS. Light‐Harvesting Nanoparticle Probes for FRET‐Based Detection of Oligonucleotides with Single‐Molecule Sensitivity. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201913804] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Nina Melnychuk
- Laboratoire de Bioimagerie et PathologiesUMR 7021 CNRSFaculté de PharmacieUniversité de Strasbourg 74, Route du Rhin 67401 Illkirch France
| | - Sylvie Egloff
- Laboratoire de Bioimagerie et PathologiesUMR 7021 CNRSFaculté de PharmacieUniversité de Strasbourg 74, Route du Rhin 67401 Illkirch France
| | - Anne Runser
- Laboratoire de Bioimagerie et PathologiesUMR 7021 CNRSFaculté de PharmacieUniversité de Strasbourg 74, Route du Rhin 67401 Illkirch France
| | - Andreas Reisch
- Laboratoire de Bioimagerie et PathologiesUMR 7021 CNRSFaculté de PharmacieUniversité de Strasbourg 74, Route du Rhin 67401 Illkirch France
| | - Andrey S. Klymchenko
- Laboratoire de Bioimagerie et PathologiesUMR 7021 CNRSFaculté de PharmacieUniversité de Strasbourg 74, Route du Rhin 67401 Illkirch France
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Ali H, Ni H, Xu X. Near-UV luminescence tomography with an aperture-free meta super oscillatory lens for single molecule detection. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2020; 37:621-628. [PMID: 32400541 DOI: 10.1364/josaa.383854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/22/2020] [Indexed: 06/11/2023]
Abstract
Medical physics offers super oscillatory lenses (SOL) to attain subwavelength focusing for efficient image resolution in the detection of a single molecule. In this paper, we propose a negative-indexed permeability-controlled meta SOL, which restores the light concentration via exciting surface plasmon resonance and enhances luminescence at our region of interest, i.e., fluid sample (${S_L}$SL). The meta SOL is aperture-free in comparison with other techniques (zero-mode waveguides and nano antennas) and hence avoids the constraints, which are posed by nano apertures, to insert a small volume of $ S_L $SL into these nano apertures for detection purposes. The meta SOL is a unique combination of gold split rings mounted on silicon dioxide (${{\rm SiO}_2}$SiO2) substrate and operational in the near-ultraviolet (UV) region. We utilized the phenomena of negative index of refraction, and our simulated trails exploit the magnetic (${\mu _r}$μr) response of the meta SOL by analyzing its transmission spectra in the frequency range from 3.53 to 3.57 Peta Hz. We observe the methodical response of the meta SOL with its ample potential to surpass the resolution at a working wavelength of $\lambda ={84.173}\;{\rm nm}$λ=84.173nm, which enhances luminescence by restoring the evanescent UV magnetic field (${B_{\rm UV}}$BUV) at ${S_L}$SL. This technique will offer a new and easy approach to uplift the efficiency of super oscillatory lenses in the near-UV regime to benefit single molecule detection techniques and thus the novelty.
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Affiliation(s)
- Si-Min Lu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yue-Yi Peng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
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81
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Melnychuk N, Egloff S, Runser A, Reisch A, Klymchenko AS. Light‐Harvesting Nanoparticle Probes for FRET‐Based Detection of Oligonucleotides with Single‐Molecule Sensitivity. Angew Chem Int Ed Engl 2020; 59:6811-6818. [DOI: 10.1002/anie.201913804] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/30/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Nina Melnychuk
- Laboratoire de Bioimagerie et PathologiesUMR 7021 CNRSFaculté de PharmacieUniversité de Strasbourg 74, Route du Rhin 67401 Illkirch France
| | - Sylvie Egloff
- Laboratoire de Bioimagerie et PathologiesUMR 7021 CNRSFaculté de PharmacieUniversité de Strasbourg 74, Route du Rhin 67401 Illkirch France
| | - Anne Runser
- Laboratoire de Bioimagerie et PathologiesUMR 7021 CNRSFaculté de PharmacieUniversité de Strasbourg 74, Route du Rhin 67401 Illkirch France
| | - Andreas Reisch
- Laboratoire de Bioimagerie et PathologiesUMR 7021 CNRSFaculté de PharmacieUniversité de Strasbourg 74, Route du Rhin 67401 Illkirch France
| | - Andrey S. Klymchenko
- Laboratoire de Bioimagerie et PathologiesUMR 7021 CNRSFaculté de PharmacieUniversité de Strasbourg 74, Route du Rhin 67401 Illkirch France
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82
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Zhu W, Gao MY, Zhu Q, Chi B, Zeng LW, Hu JM, Shen AG. Monodispersed plasmonic Prussian blue nanoparticles for zero-background SERS/MRI-guided phototherapy. NANOSCALE 2020; 12:3292-3301. [PMID: 31971195 DOI: 10.1039/c9nr08471a] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Surface-enhanced Raman scattering (SERS) and magnetic resonance imaging (MRI)-guided phototherapy are new breakthroughs in cancer therapeutics due to their complementary advantages, such as enhanced imaging spatial resolution and depth. Herein, we synthesized monodispersed Prussian blue-encapsulated gold nanoparticles (Au@PB NPs), in which the plasmonic gold core plus coordination polymer of cyanide (C[triple bond, length as m-dash]N) and iron ions coincidently become a superexcellent contrast agent for both MRI and zero-background SERS imaging. PB, as a signal source for MR and SERS, can be easily assembled onto single Au NPs, of which iron ions possess high relaxation efficiency for in vivo MRI, e.g., the longitudinal and transversal relaxation efficiency values are 0.86 mM-1 s-1 (r1) and 5.42 mM-1 s-1 (r2), respectively. Furthermore, with the help of the plasmonic enhancement of the gold core, the C[triple bond, length as m-dash]N groups exhibit a specific, strong, and stable (3S) SERS emission in the Raman-silent region (1800-2800 cm-1), allowing accurate in vivo imaging at the single or even subcellular level. More importantly, PB has remarkable absorption properties in the near infrared region, and can be used as a photosensitizer for photothermal (PT) and photodynamic (PD) therapy simultaneously. Hence, the ideal integration of a plasmonic Au core and PB shell into a single monodispersed MR-guided NP, with zero-background SERS signals, is an important candidate for both tumor navigation and in situ PT/PD treatment guided by SERS/MR dual-mode imaging.
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Affiliation(s)
- Wei Zhu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
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83
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Bandarkar P, Yang H, Henley RY, Wanunu M, Whitford PC. How Nanopore Translocation Experiments Can Measure RNA Unfolding. Biophys J 2020; 118:1612-1620. [PMID: 32075749 DOI: 10.1016/j.bpj.2020.01.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 01/29/2020] [Accepted: 01/30/2020] [Indexed: 10/25/2022] Open
Abstract
Electrokinetic translocation of biomolecules through solid-state nanopores represents a label-free single-molecule technique that may be used to measure biomolecular structure and dynamics. Recent investigations have attempted to distinguish individual transfer RNA (tRNA) species based on the associated pore translocation times, ion-current noise, and blockage currents. By manufacturing sufficiently smaller pores, each tRNA is required to undergo a deformation to translocate. Accordingly, differences in nanopore translocation times and distributions may be used to infer the mechanical properties of individual tRNA molecules. To bridge our understanding of tRNA structural dynamics and nanopore measurements, we apply molecular dynamics simulations using a simplified "structure-based" energetic model. Calculating the free-energy landscape for distinct tRNA species implicates transient unfolding of the terminal RNA helix during nanopore translocation. This provides a structural and energetic framework for interpreting current experiments, which can aid the design of methods for identifying macromolecules using nanopores.
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Affiliation(s)
- Prasad Bandarkar
- Department of Physics, Northeastern University, Boston, Massachusetts
| | - Huan Yang
- Department of Physics, Northeastern University, Boston, Massachusetts
| | - Robert Y Henley
- Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts.
| | - Paul C Whitford
- Department of Physics, Northeastern University, Boston, Massachusetts.
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84
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Wang S, Liang L, Tang J, Cai Y, Zhao C, Fang S, Wang H, Weng T, Wang L, Wang D. Label-free single-molecule identification of telomere G-quadruplexes with a solid-state nanopore sensor. RSC Adv 2020; 10:27215-27224. [PMID: 35515777 PMCID: PMC9055465 DOI: 10.1039/d0ra05083k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 07/06/2020] [Indexed: 12/14/2022] Open
Abstract
Telomere sequences can spontaneously form G-quadruplexes (G4) in the presence of some cations. In view of their relevance to genetic processes and potential as therapeutic-targets, hitherto, a wealth of conventional techniques have been reported for interrogation of G4 conformation diversity and corresponding folding kinetics, most of which are limited in precision and sensitivity. This work introduces a label-free solid-state nanopore (SSN) approach for the determination of inter-, intra- and tandem molecular G4 with distinct base permutation in various cation buffers with a tailored aperture and meanwhile captures the single-molecule G4 folding process. SSN translocation properties elucidated that both inter- and intramolecular G4 generated higher current blockage with longer duration than flexible homopolymer nucleotide, and intramolecular G4 are structurally more stable with higher event frequency and longer blockage time than intermolecular ones; base arrangement played weak role in translocation behaviors; the same sequences with one, two and three G4 skeletons displayed an increase in current blockage and a gradual extension in dwell time with the increase of molecule size recorded in the same nanopore. We observed the conformation change of single-molecule G4 which indicated the existence of folding/unfolding equilibration in nanopore, and real-time test suggested a gradual formation of G4 with time. Our results could provide a continued and improved understanding of the underlying relevance of structural stability and G4 folding process by utilizing SSN platform which exhibits strategic potential advances over the other methods with high spatial and temporal resolution. Nanopore detection of single-molecule G-quadruplexes.![]()
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85
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Nan J, Zhu S, Ye S, Sun W, Yue Y, Tang X, Shi J, Xu X, Zhang J, Yang B. Ultrahigh-Sensitivity Sandwiched Plasmon Ruler for Label-Free Clinical Diagnosis. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1905927. [PMID: 31782568 DOI: 10.1002/adma.201905927] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/14/2019] [Indexed: 06/10/2023]
Abstract
Optical biosensors, especially those based on plasmonic structures, have emerged recently as a potential tool for disease diagnostics. Plasmonic biosensors have demonstrated impressive benefits for the label-free detection of trace biomarkers in human serum. However, widespread applications of these technologies are hindered because of their insufficient sensitivity, their relatively complex chemical immobilization processes, and the use of prism couplers. Accordingly, a sandwiched plasmon ruler (SW-PR) based on a Au nanohole array with ultrahigh sensitivity arising from the plasmonic coupling effect is developed. Highly confined surface charges caused by Bloch wave surface plasmon polarizations substantially increase the coupling efficiency. This platform exhibits thickness sensitivity as high as 61 nm nm-1 and can detect at least 200 000-fold lower analyte concentrations than a nanowell sensing platform with the same wavelength shift. Additionally, the sandwiched plasmonic biosensor allows precise and label-free testing of clinical biomarkers, namely C-reactive protein and procalcitonin, in patient serum samples without requiring a sophisticated prism coupler, extra antibodies, or a chemical immobilization technique. This study yields new insight into the structural design of plasmon rulers and will open exciting avenues for disease diagnosis and therapy follow-up at the point-of-care.
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Affiliation(s)
- Jingjie Nan
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130021, P. R. China
| | - Shoujun Zhu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130021, P. R. China
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, 130061, P. R. China
| | - Shunsheng Ye
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200438, P. R. China
| | - Weihong Sun
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130021, P. R. China
| | - Ying Yue
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130021, P. R. China
| | - Xiaoduo Tang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130021, P. R. China
| | - Jingwei Shi
- Department of Clinical Laboratory, China-Japan Union Hospital of Jilin University, Changchun, 130033, P. R. China
| | - Xuesong Xu
- Department of Clinical Laboratory, China-Japan Union Hospital of Jilin University, Changchun, 130033, P. R. China
| | - Junhu Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130021, P. R. China
| | - Bai Yang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130021, P. R. China
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86
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Akkilic N, Geschwindner S, Höök F. Single-molecule biosensors: Recent advances and applications. Biosens Bioelectron 2019; 151:111944. [PMID: 31999573 DOI: 10.1016/j.bios.2019.111944] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/26/2019] [Accepted: 11/29/2019] [Indexed: 02/07/2023]
Abstract
Single-molecule biosensors serve the unmet need for real time detection of individual biological molecules in the molecular crowd with high specificity and accuracy, uncovering unique properties of individual molecules which are hidden when measured using ensemble averaging methods. Measuring a signal generated by an individual molecule or its interaction with biological partners is not only crucial for early diagnosis of various diseases such as cancer and to follow medical treatments but also offers a great potential for future point-of-care devices and personalized medicine. This review summarizes and discusses recent advances in nanosensors for both in vitro and in vivo detection of biological molecules offering single-molecule sensitivity. In the first part, we focus on label-free platforms, including electrochemical, plasmonic, SERS-based and spectroelectrochemical biosensors. We review fluorescent single-molecule biosensors in the second part, highlighting nanoparticle-amplified assays, digital platforms and the utilization of CRISPR technology. We finally discuss recent advances in the emerging nanosensor technology of important biological species as well as future perspectives of these sensors.
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Affiliation(s)
- Namik Akkilic
- Structure, Biophysics and Fragment-based Lead Generation, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden.
| | - Stefan Geschwindner
- Structure, Biophysics and Fragment-based Lead Generation, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Fredrik Höök
- Department of Applied Physics, Division of Biological Physics, Chalmers University of Technology, Gothenburg, Sweden.
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87
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Eggenberger OM, Ying C, Mayer M. Surface coatings for solid-state nanopores. NANOSCALE 2019; 11:19636-19657. [PMID: 31603455 DOI: 10.1039/c9nr05367k] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Since their introduction in 2001, solid-state nanopores have been increasingly exploited for the detection and characterization of biomolecules ranging from single DNA strands to protein complexes. A major factor that enables the application of nanopores to the analysis and characterization of a broad range of macromolecules is the preparation of coatings on the pore wall to either prevent non-specific adhesion of molecules or to facilitate specific interactions of molecules of interest within the pore. Surface coatings can therefore be useful to minimize clogging of nanopores or to increase the residence time of target analytes in the pore. This review article describes various coatings and their utility for changing pore diameters, increasing the stability of nanopores, reducing non-specific interactions, manipulating surface charges, enabling interactions with specific target molecules, and reducing the noise of current recordings through nanopores. We compare the coating methods with respect to the ease of preparing the coating, the stability of the coating and the requirement for specialized equipment to prepare the coating.
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Affiliation(s)
- Olivia M Eggenberger
- Adolphe Merkle Institute, Chemin des Verdiers 4, University of Fribourg, Fribourg, Switzerland.
| | - Cuifeng Ying
- Adolphe Merkle Institute, Chemin des Verdiers 4, University of Fribourg, Fribourg, Switzerland.
| | - Michael Mayer
- Adolphe Merkle Institute, Chemin des Verdiers 4, University of Fribourg, Fribourg, Switzerland.
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88
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Garoli D, Yamazaki H, Maccaferri N, Wanunu M. Plasmonic Nanopores for Single-Molecule Detection and Manipulation: Toward Sequencing Applications. NANO LETTERS 2019; 19:7553-7562. [PMID: 31587559 DOI: 10.1021/acs.nanolett.9b02759] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Solid-state nanopore-based sensors are promising platforms for next-generation sequencing technologies, featuring label-free single-molecule sensitivity, rapid detection, and low-cost manufacturing. In recent years, solid-state nanopores have been explored due to their miscellaneous fabrication methods and their use in a wide range of sensing applications. Here, we highlight a novel family of solid-state nanopores which have recently appeared, namely plasmonic nanopores. The use of plasmonic nanopores to engineer electromagnetic fields around a nanopore sensor allows for enhanced optical spectroscopies, local control over temperature, thermophoresis of molecules and ions to/from the sensor, and trapping of entities. This Mini Review offers a comprehensive understanding of the current state-of-the-art plasmonic nanopores for single-molecule detection and biomolecular sequencing applications and discusses the latest advances and future perspectives on plasmonic nanopore-based technologies.
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Affiliation(s)
- Denis Garoli
- Istituto Italiano di Tecnologia , via Morego 30 , I-16163 , Genova , Italy
| | - Hirohito Yamazaki
- Department of Physics , Northeastern University , 360 Huntington Avenue , Boston , Massachusetts 02115 , United States
| | - Nicolò Maccaferri
- Physics and Materials Science Research Unit , University of Luxembourg , 162a avenue de la Faïencerie , L-1511 Luxembourg , Luxembourg
| | - Meni Wanunu
- Department of Physics , Northeastern University , 360 Huntington Avenue , Boston , Massachusetts 02115 , United States
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89
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Malekian B, Xiong K, Kang ESH, Andersson J, Emilsson G, Rommel M, Sannomiya T, Jonsson MP, Dahlin A. Optical properties of plasmonic nanopore arrays prepared by electron beam and colloidal lithography. NANOSCALE ADVANCES 2019; 1:4282-4289. [PMID: 36134417 PMCID: PMC9418017 DOI: 10.1039/c9na00585d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 10/05/2019] [Indexed: 05/24/2023]
Abstract
Solid state nanopores are central structures for many applications. To date, much effort has been spent on controlled fabrication of single nanopores, while relatively little work has focused on large scale fabrication of arrays of nanopores. In this work we show wafer-scale fabrication of plasmonic nanopores in 50 nm thick silicon nitride membranes with one or two 30 nm gold films, using electron beam lithography with a negative resist or a new version of colloidal lithography. Both approaches offer good control of pore diameter (even below 100 nm) and with high yield (>90%) of intact membranes. Colloidal lithography has the advantage of parallel patterning without expensive equipment. Despite its serial nature, electron beam lithography provides high throughput and can make arbitrary array patterns. Importantly, both methods prevent metal from ending up on the membrane pore sidewalls. The new fabrication methods make it possible to compare the optical properties of structurally identical plasmonic nanopore arrays with either long-range order (e-beam) or short-range order (colloidal). The resonance features in the extinction spectrum are very similar for both structures when the pitch is the same as the characteristic spacing in the self-assembled colloidal pattern. Long-range ordering slightly enhances the magnitude of the extinction maximum and blueshift the transmission maximum by tens of nm. Upon reducing the diameter in long-range ordered arrays, the resonance is reduced in magnitude and the transmission maximum is further blue shifted, just like for short-range ordered arrays. These effects are well explained by interpreting the spectra as Fano interference between the grating-type excitation of propagating surface plasmons and the broad transmission via individual pores in the metal film. Furthermore, we find that only the short-range ordered arrays scatter light, which we attribute to the highly limited effective period in the short-range ordered system and the corresponding lack of coherent suppression of scattering by interference effects.
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Affiliation(s)
- Bita Malekian
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology 41296 Gothenburg Sweden
| | - Kunli Xiong
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology 41296 Gothenburg Sweden
| | - Evan S H Kang
- Laboratory of Organic Electronics, Linköping University 60174 Norrköping Sweden
| | - John Andersson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology 41296 Gothenburg Sweden
| | - Gustav Emilsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology 41296 Gothenburg Sweden
| | - Marcus Rommel
- Department of Microtechnology and Nanoscience, Chalmers University of Technology 41296 Gothenburg Sweden
| | - Takumi Sannomiya
- Department of Materials Science and Engineering 4259 Nagatsuta Midoriku Yokohama 226-8503 Japan
| | - Magnus P Jonsson
- Laboratory of Organic Electronics, Linköping University 60174 Norrköping Sweden
| | - Andreas Dahlin
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology 41296 Gothenburg Sweden
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90
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Peri SSS, Sabnani MK, Raza MU, Ghaffari S, Gimlin S, Wawro DD, Lee JS, Kim MJ, Weidanz J, Alexandrakis G. Detection of specific antibody-ligand interactions with a self-induced back-action actuated nanopore electrophoresis sensor. NANOTECHNOLOGY 2019; 31:085502. [PMID: 31675752 DOI: 10.1088/1361-6528/ab53a7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Recent advances in plasmonic nanopore technologies have enabled the use of concurrently acquired bimodal optical-electrical data for improved quantification of molecular interactions. This work presents the use of a new plasmonic nanosensor employing self-induced back-action (SIBA) for optical trapping to enable SIBA-actuated nanopore electrophoresis (SANE) for quantifying antibody-ligand interactions. T-cell receptor-like antibodies (TCRmAbs) engineered to target peptide-presenting major histocompatibility complex (pMHC) ligands, representing a model of target ligands presented on the surface of cancer cells, were used to test the SANE sensor's ability to identify specific antibody-ligand binding. Cancer-irrelevant TCRmAbs targeting the same pMHCs were also tested as a control. It was found that the sensor could provide bimodal molecular signatures that could differentiate between antibody, ligand and the complexes that they formed, as well as distinguish between specific and non-specific interactions. Furthermore, the results suggested an interesting phenomenon of increased antibody-ligand complex bound fraction detected by the SANE sensor compared to that expected for corresponding bulk solution concentrations. A possible physical mechanism and potential advantages for the sensor's ability to augment complex formation near its active sensing volume at concentrations lower than the free solution equilibrium binding constant (K D ) are discussed.
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Affiliation(s)
- Sai Santosh Sasank Peri
- Department of Electrical Engineering, University of Texas at Arlington, Arlington, TX, United States of America
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