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Rathnayaka C, Chandrosoma IA, Choi J, Childers K, Chibuike M, Akabirov K, Shiri F, Hall AR, Lee M, McKinney C, Verber M, Park S, Soper SA. Detection and identification of single ribonucleotide monophosphates using a dual in-plane nanopore sensor made in a thermoplastic via replication. Lab Chip 2024; 24:2721-2735. [PMID: 38656267 DOI: 10.1039/d3lc01062g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
We report the generation of ∼8 nm dual in-plane pores fabricated in a thermoplastic via nanoimprint lithography (NIL). These pores were connected in series with nanochannels, one of which served as a flight tube to allow the identification of single molecules based on their molecular-dependent apparent mobilities (i.e., dual in-plane nanopore sensor). Two different thermoplastics were investigated including poly(methyl methacrylate), PMMA, and cyclic olefin polymer, COP, as the substrate for the sensor both of which were sealed using a low glass transition cover plate (cyclic olefin co-polymer, COC) that could be thermally fusion bonded to the PMMA or COP substrate at a temperature minimizing nanostructure deformation. Unique to these dual in-plane nanopore sensors was two pores flanking each side of the nanometer flight tube (50 × 50 nm, width × depth) that was 10 μm in length. The utility of this dual in-plane nanopore sensor was evaluated to not only detect, but also identify single ribonucleotide monophosphates (rNMPs) by using the travel time (time-of-flight, ToF), the resistive pulse event amplitude, and the dwell time. In spite of the relatively large size of these in-plane pores (∼8 nm effective diameter), we could detect via resistive pulse sensing (RPS) single rNMP molecules at a mass load of 3.9 fg, which was ascribed to the unique structural features of the nanofluidic network and the use of a thermoplastic with low relative dielectric constants, which resulted in a low RMS noise level in the open pore current. Our data indicated that the identification accuracy of individual rNMPs was high, which was ascribed to an improved chromatographic contribution to the nano-electrophoresis apparent mobility. With the ToF data only, the identification accuracy was 98.3%. However, when incorporating the resistive pulse sensing event amplitude and dwell time in conjunction with the ToF and analyzed via principal component analysis (PCA), the identification accuracy reached 100%. These findings pave the way for the realization of a novel chip-based single-molecule RNA sequencing technology.
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Affiliation(s)
- Chathurika Rathnayaka
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA.
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Indu A Chandrosoma
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA.
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Junseo Choi
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Katie Childers
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
| | - Maximillian Chibuike
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA.
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Khurshed Akabirov
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA.
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Farhad Shiri
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA.
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Adam R Hall
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Virginia Tech-Wake Forest School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston Salem, NC 27101, USA
- Atrium Wake Forest Baptist Comprehensive Cancer Center, Wake Forest School of Medicine, Winston Salem, NC 27157, USA.
| | - Maxwell Lee
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Virginia Tech-Wake Forest School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston Salem, NC 27101, USA
| | - Collin McKinney
- Department of Chemistry, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Matthew Verber
- Department of Chemistry, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sunggook Park
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Steven A Soper
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA.
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Department of Mechanical Engineering, The University of Kansas, Lawrence, KS 66045, USA
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
- KU Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160, USA
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Guo L, Han Y, Yang H, Fu J, Li W, Xie R, Zhang Y, Wang K, Xia XH. Single-Molecule Discrimination of Saccharides Using Carbon Nitride Nanopores. Nano Lett 2024; 24:5639-5646. [PMID: 38668743 DOI: 10.1021/acs.nanolett.4c01223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2024]
Abstract
Structural complexity brings a huge challenge to the analysis of sugar chains. As a single-molecule sensor, nanopores have the potential to provide fingerprint information on saccharides. Traditionally, direct single-molecule saccharide detection with nanopores is hampered by their small size and weak affinity. Here, a carbon nitride nanopore device is developed to discern two types of trisaccharide molecules (LeApN and SLeCpN) with minor structural differences. The resolution of LeApN and SLeCpN in the mixture reaches 0.98, which has never been achieved in solid-state nanopores so far. Monosaccharide (GlcNAcpN) and disaccharide (LacNAcpN) can also be discriminated using this system, indicating that the versatile carbon nitride nanopores possess a monosaccharide-level resolution. This study demonstrates that the carbon nitride nanopores have the potential for conducting structure analysis on single-molecule saccharides.
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Affiliation(s)
- Linru Guo
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yida Han
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Hong Yang
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Jie Fu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Wang Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Ran Xie
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, China
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Yuanjian Zhang
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, 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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Ju H, Cheng L, Li M, Mei K, He S, Jia C, Guo X. Single-Molecule Electrical Profiling of Peptides and Proteins. Adv Sci (Weinh) 2024:e2401877. [PMID: 38639403 DOI: 10.1002/advs.202401877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/03/2024] [Indexed: 04/20/2024]
Abstract
In recent decades, there has been a significant increase in the application of single-molecule electrical analysis platforms in studying proteins and peptides. These advanced analysis methods have the potential for deep investigation of enzymatic working mechanisms and accurate monitoring of dynamic changes in protein configurations, which are often challenging to achieve in ensemble measurements. In this work, the prominent research progress in peptide and protein-related studies are surveyed using electronic devices with single-molecule/single-event sensitivity, including single-molecule junctions, single-molecule field-effect transistors, and nanopores. In particular, the successful commercial application of nanopores in DNA sequencing has made it one of the most promising techniques in protein sequencing at the single-molecule level. From single peptides to protein complexes, the correlation between their electrical characteristics, structures, and biological functions is gradually being established. This enables to distinguish different molecular configurations of these biomacromolecules through real-time electrical monitoring of their life activities, significantly improving the understanding of the mechanisms underlying various life processes.
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Affiliation(s)
- Hongyu Ju
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, P. R. China
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Li Cheng
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Mengmeng Li
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Kunrong Mei
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Suhang He
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Chuancheng Jia
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Xuefeng Guo
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
- Beijing National Laboratory for Molecular Sciences, National Biomedical Imaging Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
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Cheng P, Zhao C, Pan Q, Xiong Z, Chen Q, Miao X, He Y. Detection of Biomolecules Using Solid-State Nanopores Fabricated by Controlled Dielectric Breakdown. Sensors (Basel) 2024; 24:2420. [PMID: 38676038 PMCID: PMC11053845 DOI: 10.3390/s24082420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/07/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024]
Abstract
Nanopore sensor technology is widely used in biomolecular detection due to its advantages of low cost and easy operation. In a variety of nanopore manufacturing methods, controlled dielectric breakdown has the advantages of a simple manufacturing process and low cost under the premise of ensuring detection performance. In this paper, we have made enhancements to the applied pulses in controlled dielectric breakdown and utilized the improved dielectric breakdown technique to fabricate silicon nitride nanopores with diameters of 5 to 15 nm. Our improved fabrication method offers the advantage of precise control over the nanopore diameter (±0.4 nm) and enhances the symmetry of the nanopore. After fabrication, we performed electrical characterization on the nanopores, and the IV characteristics exhibited high linearity. Subsequently, we conducted detection experiments for DNA and protein using the prepared nanopores to assess the detection performance of the nanopores fabricated using our method. In addition, we also give a physical model of molecule translocation through the nanopores to give a reasonable explanation of the data processing results.
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Affiliation(s)
| | | | | | | | - Qi Chen
- Hubei Yangtze Memory Laboratories, School of Integrated Circuit, Huazhong University of Science and Technology, Wuhan 430074, China
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5
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Si W, Zhang Z, Chen J, Wu G, Zhang Y, Sha J. Protein Deceleration and Sequencing Using Si 3N 4-CNT Hybrid Nanopores. Chemphyschem 2024; 25:e202300866. [PMID: 38267372 DOI: 10.1002/cphc.202300866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/24/2024] [Accepted: 01/24/2024] [Indexed: 01/26/2024]
Abstract
Protein sequencing is crucial for understanding the complex mechanisms driving biological functions and is of utmost importance in molecular diagnostics and medication development. Nanopores have become an effective tool for single molecule sensing, however, the weak charge and non-uniform charge distribution of protein make capturing and sensing very challenging, which poses a significant obstacle to the development of nanopore-based protein sequencing. In this study, to facilitate capturing of the unfolded protein, highly charged peptide was employed in our simulations, we found that the velocity of unfolded peptide translocating through a hybrid nanopore composed of silicon nitride membrane and carbon nanotube is much slower compared to bare silicon nitride nanopore, it is due to the significant interaction between amino acids and the surface of carbon nanotube. Moreover, by introducing variations in the charge states at the boundaries of carbon nanotube nanopores, the competition and combination of the electrophoretic and electroosmotic flows through the nanopores could be controlled, we then successfully regulated the translocation velocity of unfolded proteins through the hybrid nanopores. The proposed hybrid nanopore effectively retards the translocation velocity of protein through it, facilitates the acquisition of ample information for accurate amino acid identification.
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Affiliation(s)
- Wei Si
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, 211100, China
| | - Zhen Zhang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, 211100, China
| | - Jiayi Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, 211100, China
| | - Gensheng Wu
- School of Mechanical and Electronic Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Yin Zhang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, 211100, China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, 211100, China
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6
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Yuan Z, Lin Y, Hu J, Wang C. Controllable Fabrication of Sub-10 nm Graphene Nanopores via Helium Ion Microscopy and DNA Detection. Biosensors (Basel) 2024; 14:158. [PMID: 38667151 PMCID: PMC11048673 DOI: 10.3390/bios14040158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 03/17/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024]
Abstract
Solid-state nanopores have become a prominent tool in the field of single-molecule detection. Conventional solid-state nanopores are thick, which affects the spatial resolution of the detection results. Graphene is the thinnest 2D material and has the highest spatial detection resolution. In this study, a graphene membrane chip was fabricated by combining a MEMS process with a 2D material wet transfer process. Raman spectroscopy was used to assess the quality of graphene after the transfer. The mechanism behind the influence of the processing dose and residence time of the helium ion beam on the processed pore size was investigated. Subsequently, graphene nanopores with diameters less than 10 nm were fabricated via helium ion microscopy. DNA was detected using a 5.8 nm graphene nanopore chip, and the appearance of double-peak signals on the surface of 20 mer DNA was successfully detected. These results serve as a valuable reference for nanopore fabrication using 2D material for DNA analysis.
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Affiliation(s)
- Zhishan Yuan
- School of Electro-Mechanical Engineering, Guangdong University of Technology, Guangzhou 510006, China; (Y.L.); (J.H.); (C.W.)
- Guangdong Provincial Key Laboratory of Minimally Invasive Surgical Instruments and Manufacturing Technology, Guangdong University of Technology, Guangzhou 510006, China
- State Key Laboratory for High Performance Tools, Guangdong University of Technology, Guangzhou 510006, China
- Smart Medical Innovation Technology Center, Guangdong University of Technology, Guangzhou 510006, China
| | - Yanbang Lin
- School of Electro-Mechanical Engineering, Guangdong University of Technology, Guangzhou 510006, China; (Y.L.); (J.H.); (C.W.)
- Guangdong Provincial Key Laboratory of Minimally Invasive Surgical Instruments and Manufacturing Technology, Guangdong University of Technology, Guangzhou 510006, China
- State Key Laboratory for High Performance Tools, Guangdong University of Technology, Guangzhou 510006, China
- Smart Medical Innovation Technology Center, Guangdong University of Technology, Guangzhou 510006, China
| | - Jieming Hu
- School of Electro-Mechanical Engineering, Guangdong University of Technology, Guangzhou 510006, China; (Y.L.); (J.H.); (C.W.)
- Guangdong Provincial Key Laboratory of Minimally Invasive Surgical Instruments and Manufacturing Technology, Guangdong University of Technology, Guangzhou 510006, China
- State Key Laboratory for High Performance Tools, Guangdong University of Technology, Guangzhou 510006, China
- Smart Medical Innovation Technology Center, Guangdong University of Technology, Guangzhou 510006, China
| | - Chengyong Wang
- School of Electro-Mechanical Engineering, Guangdong University of Technology, Guangzhou 510006, China; (Y.L.); (J.H.); (C.W.)
- Guangdong Provincial Key Laboratory of Minimally Invasive Surgical Instruments and Manufacturing Technology, Guangdong University of Technology, Guangzhou 510006, China
- State Key Laboratory for High Performance Tools, Guangdong University of Technology, Guangzhou 510006, China
- Smart Medical Innovation Technology Center, Guangdong University of Technology, Guangzhou 510006, China
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Fang S, Zeng D, He S, Li Y, Pang Z, Wang Y, Liang L, Weng T, Xie W, Wang D. Fast Fabrication Nanopores on a PMMA Membrane by a Local High Electric Field Controlled Breakdown. Sensors (Basel) 2024; 24:2109. [PMID: 38610321 PMCID: PMC11013984 DOI: 10.3390/s24072109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/18/2024] [Accepted: 03/24/2024] [Indexed: 04/14/2024]
Abstract
The sensitivity and accuracy of nanopore sensors are severely hindered by the high noise associated with solid-state nanopores. To mitigate this issue, the deposition of organic polymer materials onto silicon nitride (SiNx) membranes has been effective in obtaining low-noise measurements. Nonetheless, the fabrication of nanopores sub-10 nm on thin polymer membranes remains a significant challenge. This work proposes a method for fabricating nanopores on polymethyl methacrylate (PMMA) membrane by the local high electrical field controlled breakdown, exploring the impact of voltage and current on the breakdown of PMMA membranes and discussing the mechanism underlying the breakdown voltage and current during the formation of nanopores. By improving the electric field application method, transient high electric fields that are one-seven times higher than the breakdown electric field can be utilized to fabricate nanopores. A comparative analysis was performed on the current noise levels of nanopores in PMMA-SiNx composite membranes and SiNx nanopores with a 5 nm diameter. The results demonstrated that the fast fabrication of nanopores on PMMA-SiNx membranes exhibited reduced current noise compared to SiNx nanopores. This finding provides evidence supporting the feasibility of utilizing this technology for efficiently fabricating low-noise nanopores on polymer composite membranes.
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Affiliation(s)
- Shaoxi Fang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (S.F.); (S.H.); (Y.W.); (L.L.); (T.W.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Delin Zeng
- School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing 400065, China; (D.Z.); (Y.L.); (Z.P.)
| | - Shixuan He
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (S.F.); (S.H.); (Y.W.); (L.L.); (T.W.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Yadong Li
- School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing 400065, China; (D.Z.); (Y.L.); (Z.P.)
| | - Zichen Pang
- School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing 400065, China; (D.Z.); (Y.L.); (Z.P.)
| | - Yunjiao Wang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (S.F.); (S.H.); (Y.W.); (L.L.); (T.W.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Liyuan Liang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (S.F.); (S.H.); (Y.W.); (L.L.); (T.W.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Ting Weng
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (S.F.); (S.H.); (Y.W.); (L.L.); (T.W.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Wanyi Xie
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (S.F.); (S.H.); (Y.W.); (L.L.); (T.W.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Deqiang Wang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (S.F.); (S.H.); (Y.W.); (L.L.); (T.W.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing 400065, China; (D.Z.); (Y.L.); (Z.P.)
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Dorey A, Howorka S. Nanopore DNA sequencing technologies and their applications towards single-molecule proteomics. Nat Chem 2024; 16:314-334. [PMID: 38448507 DOI: 10.1038/s41557-023-01322-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 07/14/2023] [Indexed: 03/08/2024]
Abstract
Sequencing of nucleic acids with nanopores has emerged as a powerful tool offering rapid readout, high accuracy, low cost and portability. This label-free method for sequencing at the single-molecule level is an achievement on its own. However, nanopores also show promise for the technologically even more challenging sequencing of polypeptides, something that could considerably benefit biological discovery, clinical diagnostics and homeland security, as current techniques lack portability and speed. Here we survey the biochemical innovations underpinning commercial and academic nanopore DNA/RNA sequencing techniques, and explore how these advances can fuel developments in future protein sequencing with nanopores.
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Affiliation(s)
- Adam Dorey
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK.
| | - Stefan Howorka
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK.
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Bandara YMNDY, Karawdeniya BI, Dutt S, Kluth P, Tricoli A. Nanopore Fabrication Made Easy: A Portable, Affordable Microcontroller-Assisted Approach for Tailored Pore Formation via Controlled Breakdown. Anal Chem 2024; 96:2124-2134. [PMID: 38277343 DOI: 10.1021/acs.analchem.3c04860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Abstract
With growing interest in solid-state nanopore sensing─a single-molecule technique capable of profiling a host of analyte classes─establishing facile and scalable approaches for fabricating molecular-size pores is becoming increasingly important. The introduction of nanopore fabrication by controlled breakdown (CBD) has transformed the economics and accessibility of nanopore fabrication. Here, we introduce the design of an Arduino-based, portable USB-powered CBD device, with an estimated cost of <150 USD, which is ≈10-100× cheaper than most commercial solutions, capable of fabricating single nanopores conducive for single molecule sensing experiments. We demonstrate the facile fabrication of 60 tailored nanopores (∼2.6-12.6 nm) with ∼80% of the pores within 1 nm of the target diameter. Selected pores were then tested with double-stranded DNA, the canonical molecular ruler, demonstrating their performance for single-molecule sensing applications. The device is constructed with off-the-shelf readily available components and controlled using a highly customizable MATLAB application, which has capabilities encompassing pore fabrication, pore enlargement, and current-voltage acquisition for pore size estimation. When combined with a portable amplifier, this device also provides a fully portable sensing platform, an important step toward portable solid-state nanopore sensing applications.
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Affiliation(s)
- Y M Nuwan D Y Bandara
- Nanotechnology Research Laboratory, Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
| | - Buddini I Karawdeniya
- Department of Electronic Materials Engineering, Research School of Physics, The Australian National University, Canberra, ACT 2601, Australia
| | - Shankar Dutt
- Department of Materials Physics, Research School of Physics, The Australian National University, Canberra, ACT 2601, Australia
| | - Patrick Kluth
- Department of Materials Physics, Research School of Physics, The Australian National University, Canberra, ACT 2601, Australia
| | - Antonio Tricoli
- Nanotechnology Research Laboratory, Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
- Nanotechnology Research Laboratory, School of Biomedical Engineering, Faculty of Engineering, University of Sydney, NSW 2008, Australia
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10
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Dai B, Su Y, Guo Y, Wu C, Xie Y. Recent Strategies for the Synthesis of Phase-Pure Ultrathin 1T/1T' Transition Metal Dichalcogenide Nanosheets. Chem Rev 2024; 124:420-454. [PMID: 38146851 DOI: 10.1021/acs.chemrev.3c00422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
The past few decades have witnessed a notable increase in transition metal dichalcogenide (TMD) related research not only because of the large family of TMD candidates but also because of the various polytypes that arise from the monolayer configuration and layer stacking order. The peculiar physicochemical properties of TMD nanosheets enable an enormous range of applications from fundamental science to industrial technologies based on the preparation of high-quality TMDs. For polymorphic TMDs, the 1T/1T' phase is particularly intriguing because of the enriched density of states, and thus facilitates fruitful chemistry. Herein, we comprehensively discuss the most recent strategies for direct synthesis of phase-pure 1T/1T' TMD nanosheets such as mechanical exfoliation, chemical vapor deposition, wet chemical synthesis, atomic layer deposition, and more. We also review frequently adopted methods for phase engineering in TMD nanosheets ranging from chemical doping and alloying, to charge injection, and irradiation with optical or charged particle beams. Prior to the synthesis methods, we discuss the configuration of TMDs as well as the characterization tools mostly used in experiments. Finally, we discuss the current challenges and opportunities as well as emphasize the promising fields for the future development.
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Affiliation(s)
- Baohu Dai
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Yueqi Su
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Yuqiao Guo
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Changzheng Wu
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Yi Xie
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
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11
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Xiong M, Athreya N, Chakraborty R, Leburton JP. Ion Trapping and Thermionic Emission across Sub-nm Pores. Nano Lett 2023; 23:11719-11726. [PMID: 38078825 DOI: 10.1021/acs.nanolett.3c03592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
Ionic transport through a graphene biomimetic subnanometer (sub-nm) pore of arbitrary shape and realistically decorated by intrinsic negatively charged sites is investigated by all-atom molecular dynamics (MD) simulations. In the presence of external electric fields, cation trapping-assisted translocation occurs in the vicinity of the 2D subnanometer pore, while the anion current is blocked by the negative charges. The adsorbed cations in such asymmetrically charged nanopores are located on the top of the nanopore instead of blocking the pore, as suggested previously in highly symmetric pores such as crown ethers. Our analysis of the different types of energy involved in ion translocations indicates that electrostatics is the dominant factor controlling ion transfer across these sub-nm pores. A physical model based on the thermionic emission formalism to account for the free energy barriers to ion flow reproduces the I-V characteristics.
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12
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Wu J, Choi J, Uba FI, Soper SA, Park S. Engineering inlet structures to enhance DNA capture into nanochannels in a polymer nanofluidic device produced via nanoimprint lithography. Micro Nano Eng 2023; 21:100230. [PMID: 38737190 PMCID: PMC11085012 DOI: 10.1016/j.mne.2023.100230] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
Operating nanofluidic biosensors requires threading single molecules to be analyzed from microfluidic networks into nanostructures, mostly nanochannels or nanopores. Different inlet structures have been employed as a means of enhancing the number of the capture events into nanostructures. Here, we systematically investigated the effects of various engineered inlet structures formed at the micro/nanochannel interface on the capture of single λ-DNA molecules into the nanochannels. Different inlet geometries were evaluated and ranked in order of their effectiveness. Adding an inlet structure prior to a nanochannel effectively improved the DNA capture rate by 190 - 700 % relative to that for the abrupt micro/nanochannel interface. The capture of DNA from the microchannel to various inlets was determined mainly by the capture volumes of the inlet structures and the geometrically modified electric field in the inlet structure. However, as the width of the inlet structure increased, the hydrodynamic flow existing in the microchannel negatively influenced the DNA capture by dragging some DNA molecules deep into the inlet structure back to the microchannel. Our results indicate that engineering inlet structures is an effective means of controlling the capture of DNA molecules into nanostructures, which is important for operation of nanofluidic biosensors.
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Affiliation(s)
- Jiahao Wu
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, LA 70803, USA
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Junseo Choi
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, LA 70803, USA
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Franklin I. Uba
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, USA
| | - Steven A. Soper
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
- Center of BioModular Multiscale Systems for Precision Medicine, USA
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA
- Department of Mechanical Engineering, The University of Kansas, Lawrence, KS 66045, USA
- KU Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Sunggook Park
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, LA 70803, USA
- Center of BioModular Multiscale Systems for Precision Medicine, USA
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13
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Abstract
Solid-state nanopores have wide applications in DNA sequencing, energy conversion and storage, seawater desalination, sensors, and reactors due to their high stability, controllable geometry, and a variety of pore-forming materials. Solid-state nanopore sensors can be used for qualitative and quantitative analyses of ions, small molecules, proteins, and nucleic acids. The combination of nucleic acid amplification and solid-state nanopores to achieve trace detection of analytes is gradually attracting attention. This review outlines nucleic acid amplification strategies for enhancing the sensitivity of solid-state nanopore sensors by summarizing the articles published in the past 10 years. The future development prospects and challenges of nucleic acid amplification in solid-state nanopore sensors are discussed. This review helps readers better understand the field of solid-state nanopore sensors. We believe that solid-state nanopore sensors will break through the bottleneck of traditional detection and become a powerful single-molecule detection platform.
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Affiliation(s)
- Xiaojin Zhang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Huimin Dou
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Xiaorui Chen
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Meihua Lin
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Yu Dai
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
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14
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Si L, Wu Y, Xiao H, Xing W, Song R, Li Y, Wang S, Liang X, Yu W, Song J, Shen S. A superstable, flexible, and scalable nanofluidic ion regulation composite membrane. Sci Bull (Beijing) 2023; 68:2344-2353. [PMID: 37684133 DOI: 10.1016/j.scib.2023.08.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 05/25/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023]
Abstract
Two-dimensional layered membranes with high and stable ion transport properties have various applications in nanofluidic devices; however, their construction remains a considerable challenge. Herein, we develop a superstable aramid nanofiber/graphite composite membrane with numerous one-dimensional and two-dimensional nano-confined interspaces for ultrafast ion transport. The fabricated flexible and scalable membrane exhibits high tensile strength (∼115.3 MPa) even after immersion in water for 90 days. Further, the aramid nanofiber/graphite conductor features the surface-charge-governed ion transport behavior. The ionic conductivity of the membrane at a low potassium chloride concentration of 10-4 mol/L can be enhanced by 16 times that of the bulk counterpart. More importantly, its structure and ionic conductivity remain unchanged even after immersion in different harsh solutions (e.g., acid, base, and ethanol) for over 30 days. Molecular dynamics simulations reveal that the superstability of the membrane is attributable to the robust interchain interactions within the aramid nanofibers and the strong interfacial interactions between the aramid nanofibers and graphite nanosheets. This study highlights the superior structural stability of the proposed flexible and scalable aramid nanofiber/graphite composite membrane, which could be employed in advanced nanofluidic devices for application under extreme working environments.
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Affiliation(s)
- Lianmeng Si
- State Key Laboratory for Strength and Vibration of Mechanical Structures, School of Aerospace Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yihan Wu
- State Key Laboratory for Strength and Vibration of Mechanical Structures, School of Aerospace Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Hong Xiao
- State Key Laboratory for Strength and Vibration of Mechanical Structures, School of Aerospace Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Wensi Xing
- State Key Laboratory for Strength and Vibration of Mechanical Structures, School of Aerospace Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Rui Song
- State Key Laboratory for Strength and Vibration of Mechanical Structures, School of Aerospace Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yiju Li
- Department of Mechanical and Energy Engineering, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Sha Wang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, China
| | - Xu Liang
- State Key Laboratory for Strength and Vibration of Mechanical Structures, School of Aerospace Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Wenshan Yu
- State Key Laboratory for Strength and Vibration of Mechanical Structures, School of Aerospace Engineering, Xi'an Jiaotong University, Xi'an 710049, China.
| | - Jianwei Song
- State Key Laboratory for Strength and Vibration of Mechanical Structures, School of Aerospace Engineering, Xi'an Jiaotong University, Xi'an 710049, China.
| | - Shengping Shen
- State Key Laboratory for Strength and Vibration of Mechanical Structures, School of Aerospace Engineering, Xi'an Jiaotong University, Xi'an 710049, China
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15
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Datar A, Tanyhin B, Melchionna S, Fyta M. Influence of nanopore coating patterns on the translocation dynamics of polyelectrolytes. J Chem Phys 2023; 159:134901. [PMID: 37787143 DOI: 10.1063/5.0164355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/11/2023] [Indexed: 10/04/2023] Open
Abstract
Polyelectrolytes can electrophoretically be driven through nanopores in order to be detected. The respective translocation events are often very fast and the process needs to be controlled to promote efficient detection. To this end, we attempt to control the translocation dynamics by coating the inner surface of a nanopore. For this, different charge distributions are chosen that result in substantial variations of the pore-polymer interactions. In addition and in view of the existing detection modalities, experimental settings, and nanopore materials, different types of sensors inside the nanopore have been considered to probe the translocation process and its temporal spread. The respective transport of polyelectrolytes through the coated nanopores is modeled through a multi-physics computational scheme that incorporates a mesoscopic/electrokinetic description for the solvent and particle-based scheme for the polymer. This investigation could underline the interplay between sensing modality, nanopore material, and detection accuracy. The electro-osmotic flow and electrophoretic motion in a pore are analyzed together with the polymeric temporal and spatial fluctuations unraveling their correlations and pathways to optimize the translocation speed and dynamics. Accordingly, this work sketches pathways in order to tune the pore-polymer interactions in order to control the translocation dynamics and, in the long run, errors in their measurements.
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Affiliation(s)
- Adwait Datar
- Institute for Computational Physics, Universität Stuttgart, Allmandring 3, Stuttgart 70569, Germany
- Institute of Data-Science Foundations, Hamburg University of Technology, Hamburg 21073, Germany
| | - Bohdan Tanyhin
- IAC-CNR, Istituto per le Applicazioni del Calcolo "M. Picone," 19 Via dei Taurini, Rome 00185, Italy
- Lexma Technology LLC, 20 School St., Belmont, Massachusetts 02478, USA
| | - Simone Melchionna
- IAC-CNR, Istituto per le Applicazioni del Calcolo "M. Picone," 19 Via dei Taurini, Rome 00185, Italy
- Lexma Technology LLC, 20 School St., Belmont, Massachusetts 02478, USA
| | - Maria Fyta
- Institute for Computational Physics, Universität Stuttgart, Allmandring 3, Stuttgart 70569, Germany
- Computational Biotechnology, RWTH Aachen, Worringerweg, Aachen 52074, Germany
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16
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Wang J, Gui C, Zhu J, Zhu B, Zhu Z, Jiang X, Chen D. A novel design of DNA duplex containing programmable sensing sites for nanopore-based length-resolution reading and applications for Pb 2+ and cfDNA analysis. Analyst 2023; 148:4346-4355. [PMID: 37581252 DOI: 10.1039/d3an01126g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
Glass nanopore is an ideal candidate for biosensors due to its unique advantages such as label-free analysis, single-molecule sensitivity, and easy operation. Previous studies have shown that glass nanopores can distinguish different lengths of double-stranded DNA (dsDNA) at the same time with the length-resolution ability. Based on this, we proposed a novel design of a dsDNA block containing a programmable sensing site inside, which can be programmed to respond to different target molecules and cleaved into two smaller DNA blocks. When programming the sensing site with different sequences, for example, programming it as the substrate of GR-5 DNAzyme and CRISPR-Cas12a system, the DNA block could realize Pb2+ and cfDNA detection with the length-resolution ability of the glass nanopore. This strategy achieved a Pb2+ detection range from 0.5 nM to 100 nM, with a detection limit of 0.4 nM, and a BRCA-1 detection range from 1 pM to 10 pM, with a detection limit of 1 pM. The programable sensing site is easy to design and has strong expandability, which gives full play to the advantages of glass nanopore in length-resolution ability for dsDNA, and is expected to become an optional design for biosensing strategy for the glass nanopore as a biosensing platform.
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Affiliation(s)
- Jiahai Wang
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China.
| | - Cenlin Gui
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China.
| | - Jianji Zhu
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China.
| | - Baian Zhu
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China.
| | - Zhuobin Zhu
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China.
| | - Xiwen Jiang
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Daqi Chen
- School of Chemistry and Chemical Engineering, School of Mechanical and Electrical Engineering, Guangzhou University, Guangzhou, Guangdong, 510006, China.
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17
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Xing Y, Rottensteiner A, Ciccone J, Howorka S. Functional Nanopores Enabled with DNA. Angew Chem Int Ed Engl 2023; 62:e202303103. [PMID: 37186432 DOI: 10.1002/anie.202303103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/17/2023]
Abstract
Membrane-spanning nanopores are used in label-free single-molecule sensing and next-generation portable nucleic acid sequencing, and as powerful research tools in biology, biophysics, and synthetic biology. Naturally occurring protein and peptide pores, as well as synthetic inorganic nanopores, are used in these applications, with their limitations. The structural and functional repertoire of nanopores can be considerably expanded by functionalising existing pores with DNA strands and by creating an entirely new class of nanopores with DNA nanotechnology. This review outlines progress in this area of functional DNA nanopores and outlines developments to open up new applications.
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Affiliation(s)
- Yongzheng Xing
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
| | - Alexia Rottensteiner
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
| | - Jonah Ciccone
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
| | - Stefan Howorka
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
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18
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Yanagi I, Akahori R, Takeda KI. Dwell Time Prolongation and Identification of Single Nucleotides Passing through a Solid-State Nanopore by Using Ammonium Sulfate Aqueous Solution. ACS Omega 2023; 8:21285-21292. [PMID: 37332803 PMCID: PMC10268630 DOI: 10.1021/acsomega.3c02703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 05/22/2023] [Indexed: 06/20/2023]
Abstract
The ionic current blockades when poly(dT)60 or dNTPs passed through SiN nanopores in an aqueous solution containing (NH4)2SO4 were investigated. The dwell time of poly(dT)60 in the nanopores in an aqueous solution containing (NH4)2SO4 was significantly longer compared to that in an aqueous solution that did not contain (NH4)2SO4. This dwell time prolongation effect due to the aqueous solution containing (NH4)2SO4 was also confirmed when dCTP passed through the nanopores. In addition, when the nanopores were fabricated via dielectric breakdown in the aqueous solution containing (NH4)2SO4, the dwell time prolongation effect for dCTP still occurred even after the aqueous solution was displaced with the aqueous solution without (NH4)2SO4. Furthermore, we measured the ionic current blockades when the four types of dNTPs passed through the same nanopore, and the four types of dNTPs could be statistically identified according to their current blockade values.
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Affiliation(s)
- Itaru Yanagi
- Center
for Exploratory Research, Research & Development Group, Hitachi, Ltd., 1-280, Higashi-koigakubo, Kokubunji, Tokyo 185-8603, Japan
| | - Rena Akahori
- Center
for Technology Innovation - Healthcare, Research & Development
Group, Hitachi, Ltd., 1-280, Higashi-koigakubo, Kokubunji, Tokyo 185-8603, Japan
| | - Ken-ichi Takeda
- Center
for Technology Innovation - Healthcare, Research & Development
Group, Hitachi, Ltd., 1-280, Higashi-koigakubo, Kokubunji, Tokyo 185-8603, Japan
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19
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Liu M, Li J, Tan CS. Unlocking the Power of Nanopores: Recent Advances in Biosensing Applications and Analog Front-End. Biosensors (Basel) 2023; 13:598. [PMID: 37366963 DOI: 10.3390/bios13060598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/24/2023] [Accepted: 05/29/2023] [Indexed: 06/28/2023]
Abstract
The biomedical field has always fostered innovation and the development of various new technologies. Beginning in the last century, demand for picoampere-level current detection in biomedicine has increased, leading to continuous breakthroughs in biosensor technology. Among emerging biomedical sensing technologies, nanopore sensing has shown great potential. This paper reviews nanopore sensing applications, such as chiral molecules, DNA sequencing, and protein sequencing. However, the ionic current for different molecules differs significantly, and the detection bandwidths vary as well. Therefore, this article focuses on current sensing circuits, and introduces the latest design schemes and circuit structures of different feedback components of transimpedance amplifiers mainly used in nanopore DNA sequencing.
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Affiliation(s)
- Miao Liu
- Medical College, Tianjin University, Tianjin 300072, China
| | - Junyang Li
- Medical College, Tianjin University, Tianjin 300072, China
| | - Cherie S Tan
- Medical College, Tianjin University, Tianjin 300072, China
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20
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Wang F, Zhao C, Zhao P, Chen F, Qiao D, Feng J. MoS 2 nanopore identifies single amino acids with sub-1 Dalton resolution. Nat Commun 2023; 14:2895. [PMID: 37210427 DOI: 10.1038/s41467-023-38627-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/09/2023] [Indexed: 05/22/2023] Open
Abstract
The sequencing of single protein molecules using nanopores is faced with a huge challenge due to the lack of resolution needed to resolve single amino acids. Here we report the direct experimental identification of single amino acids in nanopores. With atomically engineered regions of sensitivity comparable to the size of single amino acids, MoS2 nanopores provide a sub-1 Dalton resolution for discriminating the chemical group difference of single amino acids, including recognizing the amino acid isomers. This ultra-confined nanopore system is further used to detect the phosphorylation of individual amino acids, demonstrating its capability for reading post-translational modifications. Our study suggests that a sub-nanometer engineered pore has the potential to be applied in future chemical recognition and de novo protein sequencing at the single-molecule level.
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Affiliation(s)
- Fushi Wang
- Laboratory of Experimental Physical Biology, Department of Chemistry, Zhejiang University, 310027, Hangzhou, China
| | - Chunxiao Zhao
- Laboratory of Experimental Physical Biology, Department of Chemistry, Zhejiang University, 310027, Hangzhou, China
| | - Pinlong Zhao
- Laboratory of Experimental Physical Biology, Department of Chemistry, Zhejiang University, 310027, Hangzhou, China
| | - Fanfan Chen
- Laboratory of Experimental Physical Biology, Department of Chemistry, Zhejiang University, 310027, Hangzhou, China
| | - Dan Qiao
- Laboratory of Experimental Physical Biology, Department of Chemistry, Zhejiang University, 310027, Hangzhou, China
| | - Jiandong Feng
- Laboratory of Experimental Physical Biology, Department of Chemistry, Zhejiang University, 310027, Hangzhou, China.
- Research Center for Quantum Sensing, Research Institute of Intelligent Sensing, Zhejiang Lab, 311121, Hangzhou, China.
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21
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Yu C, Wang Y, Wu R, Li B. Single Molecular Nanopores as a Label-Free Method for Homogeneous Conformation Investigation and Anti-Interference Molecular Analysis. ACS Appl Mater Interfaces 2023; 15:23602-23612. [PMID: 37141628 DOI: 10.1021/acsami.3c01884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
In this paper, we propose a "reciprocal strategy" that, on the one hand, explores the ability of solid-state nanopores in a homogeneous high-fidelity characterization of nucleic acid assembly and, on the other hand, the formed nucleic acid assembly with a large size serves as an amplifier to provide a highly distinguished and anti-interference signal for molecular sensing. Four-hairpin hybridization chain reaction (HCR) with G-rich tail tags is taken as the proof-of-concept demonstration. G-rich tail tags are commonly used to form G-quadruplex signal probes on the side chain of HCR duplex concatemers. When such G-tailed HCR concatemers translocate the nanopore, abnormal, much higher nanopore signals over normal duplexes can be observed. Combined with atomic force microscopy, we reveal the G-rich tail may easily induce the "intermolecular interaction" between HCR concatemers to form "branched assembly structure (BAS)". To the best of our knowledge, this is the first evidence for the formation BAS of the G tailed HCR concatemers in a homogeneous solution. Systematic nanopore measurements further suggest the formation of these BASs is closely related to the types of salt ions, the amount of G, the concentration of substrate hairpins, the reaction time, and so forth. Under optimized conditions, these BASs can be grown to just the right size without being too large to block the pores, while producing a current 14 times that of conventional double-stranded chains. Here, these very abnormal large current blockages have, in turn, been taken as an anti-interference signal indicator for small targets in order to defend the high noises resulting from co-existing big species (e.g., enzymes or other long double-stranded DNA).
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Affiliation(s)
- Chunmiao Yu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, P. R. China
| | - Yesheng Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, P. R. China
| | - Ruiping Wu
- Department of Laboratory Medicine, The First Affiliated Hospital of Xi'an Medical University, Xi'an, Shaanxi 710077, P. R. China
| | - Bingling Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, P. R. China
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22
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Xie W, He S, Fang S, Yin B, Tian R, Wang Y, Wang D. Analysis of starch dissolved in ionic liquid by glass nanopore at single molecular level. Int J Biol Macromol 2023; 239:124271. [PMID: 37019197 DOI: 10.1016/j.ijbiomac.2023.124271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/06/2023] [Accepted: 03/27/2023] [Indexed: 04/05/2023]
Abstract
In this paper, the glass nanopore technology was proposed to detect a single molecule of starch dissolved in ionic liquid [1-butyl-3-methylimidazolium chloride (BmimCl)]. Firstly, the influence of BmimCl on nanopore detection is discussed. It is found that a certain amount of strong polar ionic liquids will disturb the charge distribution in nanopores and increase the detection noise. Then, by analysis of the characteristic current signal of the conical nanopore, the motion behaviour of starch near the entrance of the nanopore was studied and analysis the dominant ion of starch in the BmimCl dissolution process. Finally, based on nuclear magnetic resonance (NMR) and Fourier transform infrared (FTIR) spectroscopy simply discussed the mechanism of amylose and amylopectin dissolved in BmimCl. These results confirm that branched chain structure would affect the dissolution of polysaccharides in ionic liquids and the contribution of anions to the dissolution of polysaccharides are dominant. It is further proved that the current signal can be used to judge the charge and structure information of the analyte, and the dissolution mechanism can be assist analyzed at the single molecule level.
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23
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Singh SL, Chauhan K, Bharadwaj AS, Kishore V, Laux P, Luch A, Singh AV. Polymer Translocation and Nanopore Sequencing: A Review of Advances and Challenges. Int J Mol Sci 2023; 24:6153. [PMID: 37047125 PMCID: PMC10094227 DOI: 10.3390/ijms24076153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/01/2023] [Accepted: 02/28/2023] [Indexed: 03/31/2023] Open
Abstract
Various biological processes involve the translocation of macromolecules across nanopores; these pores are basically protein channels embedded in membranes. Understanding the mechanism of translocation is crucial to a range of technological applications, including DNA sequencing, single molecule detection, and controlled drug delivery. In this spirit, numerous efforts have been made to develop polymer translocation-based sequencing devices, these efforts include findings and insights from theoretical modeling, simulations, and experimental studies. As much as the past and ongoing studies have added to the knowledge, the practical realization of low-cost, high-throughput sequencing devices, however, has still not been realized. There are challenges, the foremost of which is controlling the speed of translocation at the single monomer level, which remain to be addressed in order to use polymer translocation-based methods for sensing applications. In this article, we review the recent studies aimed at developing control over the dynamics of polymer translocation through nanopores.
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Affiliation(s)
- Swarn Lata Singh
- Department of Physics, Mahila Mahavidyalaya (MMV), Banaras Hindu University, Varanasi 221005, UP, India
| | - Keerti Chauhan
- Department of Physics, Banaras Hindu University, Varanasi 221005, UP, India
| | - Atul S. Bharadwaj
- Department of Physics, CMP Degree College, University of Allahabad, Prayagraj 211002, UP, India
| | - Vimal Kishore
- Department of Physics, Banaras Hindu University, Varanasi 221005, UP, India
| | - Peter Laux
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR) Maxdohrnstrasse 8-10, 10589 Berlin, Germany
| | - Andreas Luch
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR) Maxdohrnstrasse 8-10, 10589 Berlin, Germany
| | - Ajay Vikram Singh
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR) Maxdohrnstrasse 8-10, 10589 Berlin, Germany
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24
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Aluru NR, Aydin F, Bazant MZ, Blankschtein D, Brozena AH, de Souza JP, Elimelech M, Faucher S, Fourkas JT, Koman VB, Kuehne M, Kulik HJ, Li HK, Li Y, Li Z, Majumdar A, Martis J, Misra RP, Noy A, Pham TA, Qu H, Rayabharam A, Reed MA, Ritt CL, Schwegler E, Siwy Z, Strano MS, Wang Y, Yao YC, Zhan C, Zhang Z. Fluids and Electrolytes under Confinement in Single-Digit Nanopores. Chem Rev 2023; 123:2737-2831. [PMID: 36898130 PMCID: PMC10037271 DOI: 10.1021/acs.chemrev.2c00155] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Confined fluids and electrolyte solutions in nanopores exhibit rich and surprising physics and chemistry that impact the mass transport and energy efficiency in many important natural systems and industrial applications. Existing theories often fail to predict the exotic effects observed in the narrowest of such pores, called single-digit nanopores (SDNs), which have diameters or conduit widths of less than 10 nm, and have only recently become accessible for experimental measurements. What SDNs reveal has been surprising, including a rapidly increasing number of examples such as extraordinarily fast water transport, distorted fluid-phase boundaries, strong ion-correlation and quantum effects, and dielectric anomalies that are not observed in larger pores. Exploiting these effects presents myriad opportunities in both basic and applied research that stand to impact a host of new technologies at the water-energy nexus, from new membranes for precise separations and water purification to new gas permeable materials for water electrolyzers and energy-storage devices. SDNs also present unique opportunities to achieve ultrasensitive and selective chemical sensing at the single-ion and single-molecule limit. In this review article, we summarize the progress on nanofluidics of SDNs, with a focus on the confinement effects that arise in these extremely narrow nanopores. The recent development of precision model systems, transformative experimental tools, and multiscale theories that have played enabling roles in advancing this frontier are reviewed. We also identify new knowledge gaps in our understanding of nanofluidic transport and provide an outlook for the future challenges and opportunities at this rapidly advancing frontier.
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Affiliation(s)
- Narayana R Aluru
- Oden Institute for Computational Engineering and Sciences, Walker Department of Mechanical Engineering, The University of Texas at Austin, Austin, 78712TexasUnited States
| | - Fikret Aydin
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
| | - Martin Z Bazant
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Daniel Blankschtein
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Alexandra H Brozena
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland20742, United States
| | - J Pedro de Souza
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Menachem Elimelech
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut06520-8286, United States
| | - Samuel Faucher
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - John T Fourkas
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland20742, United States
- Institute for Physical Science and Technology, University of Maryland, College Park, Maryland20742, United States
- Maryland NanoCenter, University of Maryland, College Park, Maryland20742, United States
| | - Volodymyr B Koman
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Matthias Kuehne
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Hao-Kun Li
- Department of Mechanical Engineering, Stanford University, Stanford, California94305, United States
| | - Yuhao Li
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
| | - Zhongwu Li
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
| | - Arun Majumdar
- Department of Mechanical Engineering, Stanford University, Stanford, California94305, United States
| | - Joel Martis
- Department of Mechanical Engineering, Stanford University, Stanford, California94305, United States
| | - Rahul Prasanna Misra
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - Aleksandr Noy
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
- School of Natural Sciences, University of California Merced, Merced, California95344, United States
| | - Tuan Anh Pham
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
| | - Haoran Qu
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland20742, United States
| | - Archith Rayabharam
- Oden Institute for Computational Engineering and Sciences, Walker Department of Mechanical Engineering, The University of Texas at Austin, Austin, 78712TexasUnited States
| | - Mark A Reed
- Department of Electrical Engineering, Yale University, 15 Prospect Street, New Haven, Connecticut06520, United States
| | - Cody L Ritt
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut06520-8286, United States
| | - Eric Schwegler
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
| | - Zuzanna Siwy
- Department of Physics and Astronomy, Department of Chemistry, Department of Biomedical Engineering, University of California, Irvine, Irvine92697, United States
| | - Michael S Strano
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts02139, United States
| | - YuHuang Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland20742, United States
- Maryland NanoCenter, University of Maryland, College Park, Maryland20742, United States
| | - Yun-Chiao Yao
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
- School of Natural Sciences, University of California Merced, Merced, California95344, United States
| | - Cheng Zhan
- Materials Science Division, Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, California94550, United States
| | - Ze Zhang
- Department of Mechanical Engineering, Stanford University, Stanford, California94305, United States
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25
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Abstract
Nanopores in thin membranes play important roles in science and industry. Single nanopores have provided a step-change in portable DNA sequencing and understanding nanoscale transport while multipore membranes facilitate food processing and purification of water and medicine. Despite the unifying use of nanopores, the fields of single nanopores and multipore membranes differ - to varying degrees - in terms of materials, fabrication, analysis, and applications. Such a partial disconnect hinders scientific progress as important challenges are best resolved together. This Viewpoint suggests how synergistic crosstalk between the two fields can provide considerable mutual benefits in fundamental understanding and the development of advanced membranes. We first describe the main differences including the atomistic definition of single pores compared to the less defined conduits in multipore membranes. We then outline steps to improve communication between the two fields such as harmonizing measurements and modelling of transport and selectivity. The resulting insight is expected to improve the rational design of porous membranes. The Viewpoint concludes with an outlook of other developments that can be best achieved by collaboration across the two fields to advance the understanding of transport in nanopores and create next-generation porous membranes tailored for sensing, filtration, and other applications.
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Affiliation(s)
- Zuzanna S Siwy
- Department of Physics and Astronomy, University of California, Irvine, USA.
| | - Merlin L Bruening
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, USA.
| | - Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, UK.
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26
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Abstract
Thin membranes are highly sought-after for nanopore-based single-molecule sensing, and fabrication of such membranes becomes challenging in the ≲10 nm thickness regime where a plethora of useful molecule information can be acquired by nanopore sensing. In this work, we present a scalable and controllable method to fabricate silicon nitride (SixNy) membranes with effective thickness down to ∼1.5 nm using standard silicon processing and chemical etching using hydrofluoric acid (HF). Nanopores were fabricated using the controlled breakdown method with estimated pore diameters down to ∼1.8 nm yielding events >500,000 and >1,800,000 from dsDNA and bovine serum albumin (BSA) protein, respectively, demonstrating the high-performance and extended lifetime of the pores fabricated through our membranes. We used two different compositions of SixNy for membrane fabrication (near-stoichiometric and silicon-rich SixNy) and compared them against commercial membranes. The final thicknesses of the membranes were measured using ellipsometry and were in good agreement with the values calculated from the bulk etch rates and DNA translocation characteristics. The stoichiometry and the density of the membrane layers were characterized with Rutherford backscattering spectrometry while the nanopores were characterized using pH-conductance, conductivity-conductance, and power spectral density (PSD) graphs.
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Affiliation(s)
- Shankar Dutt
- Department of Materials Physics, Research School of Physics, The Australian National University, Canberra, ACT 2601, Australia
| | - Buddini I Karawdeniya
- Department of Electronic Materials Engineering, Research School of Physics, The Australian National University, Canberra, ACT 2601, Australia
| | - Y M Nuwan D Y Bandara
- Department of Materials Physics, Research School of Physics, The Australian National University, Canberra, ACT 2601, Australia.,Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
| | - Nahid Afrin
- Department of Materials Physics, Research School of Physics, The Australian National University, Canberra, ACT 2601, Australia
| | - Patrick Kluth
- Department of Materials Physics, Research School of Physics, The Australian National University, Canberra, ACT 2601, Australia
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27
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Hu G, Yan H, Xi G, Gao Z, Wu Z, Lu Z, Tu J. Nanopore sensors for single molecular protein detection: Research progress based on computer simulations. IET Nanobiotechnol 2023; 17:257-268. [PMID: 36924083 DOI: 10.1049/nbt2.12124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/20/2023] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
As biological macromolecules, proteins are involved in important cellular functions ranging from DNA replication and biosynthesis to metabolic signalling and environmental sensing. Protein sequencing can help understand the relationship between protein function and structure, and provide key information for disease diagnosis and new drug design. Nanopore sensors are a novel technology to achieve the goal of label-free and high-throughput protein sequencing. In recent years, nanopore-based biosensors have been widely used in the detection and analysis of biomolecules such as DNA, RNA, and proteins. At the same time, computer simulations can describe the transport of proteins through nanopores at the atomic level. This paper reviews the applications of nanopore sensors in protein sequencing over the past decade and the solutions to key problems from a computer simulation perspective, with the aim of pointing the way to the future of nanopore protein sequencing.
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Affiliation(s)
- Gang Hu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Han Yan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Guohao Xi
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Zhuwei Gao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Ziqing Wu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Jing Tu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
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28
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Chen K, Choudhary A, Sandler SE, Maffeo C, Ducati C, Aksimentiev A, Keyser UF. Super-Resolution Detection of DNA Nanostructures Using a Nanopore. Adv Mater 2023; 35:e2207434. [PMID: 36630969 DOI: 10.1002/adma.202207434] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/28/2022] [Indexed: 06/17/2023]
Abstract
High-resolution analysis of biomolecules has brought unprecedented insights into fundamental biological processes and dramatically advanced biosensing. Notwithstanding the ongoing resolution revolution in electron microscopy and optical imaging, only a few methods are presently available for high-resolution analysis of unlabeled single molecules in their native states. Here, label-free electrical sensing of structured single molecules with a spatial resolution down to single-digit nanometers is demonstrated. Using a narrow solid-state nanopore, the passage of a series of nanostructures attached to a freely translocating DNA molecule is detected, resolving individual nanostructures placed as close as 6 nm apart and with a surface-to-surface gap distance of only 2 nm. Such super-resolution ability is attributed to the nanostructure-induced enhancement of the electric field at the tip of the nanopore. This work demonstrates a general approach to improving the resolution of single-molecule nanopore sensing and presents a critical advance towards label-free, high-resolution DNA sequence mapping, and digital information storage independent of molecular motors.
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Affiliation(s)
- Kaikai Chen
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Adnan Choudhary
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL, 61801, USA
| | - Sarah E Sandler
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Christopher Maffeo
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL, 61801, USA
| | - Caterina Ducati
- Department of Materials Science & Metallurgy, University of Cambridge, 27 Charles Babbage Road, Cambridge, CB3 0FS, UK
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL, 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N Mathews Avenue, Urbana, IL 61801, USA
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
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29
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Alibakhshi MA, Kang X, Clymer D, Zhang Z, Vargas A, Meunier V, Wanunu M. Scaled-Up Synthesis of Freestanding Molybdenum Disulfide Membranes for Nanopore Sensing. Adv Mater 2023; 35:e2207089. [PMID: 36580439 DOI: 10.1002/adma.202207089] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 12/08/2022] [Indexed: 06/17/2023]
Abstract
2D materials are ideal for nanopores with optimal detection sensitivity and resolution. Among these, molybdenum disulfide (MoS2 ) has gained traction as a less hydrophobic material than graphene. However, experiments using 2D nanopores remain challenging due to the lack of scalable methods for high-quality freestanding membranes. Herein, a site-directed, scaled-up synthesis of MoS2 membranes on predrilled nanoapertures on 4-inch wafer substrates with 75% yields is reported. Chemical vapor deposition (CVD), which introduces sulfur and molybdenum dioxide vapors across the sub-100 nm nanoapertures results in exclusive formation of freestanding membranes that seal the apertures. Nucleation and growth near the nanoaperture edges is followed by nanoaperture decoration with MoS2 , which proceeds until a critical flake curvature is achieved, after which fully spanning freestanding membranes form. Intentional blocking of reagent flow through the apertures inhibits MoS2 nucleation around the nanoapertures, promoting the formation of large-crystal monolayer MoS2 membranes. The in situ grown membranes along with facile membrane wetting and nanopore formation using dielectric breakdown enables the recording of dsDNA translocation events at an unprecedentedly high 1 MHz bandwidth. The methods presented here are important steps toward the development of scalable single-layer membrane manufacture for 2D nanofluidics and nanopore applications.
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Affiliation(s)
| | - Xinqi Kang
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA
| | - David Clymer
- Department of Physics, Applied Physics, and Astronomy, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Zhuoyu Zhang
- School of Physics, Nankai University, Tianjin, 300071, P.R. China
| | - Anthony Vargas
- Department of Physics, Northeastern University, Boston, MA, 02115, USA
| | - Vincent Meunier
- Department of Physics, Applied Physics, and Astronomy, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, MA, 02115, USA
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA
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30
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Huang C, Li Z, Zhu X, Ma X, Li N, Fan J. Two Detection Modes of Nanoslit Sensing Based on Planar Heterostructure of Graphene/Hexagonal Boron Nitride. ACS Nano 2023; 17:3301-3312. [PMID: 36638059 DOI: 10.1021/acsnano.2c05002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Solid-state nanopore sequencing is now confronted with problems of stochastic pore clogging and too fast speed during the DNA permeation through a nanopore, although this technique is revolutionary with long readability and high efficiency. These two problems are related to controlling molecular transportation during sequencing. To control the DNA motion and identify the four bases, we propose nanoslit sensing based on the planar heterostructure of two-dimensional graphene and hexagonal boron nitride. Molecular dynamics simulations are performed on investigating the motion of DNA molecules on the heterostructure with a nanoslit sensor. Results show that the DNA molecules are confined within the hexagonal boron nitride (HBN) domain of the heterostructure. And the confinement effects of the heterostructure can be optimized by tailoring the stripe length. Besides, there are two ways of DNA permeation through nanoslits: the DNA can cross or translocate the nanoslit under applied voltages along the y and z directions. The two detection modes are named cross-slit and trans-slit, respectively. In both modes, the ionic current drops can be observed when the nanoslit is occupied by the DNA. And the ionic currents and dwell times can be simultaneously detected to identify the four different DNA bases. This study can shed light on the sensing mechanism based on the nanoslit sensor of a planar heterostructure and provide theoretical guidance on designing devices controlling molecular transportation during nanopore sequencing.
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Affiliation(s)
- Changxiong Huang
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong, 999077, China
| | - Zhen Li
- School of Materials Science and Engineering, China University of Petroleum (East China), Qingdao266580, China
| | - Xiaohong Zhu
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong, 999077, China
| | - Xinyao Ma
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong, 999077, China
| | - Na Li
- School of Chemistry and Materials Science, Key Laboratory of Magnetic Molecules and Magnetic Information Materials of Ministry of Education, Shanxi Normal University, Taiyuan030000, China
| | - Jun Fan
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon, Hong Kong, 999077, China
- Center for Advanced Nuclear Safety and Sustainable Development, City University of Hong Kong, Kowloon, Hong Kong, 999077, China
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31
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Thakur M, Cai N, Zhang M, Teng Y, Chernev A, Tripathi M, Zhao Y, Macha M, Elharouni F, Lihter M, Wen L, Kis A, Radenovic A. High durability and stability of 2D nanofluidic devices for long-term single-molecule sensing. NPJ 2D Mater Appl 2023; 7:11. [PMID: 38665480 PMCID: PMC11041726 DOI: 10.1038/s41699-023-00373-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 02/10/2023] [Indexed: 04/28/2024]
Abstract
Nanopores in two-dimensional (2D) membranes hold immense potential in single-molecule sensing, osmotic power generation, and information storage. Recent advances in 2D nanopores, especially on single-layer MoS2, focus on the scalable growth and manufacturing of nanopore devices. However, there still remains a bottleneck in controlling the nanopore stability in atomically thin membranes. Here, we evaluate the major factors responsible for the instability of the monolayer MoS2 nanopores. We identify chemical oxidation and delamination of monolayers from their underlying substrates as the major reasons for the instability of MoS2 nanopores. Surface modification of the substrate and reducing the oxygen from the measurement solution improves nanopore stability and dramatically increases their shelf-life. Understanding nanopore growth and stability can provide insights into controlling the pore size, shape and can enable long-term measurements with a high signal-to-noise ratio and engineering durable nanopore devices.
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Affiliation(s)
- Mukeshchand Thakur
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, 1015 Lausanne, Switzerland
| | - Nianduo Cai
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, 1015 Lausanne, Switzerland
| | - Miao Zhang
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, 1015 Lausanne, Switzerland
| | - Yunfei Teng
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, 1015 Lausanne, Switzerland
- CAS Key Laboratory of Bio-Inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, 100190 Beijing, China
- School of Future Technology, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Andrey Chernev
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, 1015 Lausanne, Switzerland
| | - Mukesh Tripathi
- Laboratory of Nanoscale Electronics and Structure, Institute of Electrical Engineering and Institute of Materials Science and Engineering, School of Engineering, EPFL, 1015 Lausanne, Switzerland
| | - Yanfei Zhao
- Laboratory of Nanoscale Electronics and Structure, Institute of Electrical Engineering and Institute of Materials Science and Engineering, School of Engineering, EPFL, 1015 Lausanne, Switzerland
| | - Michal Macha
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, 1015 Lausanne, Switzerland
| | - Farida Elharouni
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, 1015 Lausanne, Switzerland
| | - Martina Lihter
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, 1015 Lausanne, Switzerland
| | - Liping Wen
- CAS Key Laboratory of Bio-Inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, 100190 Beijing, China
- School of Future Technology, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Andras Kis
- Laboratory of Nanoscale Electronics and Structure, Institute of Electrical Engineering and Institute of Materials Science and Engineering, School of Engineering, EPFL, 1015 Lausanne, Switzerland
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, 1015 Lausanne, Switzerland
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32
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Xiao Y, Xiong C, Chen MM, Wang S, Fu L, Zhang X. Structure modulation of two-dimensional transition metal chalcogenides: recent advances in methodology, mechanism and applications. Chem Soc Rev 2023; 52:1215-1272. [PMID: 36601686 DOI: 10.1039/d1cs01016f] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Together with the development of two-dimensional (2D) materials, transition metal dichalcogenides (TMDs) have become one of the most popular series of model materials for fundamental sciences and practical applications. Due to the ever-growing requirements of customization and multi-function, dozens of modulated structures have been introduced in TMDs. In this review, we present a systematic and comprehensive overview of the structure modulation of TMDs, including point, linear and out-of-plane structures, following and updating the conventional classification for silicon and related bulk semiconductors. In particular, we focus on the structural characteristics of modulated TMD structures and analyse the corresponding root causes. We also summarize the recent progress in modulating methods, mechanisms, properties and applications based on modulated TMD structures. Finally, we demonstrate challenges and prospects in the structure modulation of TMDs and forecast potential directions about what and how breakthroughs can be achieved.
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Affiliation(s)
- Yao Xiao
- Collaborative Innovation Centre for Advanced Organic Chemical Materials Co-Constructed by the Province and Ministry, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, P. R. China.
| | - Chengyi Xiong
- Collaborative Innovation Centre for Advanced Organic Chemical Materials Co-Constructed by the Province and Ministry, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, P. R. China.
| | - Miao-Miao Chen
- Collaborative Innovation Centre for Advanced Organic Chemical Materials Co-Constructed by the Province and Ministry, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, P. R. China.
| | - Shengfu Wang
- Collaborative Innovation Centre for Advanced Organic Chemical Materials Co-Constructed by the Province and Ministry, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, P. R. China.
| | - Lei Fu
- The Institute for Advanced Studies (IAS), Wuhan University, Wuhan 430072, P. R. China. .,College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China.
| | - Xiuhua Zhang
- Collaborative Innovation Centre for Advanced Organic Chemical Materials Co-Constructed by the Province and Ministry, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, P. R. China.
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Liu H, Zhou Q, Wang W, Fang F, Zhang J. Solid-State Nanopore Array: Manufacturing and Applications. Small 2023; 19:e2205680. [PMID: 36470663 DOI: 10.1002/smll.202205680] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Nanopore brings extraordinary properties for a variety of potential applications in various industrial sectors. Since manufacturing of solid-state nanopore is first reported in 2001, solid-state nanopore has become a hot topic in the recent years. An increasing number of manufacturing methods have been reported, with continuously decreased sizes from hundreds of nanometers at the beginning to ≈1 nm until recently. To enable more robust, sensitive, and reliable devices required by the industry, researchers have started to explore the possible methods to manufacture nanopore array which presents unprecedented challenges on the fabrication efficiency, accuracy and repeatability, applicable materials, and cost. As a result, the exploration of fabrication of nanopore array is still in the fledging period with various bottlenecks. In this article, a wide range of methods of manufacturing nanopores are summarized along with their achievable morphologies, sizes, inner structures for characterizing the main features, based on which the manufacturing of nanopore array is further addressed. To give a more specific idea on the potential applications of nanopore array, some representative practices are introduced such as DNA/RNA sequencing, energy conversion and storage, water desalination, nanosensors, nanoreactors, and dialysis.
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Affiliation(s)
- Hongshuai Liu
- Centre of Micro/Nano Manufacturing Technology (MNMT-Dublin), School of Mechanical and Materials Engineering, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Qin Zhou
- College of Basic Medicine, Harbin Medical University, No. 157 Baojian Road, Nangang District, Harbin, Heilongjiang, 150081, China
| | - Wei Wang
- School of Mechanical and Electrical Engineering, University of Electronic Science and Technology of China, 2006 Xiyuan Ave, Chengdu, Sichuan, 611731, China
| | - Fengzhou Fang
- Centre of Micro/Nano Manufacturing Technology (MNMT-Dublin), School of Mechanical and Materials Engineering, University College Dublin, Dublin, D04 V1W8, Ireland
- State Key Laboratory of Precision Measuring Technology and Instruments, Laboratory of Micro/Nano Manufacturing Technology (MNMT), Tianjin University, Tianjin, 300072, China
| | - Jufan Zhang
- Centre of Micro/Nano Manufacturing Technology (MNMT-Dublin), School of Mechanical and Materials Engineering, University College Dublin, Dublin, D04 V1W8, Ireland
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Zhou S, Hu Y, Xin W, Fu L, Lin X, Yang L, Hou S, Kong XY, Jiang L, Wen L. Surfactant-Assisted Sulfonated Covalent Organic Nanosheets: Extrinsic Charge for Improved Ion Transport and Salinity-Gradient Energy Harvesting. Adv Mater 2023; 35:e2208640. [PMID: 36457170 DOI: 10.1002/adma.202208640] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/11/2022] [Indexed: 06/17/2023]
Abstract
Charge-governed ion transport is the vital property of nanofluidic channels for salinity-gradient energy harvesting and other electrochemical energy conversion technologies. 2D nanofluidic channels constructed by nanosheets exhibit great superiority in ion selectivity, but a high ion transport rate remains challenging due to the insufficiency of intrinsic surface charge density in nanoconfinement. Herein, extrinsic surface charge into nanofluidic channels composed of surfactant-assisted sulfonated covalent organic nanosheets (SCONs), which enable tunable ion transport behaviors, is demonstrated. The polar moiety of surfactant is embedded in SCONs to adjust in-plane surface charges, and the aggregation of nonpolar moiety results in the sol-to-gel transformation of SCON solution for membrane fabrication. The combination endows SCON/surfactant membranes with considerable water-resistance, and the designable extrinsic charges promise fast ion transport and high ion selectivity. Additionally, the SCON/surfactant membrane, serving as a power generator, exhibits huge potential in harvesting salinity-gradient energy where corresponding output power density can reach up to 9.08 W m-2 under a 50-fold salinity gradient (0.5 m NaCl|0.01 m NaCl). The approach to extrinsic surface charge provides new and promising insight into regulating ion transport behaviors.
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Affiliation(s)
- Shengyang Zhou
- Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yuhao Hu
- Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Weiwen Xin
- Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Lin Fu
- Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Xiangbin Lin
- Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Linsen Yang
- Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Shuhua Hou
- Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Xiang-Yu Kong
- Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Lei Jiang
- Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Liping Wen
- Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
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Maier FC, Fyta M. Electronic analysis of hydrogen-bonded molecular complexes: the case of DNA sensed in a functionalized nanogap. RSC Adv 2023; 13:2530-2537. [PMID: 36741157 PMCID: PMC9844209 DOI: 10.1039/d2ra06928h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/29/2022] [Indexed: 01/19/2023] Open
Abstract
DNA nucleotides can be interrogated by nanomaterials in order to be detected. With the aid of quantum-mechanical simulations, we unravel the intrinsic details of the electronic transport across nanoelectrodes functionalized with tiny modified diamond-like molecules. These electrodes generate a gap in which DNA nucleotides are placed and can be identified. The identification is strongly affected by the hydrogen bonding characteristics of the diamond-like particle and the nucleotides. The results point to the connection of the electronic transmission across the functionalized nanogap and the electronic and bonding characteristics of the molecular complexes within the nanogap. Specifically, our discussion focuses on the influence of the DNA dynamics on the electronic signals across the nanogap. We identify the molecular complex's details that hinder or promote the electronic transport through an analysis that moves from the bonding within the molecular complex up to the electronic current that this can accommodate. Accordingly, our work discusses pathways for analyzing hydrogen-bonded molecular complexes or molecules hydrogen-bonded to a material part having the optimization of the design of biosensing nanogaps and read-out nanopores in mind. The presented approach, though, is applicable to a wide range of applications utilizing exactly the bio/nano interface.
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Affiliation(s)
- Frank C. Maier
- Institute for Computational Physics, University of StuttgartAllmandring 370569 StuttgartGermany
| | - Maria Fyta
- Institute for Computational Physics, University of StuttgartAllmandring 370569 StuttgartGermany,Computational Biotechnology, RWTH Aachen UniversityWorringerweg 3AachenGermany
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Wang Y, Zhu Z, Yu C, Wu R, Zhu J, Li B. Lego-Like Catalytic Hairpin Assembly Enables Controllable DNA-Oligomer Formation and Spatiotemporal Amplification in Single Molecular Signaling. Small 2023; 19:e2206283. [PMID: 36436946 DOI: 10.1002/smll.202206283] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/14/2022] [Indexed: 06/16/2023]
Abstract
While the solid-state nanopore shows increasing potential during sensitive and label-free single molecular analysis, target concentration and signal amplification method is in urgent need. In this article, a solution via designing a model nucleic acid circuit reaction that can produce "Y" shape-structure three-way DNA oligomers with controllable size and polymerization degree is proposed. Such a so-called lego-like three-way catalytic hairpin assembly (LK-3W-CHA) can provide both concentration amplification (via CHA circuit) and programmable size control (via lego-like building mode) to enhance spatiotemporal resolution in single molecular sensing of solid-state nanopore. Oligomers containing 1-4 DNA three-way junctions (Y monomers, Y1-Y4) are designed in proof-of-concept experiments and applications. When the oligomers are applied to direct translocation measurements, Y2-Y4 can significantly increase the signal resolution and stability than that of Y1. Meanwhile, Y1 to Y4 can be used as the tags on the long DNA carrier to provide very legible secondary signals for specific identification, multiple assays, and information storage. Compared with other possible tags, Y1-Y4 provides higher signal density and amplitude, and quasi-linear "inner reference" for each other, which may provide more systematic, reliable, and controllable experimental results.
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Affiliation(s)
- Yesheng Wang
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
- University of Science & Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Zhentong Zhu
- Key Laboratory of Bioelectrochemistry & Environmental Analysis of Gansu Province, College of Chemistry & Chemical Engineering, Northwest Normal University, Lanzhou, Gansu, 730070, P. R. China
| | - Chunmiao Yu
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
- University of Science & Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Ruiping Wu
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
- University of Science & Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Jinbo Zhu
- Cavendish Lab, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Bingling Li
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
- University of Science & Technology of China, Hefei, Anhui, 230026, P. R. China
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Wang Y, Fan P, Zhang S, Wang L, Li X, Jia W, Liu Y, Wang K, Du X, Zhang P, Huang S. Discrimination of Ribonucleoside Mono-, Di-, and Triphosphates Using an Engineered Nanopore. ACS Nano 2022; 16:21356-21365. [PMID: 36475606 DOI: 10.1021/acsnano.2c09662] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Ribonucleotides, which widely exist in all living organisms and are essential to both physiological and pathological processes, can naturally appear as ribonucleoside mono-, di-, and triphosphates. Natural ribonucleotides can also dynamically switch between different phosphorylated forms, posing a great challenge for sensing. A specially engineered nanopore sensor is promising for full discrimination of all canonical ribonucleoside mono-, di-, and triphosphates. However, such a demonstration has never been reported, due to the lack of a suitable nanopore sensor that has a sufficient resolution. In this work, we utilized a phenylboronic acid (PBA) modified Mycobacterium smegmatis porin A (MspA) hetero-octamer for ribonucleotide sensing. Twelve types of ribonucleotides, including mono-, di-, and triphosphates of cytidine (CMP, CDP, CTP), uridine (UMP, UDP, UTP), adenosine (AMP, ADP, ATP), and guanosine (GMP, GDP, GTP) were simultaneously discriminated. A machine-learning algorithm was also developed, which achieved a general accuracy of 99.9% for ribonucleotide sensing. This strategy was also further applied to identify ribonucleotide components in ATP tablets and injections. This sensing strategy provides a direct, accurate, easy, and rapid solution to characterize ribonucleotide components in different phosphorylated forms.
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Affiliation(s)
- Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People's Republic of China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, People's Republic of China
| | - Pingping Fan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People's Republic of China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, People's Republic of China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People's Republic of China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, People's Republic of China
| | - Liying Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People's Republic of China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, People's Republic of China
| | - Xinyue Li
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People's Republic of China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, People's Republic of China
| | - Wendong Jia
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People's Republic of China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, People's Republic of China
| | - Yao Liu
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People's Republic of China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, People's Republic of China
| | - Kefan Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People's Republic of China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, People's Republic of China
| | - Xiaoyu Du
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People's Republic of China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, People's Republic of China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People's Republic of China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, People's Republic of China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023 Nanjing, People's Republic of China
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38
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Offenbartl‐Stiegert D, Rottensteiner A, Dorey A, Howorka S. A Light-Triggered Synthetic Nanopore for Controlling Molecular Transport Across Biological Membranes. Angew Chem Int Ed Engl 2022; 61:e202210886. [PMID: 36318092 PMCID: PMC10098474 DOI: 10.1002/anie.202210886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Indexed: 11/06/2022]
Abstract
Controlling biological molecular processes with light is of interest in biological research and biomedicine, as light allows precise and selective activation in a non-invasive and non-toxic manner. A molecular process benefitting from light control is the transport of cargo across biological membranes, which is conventionally achieved by membrane-puncturing barrel-shaped nanopores. Yet, there is also considerable gain in constructing more complex gated pores. Here, we pioneer a synthetic light-gated nanostructure which regulates transport across membranes via a controllable lid. The light-triggered nanopore is self-assembled from six pore-forming DNA strands and a lid strand carrying light-switchable azobenzene molecules. Exposure to light opens the pore to allow small-molecule transport across membranes. Our light-triggered pore advances biomimetic chemistry and DNA nanotechnology and may be used in biotechnology, biosensing, targeted drug release, or synthetic cells.
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Affiliation(s)
- Daniel Offenbartl‐Stiegert
- Department of ChemistryInstitute for Structural and Molecular BiologyUniversity College LondonWC1H0AJLondonUK
| | - Alexia Rottensteiner
- Department of ChemistryInstitute for Structural and Molecular BiologyUniversity College LondonWC1H0AJLondonUK
| | - Adam Dorey
- Department of ChemistryInstitute for Structural and Molecular BiologyUniversity College LondonWC1H0AJLondonUK
| | - Stefan Howorka
- Department of ChemistryInstitute for Structural and Molecular BiologyUniversity College LondonWC1H0AJLondonUK
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39
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Gu C, Yu Z, Li X, Zhu X, Jin C, Cao Z, Dong S, Luo J, Ye Z, Liu Y. Experimental study on single biomolecule sensing using MoS 2-graphene heterostructure nanopores. Nanoscale 2022; 15:266-274. [PMID: 36477179 DOI: 10.1039/d2nr04485d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Solid-state nanopores play an important role in sensing single-biomolecules such as DNA and proteins. However, an ultra-short translocation time hinders nanopores from acquiring more detailed information about biomolecules, and further applications such as sequencing and molecular structure analysis are limited. Related studies have shown that MoS2 has no obvious impediment to biomolecule translocation while graphene may cause obstacles to this process. By combining these two-dimensional materials, nanopores might slow the biomolecule passage. Herein, we fabricated sub-10 nm ultra-thin MoS2-graphene heterostructure nanopores with high stability and tested both dsDNA and native protein (BSA) at the single-molecule level in experiments for the first time. Some special signals with advanced order are observed, which may reflect the shape change of the BSA molecules during the slow translocation process. The results show that the translocation time of BSA is slowed down up to more than 100 ms and the signal length and form are determined by the extent of interaction between the BSA and the heterostructure nanopore. The weak interaction between the BSA and the MoS2 layer increases the translocation probability, and meanwhile, the strong interaction of the graphene layer to BSA slows down the translocation and changes its structure. Therefore, our findings indicate the possibilities of slowing down the single-biomolecule translocation and the capability of acquiring more detailed information about biomolecules using MoS2-graphene heterostructure nanopores.
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Affiliation(s)
- Chaoming Gu
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China.
- International Joint Innovation Centre, Haining 314400, P. R. China
| | - Zhoubin Yu
- State Key Laboratory of Silicon Materials, School of Materials Science and Engineering, Zhejiang University, Hangzhou 310027, P. R. China
| | - Xiaojie Li
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China.
- International Joint Innovation Centre, Haining 314400, P. R. China
| | - Xin Zhu
- Chemistry Research Laboratory, Oxford University, Oxford, OX1 3TA, UK
| | - Chuanhong Jin
- State Key Laboratory of Silicon Materials, School of Materials Science and Engineering, Zhejiang University, Hangzhou 310027, P. R. China
| | - Zhen Cao
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China.
- International Joint Innovation Centre, Haining 314400, P. R. China
| | - Shurong Dong
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China.
- International Joint Innovation Centre, Haining 314400, P. R. China
| | - Jikui Luo
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China.
- International Joint Innovation Centre, Haining 314400, P. R. China
| | - Zhi Ye
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China.
- International Joint Innovation Centre, Haining 314400, P. R. China
| | - Yang Liu
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China.
- International Joint Innovation Centre, Haining 314400, P. R. China
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40
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Zheng X, Liu J, Li M, Hua Y, Liang X, Zhang S, Zhang X, Shao Y. Dual-Nanopipettes for the Detection of Single Nanoparticles and Small Molecules. Anal Chem 2022; 94:17431-17438. [PMID: 36495265 DOI: 10.1021/acs.analchem.2c03344] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nanopore sensing is blooming due to its label-free and high sensitivity features. As a novel nanopore, a droplet is formed at the orifice of a dual-nanopipette, which allows for the translocation of analytes through the two channels at a relatively low speed and the promotion of signal-to-noise ratio. However, nanopore sensing based on the principle of current blockage requires the pore size to be comparable to that of the single entity, which poses a huge challenge for the direct detection of small molecules. In this work, gold nanoparticles (Au NPs) modified with sulfhydryl poly(ethylene glycol) (PEG-SH) or aptamers were detected successfully. The size difference of Au NPs and the interaction between Au NPs and dual-nanopipettes could be distinguished sensitively. Furthermore, Au NPs modified with designed aptamers will produce different blocking current after capturing the corresponding small molecules (e.g., dopamine and serotonin). Even non-electroactive ions, such as potassium ions, can also be detected, which is difficult to sense based on redox reactions, and further illustrates that the change of surface properties of nanoparticles is responsible for the detection. This work expands the application of nanopipette sensing for Au NPs and provides a universal platform for the small-molecule detection, which has the potential application in biosensing.
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Affiliation(s)
- Xinhe Zheng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Junjie Liu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Mingzhi Li
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yutong Hua
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xu Liang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Shudong Zhang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xianhao Zhang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yuanhua Shao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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41
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Dai Y, Zhang Y, Ma Q, Lin M, Zhang X, Xia F. Inner Wall and Outer Surface Distinguished Solid-State Nanopores for Sensing. Anal Chem 2022; 94:17343-17348. [PMID: 36473027 DOI: 10.1021/acs.analchem.2c04216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Solid-state nanopores, inspired by biological nanopores, have the advantages of good mechanical properties, stability, and easy modification. They have attracted wide attention in the fields of sequencing, sensing, molecular sieving, nanofluidic devices, nanoelectrochemistry, and energy conversion. Because of the ion/molecule transport characteristic of the pore, the research on solid-state nanopores mainly focuses on the functional modification of its inner wall. In recent years, the outer surface of nanopores has also attracted the attention of researchers, and the functional elements on the outer surface have the functions of anti-interference and ionic signal enhancement. In this perspective, we review research progress of inner wall and outer surface distinguished solid-state nanopores, highlight their processing and advantages, summarize their functions and applications in sensing, and give insight into further research.
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Affiliation(s)
- Yu Dai
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P. R. China
| | - Yiwei Zhang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P. R. China
| | - Qun Ma
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P. R. China
| | - Meihua Lin
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P. R. China
| | - Xiaojin Zhang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P. R. China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P. R. China
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42
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Xu T, Tu Y, Zhu Y, Shen Y, Yin K, Sun L. Nucleation and growth of stacking-dependent nanopores in bilayer h-BN. Nanoscale 2022; 14:17182-17187. [PMID: 36385277 DOI: 10.1039/d2nr05311j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The nucleation and growth of well-defined nanopores are presented under electron irradiation in h-BN bilayers with various stacking angles. The pores are initiated by the formation of boron vacancies in each basal layer, and then evolve into either triangular or hexagonal pores, which is dependent on the relative rotation between BN layers. The result may shed light on the rational design and fabrication of nanopores.
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Affiliation(s)
- Tao Xu
- SEU-FEI Nano-Pico Center, Key Lab of MEMS of Ministry of Education, Southeast University, Nanjing 210096, P. R. China.
| | - Yizhi Tu
- SEU-FEI Nano-Pico Center, Key Lab of MEMS of Ministry of Education, Southeast University, Nanjing 210096, P. R. China.
| | - Yatong Zhu
- SEU-FEI Nano-Pico Center, Key Lab of MEMS of Ministry of Education, Southeast University, Nanjing 210096, P. R. China.
| | - Yuting Shen
- College of Physics and Electronic Engineering, Changshu Institute of Technology, Changshu 215500, P. R. China
| | - Kuibo Yin
- SEU-FEI Nano-Pico Center, Key Lab of MEMS of Ministry of Education, Southeast University, Nanjing 210096, P. R. China.
| | - Litao Sun
- SEU-FEI Nano-Pico Center, Key Lab of MEMS of Ministry of Education, Southeast University, Nanjing 210096, P. R. China.
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Tsutsui M, Yokota K, He Y, Kawai T. Ionic Signal Amplification of DNA in a Nanopore. Small Methods 2022; 6:e2200761. [PMID: 36196624 DOI: 10.1002/smtd.202200761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/06/2022] [Indexed: 06/16/2023]
Abstract
Ionic signal amplification is a key challenge for single-molecule analyses by solid-state nanopore sensing. Here, a permittivity gradient approach for amplifying ionic blockade characteristics of DNA in a nanofluidic channel is reported. The transmembrane ionic current response is found to change substantially through modifying the liquid permittivity at one side of a pore with an organic solvent. Imposing positive liquid permittivity gradients with respect to the direction of DNA electrophoresis, this study observes the resistive ionic signals to become larger due to the varying contributions of molecular counterions. On the contrary, negative gradients render adverse effects causing conductive ionic current pulses upon polynucleotide translocations. Most importantly, both the positive and negative gradients are demonstrated to be capable of amplifying the ionic signals by an order of magnitude with a 1.3-fold difference in the transmembrane liquid dielectric constants. This phenomenon allows a novel way to enhance the single-molecule sensitivity of nanopore sensing that may be useful in analyzing secondary structures and genome sequence of DNA by ionic current measurements.
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Affiliation(s)
- Makusu Tsutsui
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka, 567-0047, Japan
| | - Kazumichi Yokota
- National Institute of Advanced Industrial Science and Technology, Takamatsu, Kagawa, 761-0395, Japan
| | - Yuhui He
- Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Tomoji Kawai
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka, 567-0047, Japan
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44
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Macha M, Marion S, Tripathi M, Thakur M, Lihter M, Kis A, Smolyanitsky A, Radenovic A. High-Throughput Nanopore Fabrication and Classification Using Xe-Ion Irradiation and Automated Pore-Edge Analysis. ACS Nano 2022; 16:16249-16259. [PMID: 36153997 DOI: 10.1021/acsnano.2c05201] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Large-area nanopore drilling is a major bottleneck in state-of-the-art nanoporous 2D membrane fabrication protocols. In addition, high-quality structural and statistical descriptions of as-fabricated porous membranes are key to predicting the corresponding membrane-wide permeation properties. In this work, we investigate Xe-ion focused ion beam as a tool for scalable, large-area nanopore fabrication on atomically thin, free-standing molybdenum disulfide. The presented irradiation protocol enables designing ultrathin membranes with tunable porosity and pore dimensions, along with spatial uniformity across large-area substrates. Fabricated nanoporous membranes are then characterized using scanning transmission electron microscopy imaging, and the observed nanopore geometries are analyzed through a pore-edge detection and analysis script. We further demonstrate that the obtained structural and statistical data can be readily passed on to computational and analytical tools to predict the permeation properties at both individual pore and membrane-wide scales. As an example, membranes featuring angstrom-scale pores are investigated in terms of their emerging water and ion flow properties through extensive all-atom molecular dynamics simulations. We believe that the combination of experimental and analytical approaches presented here will yield accurate physics-based property estimates and thus potentially enable a true function-by-design approach to fabrication for applications such as osmotic power generation and desalination/filtration.
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Affiliation(s)
- Michal Macha
- Laboratory of Nanoscale Biology, Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Sanjin Marion
- Laboratory of Nanoscale Biology, Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, 1015, Switzerland
- Interuniversity Microelectronics Centre (IMEC), Kapeldreef 75, B-3001 Leuven, Belgium
| | - Mukesh Tripathi
- Laboratory of Nanoscale Electronics and Structures, Electrical Engineering Institute and Institute of Materials Science Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Mukeshchand Thakur
- Laboratory of Nanoscale Biology, Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Martina Lihter
- Laboratory of Nanoscale Biology, Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Andras Kis
- Laboratory of Nanoscale Electronics and Structures, Electrical Engineering Institute and Institute of Materials Science Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Alex Smolyanitsky
- National Institute of Standards and Technology, Applied Chemicals and Materials Division, 325 Broadway, Boulder, Colorado 80305, United States
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, 1015, Switzerland
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45
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Sun Z, Liu X, Liu W, Li J, Yang J, Qiao F, Ma J, Sha J, Li J, Xu LQ. AutoNanopore: An Automated Adaptive and Robust Method to Locate Translocation Events in Solid-State Nanopore Current Traces. ACS Omega 2022; 7:37103-37111. [PMID: 36312336 PMCID: PMC9608407 DOI: 10.1021/acsomega.2c02927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Solid-state nanopore sequencing has shown impressive performances in several research scenarios but is still challenging, mainly due to the ultrafast speed of DNA translocation and significant noises embedded in raw signals. Hence, event detection, aiming to locate precisely these translocation events, is the fundamental step of data analysis. However, existing event detection methods use either a user-defined global threshold or an adaptive threshold determined by the data, assuming the baseline current to be stable over time. These disadvantages limit their applications in real-world application scenarios, especially considering that the results of different methods are often inconsistent. In this study, we develop an automated adaptive method called AutoNanopore, for fast and accurate event detection in current traces. The method consists of three consecutive steps: current trace segmentation, current amplitude outlier identification by straightforward statistical analyses, and event characterization. Then we propose ideas/metrics on how to quantitatively evaluate the performance of an event detection method, followed by comparing the performance of AutoNanopore against two state-of-the-art methods, OpenNanopore and EventPro. Finally, we examine if one method can detect the overlapping events detected by the other two, demonstrating that AutoNanopore has the highest coverage ratio. Moreover, AutoNanopore also performs well in detecting challenging events: e.g., those with significantly varying baselines.
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Affiliation(s)
- Zepeng Sun
- China
Mobile (Chengdu) Industrial Research Institute, Chengdu610000, People’s Republic of China
| | - Xinlong Liu
- China
Mobile (Chengdu) Industrial Research Institute, Chengdu610000, People’s Republic of China
| | - Wei Liu
- Jiangsu
Key Laboratory for Design and Manufacture of Micro-Nano Biomedical
Instruments, School of Mechanical Engineering, Southeast University, Nanjing210096, People’s Republic
of China
| | - Jiahui Li
- China
Mobile (Chengdu) Industrial Research Institute, Chengdu610000, People’s Republic of China
| | - Jing Yang
- Key
Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing210096, People’s Republic of China
| | - Feng Qiao
- China
Mobile (Chengdu) Industrial Research Institute, Chengdu610000, People’s Republic of China
| | - Jianjun Ma
- China
Mobile (Chengdu) Industrial Research Institute, Chengdu610000, People’s Republic of China
| | - Jingjie Sha
- Jiangsu
Key Laboratory for Design and Manufacture of Micro-Nano Biomedical
Instruments, School of Mechanical Engineering, Southeast University, Nanjing210096, People’s Republic
of China
| | - Jian Li
- Key
Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing210096, People’s Republic of China
| | - Li-Qun Xu
- China
Mobile (Chengdu) Industrial Research Institute, Chengdu610000, People’s Republic of China
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46
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Wang Y, Zhang S, Jia W, Fan P, Wang L, Li X, Chen J, Cao Z, Du X, Liu Y, Wang K, Hu C, Zhang J, Hu J, Zhang P, Chen HY, Huang S. Identification of nucleoside monophosphates and their epigenetic modifications using an engineered nanopore. Nat Nanotechnol 2022; 17:976-983. [PMID: 35851382 DOI: 10.1038/s41565-022-01169-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/01/2022] [Indexed: 05/25/2023]
Abstract
RNA modifications play critical roles in the regulation of various biological processes and are associated with many human diseases. Direct identification of RNA modifications by sequencing remains challenging, however. Nanopore sequencing is promising, but the current strategy is complicated by sequence decoding. Sequential nanopore identification of enzymatically cleaved nucleoside monophosphates may simultaneously provide accurate sequence and modification information. Here we show a phenylboronic acid-modified hetero-octameric Mycobacterium smegmatis porin A nanopore, with which direct distinguishing between monophosphates of canonical nucleosides, 5-methylcytidine, N6-methyladenosine, N7-methylguanosine, N1-methyladenosine, inosine, pseudouridine and dihydrouridine was achieved. A custom machine learning algorithm, which reports an accuracy of 0.996, was also applied to the quantitative analysis of modifications in microRNA and natural transfer RNA. It is generally suitable for sensing of a variety of other nucleoside or nucleotide derivatives and may bring new insights to epigenetic RNA sequencing.
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Affiliation(s)
- Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Wendong Jia
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Pingping Fan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Liying Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Xinyue Li
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Jialu Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Zhenyuan Cao
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Xiaoyu Du
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Yao Liu
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Kefan Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Chengzhen Hu
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Jinyue Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Jun Hu
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China.
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China.
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47
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Al Nasser HA, Kim C, Li Q, Bissett MA, Haigh SJ, Dryfe RA. The modified liquid | liquid interface: An electrochemical route for the electrode-less synthesis of MoS2 metal composite thin films. Electrochim Acta 2022. [DOI: 10.1016/j.electacta.2022.140609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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48
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Xia Z, Patchin M, McKay CP, Drndić M. Deoxyribonucleic Acid Extraction from Mars Analog Soils and Their Characterization with Solid-State Nanopores. Astrobiology 2022; 22:992-1008. [PMID: 35731031 DOI: 10.1089/ast.2021.0051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Life detection on Mars is an important topic that includes a direct search for biomarkers. This requires instruments for in situ biomarker detection that are compact, lightweight, and able to withstand operations in space. Solid-state nanopores are excellent candidates that allow fast single-molecule detection. They can withstand high temperatures and be sterilized to minimize planetary contamination. The instruments are portable with low-power requirements. We demonstrate a few key results in advancing the use of nanopores for in-space applications. First, we developed modified deoxyribonucleic acid (DNA) extraction protocols to extract DNA from Mars analog soils. Second, we used silicon nitride nanopores to demonstrate the detection of extracted DNA and corresponding current characteristics. The yields and properties of extracted DNA (e.g., estimated diameters) varied somewhat by soil types, extraction methods, and nanopores used. The yields varied from a minimum of 0.9 ng DNA/g soil for a magnesium carbonate sample from Lake Salda to a maximum of 210 ng DNA/g soil for a calcium carbonate sample from Trona Pinnacles. For a given soil type, yields from different methods varied by a factor of up to 50. These observations motivate future studies with a broader range of Mars-like soils and improved instruments to increase signal-to-noise-ratio at higher measurement bandwidths.
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Affiliation(s)
- Zehui Xia
- Goeppert LLC, Pennovation Works, Philadelphia, Pennsylvania, USA
| | - Margaret Patchin
- Goeppert LLC, Pennovation Works, Philadelphia, Pennsylvania, USA
| | - Christopher P McKay
- Space Science Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Marija Drndić
- David Rittenhouse Laboratory, Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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49
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Gu Z, He Z, Chen F, Meng L, Feng J, Zhou R. Ionic Liquid Decelerates Single-Stranded DNA Transport through Molybdenum Disulfide Nanopores. ACS Appl Mater Interfaces 2022; 14:32618-32624. [PMID: 35798544 DOI: 10.1021/acsami.2c03335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Nanopores in two-dimensional (2D) materials have emerged to offer in principle necessary spatial resolution for high-throughput DNA sequencing. However, their fidelity is severely limited by the fast DNA translocation. A recent experiment indicates that introducing ionic liquids could slow down DNA translocation in a MoS2 nanopore. However, the corresponding in-depth molecular mechanism underlying the experimental findings is not fully understood, which is crucial for the future improvement of rational DNA translocation control. Here, we computationally investigate and then experimentally identify the effect of BmimCl ionic liquid on the retardation of ssDNA translocation through a single-layer MoS2 nanopore. Our all-atom molecular dynamics simulations demonstrate that the strong interaction between Bmim+ and ssDNA offers a considerable dragging force to decelerate the electrophoretic motion of ssDNA in the BmimCl solution. Moreover, we show that Bmim+ ions exhibit preferential binding on the sulfur edges of the nanopore. These Bmim+ in the pore region can not only act as a steric blockage but also form π-π stackings with nucleobases, which provide a further restriction on the ssDNA motion. Therefore, our molecular dynamics simulation investigations deepen the understanding of the critical role of ionic liquid in DNA translocation through a nanopore from a molecular landscape, which may benefit practical implementations of ionic liquids in nanopore sequencing.
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Affiliation(s)
- Zonglin Gu
- Institute of Quantitative Biology, Department of Physics, and College of Life Sciences, Zhejiang University, 310027 Hangzhou, China
| | - Zhi He
- Institute of Quantitative Biology, Department of Physics, and College of Life Sciences, Zhejiang University, 310027 Hangzhou, China
| | - Fanfan Chen
- Laboratory of Experimental Physical Biology, Department of Chemistry, Zhejiang University, 310027 Hangzhou, China
| | - Lijun Meng
- Institute of Quantitative Biology, Department of Physics, and College of Life Sciences, Zhejiang University, 310027 Hangzhou, China
| | - Jiandong Feng
- Laboratory of Experimental Physical Biology, Department of Chemistry, Zhejiang University, 310027 Hangzhou, China
| | - Ruhong Zhou
- Institute of Quantitative Biology, Department of Physics, and College of Life Sciences, Zhejiang University, 310027 Hangzhou, China
- Shanghai Institute for Advanced Study, Zhejiang University, 201203 Shanghai, China
- Department of Chemistry, Colombia University, New York City, New York 10027, United States
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50
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Hazra S, Zhang C, Wu Q, Asheghi M, Goodson K, Dede EM, Palko J, Narumanchi S. A novel hardmask-to-substrate pattern transfer method for creating 3D, multi-level, hierarchical, high aspect-ratio structures for applications in microfluidics and cooling technologies. Sci Rep 2022; 12:12180. [PMID: 35842450 PMCID: PMC9288478 DOI: 10.1038/s41598-022-16281-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/07/2022] [Indexed: 11/14/2022] Open
Abstract
This letter solves a major hurdle that mars photolithography-based fabrication of micro-mesoscale structures in silicon. Conventional photolithography is usually performed on smooth, flat wafer surfaces to lay a 2D design and subsequently etch it to create single-level features. It is, however, unable to process non-flat surfaces or already etched wafers and create more than one level in the structure. In this study, we have described a novel cleanroom-based process flow that allows for easy creation of such multi-level, hierarchical 3D structures in a substrate. This is achieved by introducing an ultra-thin sacrificial silicon dioxide hardmask layer on the substrate which is first 3D patterned via multiple rounds of lithography. This 3D pattern is then scaled vertically by a factor of 200–300 and transferred to the substrate underneath via a single shot deep etching step. The proposed method is also easily characterizable—using features of different topographies and dimensions, the etch rates and selectivities were quantified; this characterization information was later used while fabricating specific target structures. Furthermore, this study comprehensively compares the novel pattern transfer technique to already existing methods of creating multi-level structures, like grayscale lithography and chip stacking. The proposed process was found to be cheaper, faster, and easier to standardize compared to other methods—this made the overall process more reliable and repeatable. We hope it will encourage more research into hybrid structures that hold the key to dramatic performance improvements in several micro-mesoscale devices.
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Affiliation(s)
- Sougata Hazra
- Department of Mechanical Engineering, Stanford University, Stanford, USA.
| | - Chi Zhang
- Department of Mechanical Engineering, Stanford University, Stanford, USA
| | - Qianying Wu
- Department of Mechanical Engineering, Stanford University, Stanford, USA
| | - Mehdi Asheghi
- Department of Mechanical Engineering, Stanford University, Stanford, USA
| | - Kenneth Goodson
- Department of Mechanical Engineering, Stanford University, Stanford, USA
| | - Ercan M Dede
- Electronics Research Department, Toyota Research Institute of North America, Ann Arbor, MI, USA
| | - James Palko
- Department of Mechanical Engineering, University of California-Merced, Merced, CA, USA
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