1
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Wen C, Schmid S, Dekker C. Understanding Electrophoresis and Electroosmosis in Nanopore Sensing with the Help of the Nanopore Electro-Osmotic Trap. ACS NANO 2024; 18:20449-20458. [PMID: 39051760 PMCID: PMC11308919 DOI: 10.1021/acsnano.4c04788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/11/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024]
Abstract
Nanopore technology is widely used for sequencing DNA, RNA, and peptides with single-molecule resolution, for fingerprinting single proteins, and for detecting metabolites. However, the molecular driving forces controlling the analyte capture, its residence time, and its escape have remained incompletely understood. The recently developed Nanopore Electro-Osmotic trap (NEOtrap) is well fit to study these basic physical processes in nanopore sensing, as it reveals previously missed events. Here, we use the NEOtrap to quantitate the electro-osmotic and electrophoretic forces that act on proteins inside the nanopore. We establish a physical model to describe the capture and escape processes, including the trapping energy potential. We verified the model with experimental data on CRISPR dCas9-RNA-DNA complexes, where we systematically screened crucial modeling parameters such as the size and net charge of the complex. Tuning the balance between electrophoretic and electro-osmotic forces in this way, we compare the trends in the kinetic parameters with our theoretical models. The result is a comprehensive picture of the major physical processes in nanopore trapping, which helps to guide the experiment design and signal interpretation in nanopore experiments.
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Affiliation(s)
- Chenyu Wen
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands
- Laboratory
of Biophysics, Wageningen University and
Research, Stippeneng 4, Wageningen 6708 WE, The Netherlands
| | - Sonja Schmid
- Laboratory
of Biophysics, Wageningen University and
Research, Stippeneng 4, Wageningen 6708 WE, The Netherlands
| | - Cees Dekker
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands
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2
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Burden DL, Meyer JJ, Michael RD, Anderson SC, Burden HM, Peña SM, Leong-Fern KJ, Van Ye LA, Meyer EC, Keranen-Burden LM. Confirming Silent Translocation through Nanopores with Simultaneous Single-Molecule Fluorescence and Single-Channel Electrical Recordings. Anal Chem 2023; 95:18020-18028. [PMID: 37991877 PMCID: PMC10719886 DOI: 10.1021/acs.analchem.3c02329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/24/2023]
Abstract
Most of what is known concerning the luminal passage of materials through nanopores arises from electrical measurements. Whether nanopores are biological, solid-state, synthetic, hybrid, glass-capillary-based, or protein ion channels in cells and tissues, characteristic signatures embedded in the flow of ionic current are foundational to understanding functional behavior. In contrast, this work describes passage through a nanopore that occurs without producing an electrical signature. We refer to the phenomenon as "silent translocation." By definition, silent translocations are invisible to the standard tools of electrophysiology and fundamentally require a simultaneous ancillary measurement technique for positive identification. As a result, this phenomenon has been largely unexplored in the literature. Here, we report on a derivative of Cyanine 5 (sCy5a) that passes through the α-hemolysin (αHL) nanopore silently. Simultaneously acquired single-molecule fluorescence and single-channel electrical recordings from bilayers formed over a closed microcavity demonstrate that translocation does indeed take place, albeit infrequently. We report observations of silent translocation as a function of time, dye concentration, and nanopore population in the bilayer. Lastly, measurement of the translocation rate as a function of applied potential permits estimation of an effective energy barrier for transport through the pore as well as the effective charge on the dye, all in the absence of an information-containing electrical signature.
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Affiliation(s)
- Daniel L. Burden
- Chemistry Department, Wheaton College, Wheaton, Illinois 60187, United States
| | - Joshua J. Meyer
- Chemistry Department, Wheaton College, Wheaton, Illinois 60187, United States
| | - Richard D. Michael
- Chemistry Department, Wheaton College, Wheaton, Illinois 60187, United States
| | - Sophie C. Anderson
- Chemistry Department, Wheaton College, Wheaton, Illinois 60187, United States
| | - Hannah M. Burden
- Chemistry Department, Wheaton College, Wheaton, Illinois 60187, United States
| | - Sophia M. Peña
- Chemistry Department, Wheaton College, Wheaton, Illinois 60187, United States
| | | | - Lily Anne Van Ye
- Chemistry Department, Wheaton College, Wheaton, Illinois 60187, United States
| | - Elizabeth C. Meyer
- Chemistry Department, Wheaton College, Wheaton, Illinois 60187, United States
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3
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Chen X, Zhou S, Wang Y, Zheng L, Guan S, Wang D, Wang L, Guan X. Nanopore Single-molecule Analysis of Biomarkers: Providing Possible Clues to Disease Diagnosis. Trends Analyt Chem 2023; 162:117060. [PMID: 38106545 PMCID: PMC10722900 DOI: 10.1016/j.trac.2023.117060] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Biomarker detection has attracted increasing interest in recent years due to the minimally or non-invasive sampling process. Single entity analysis of biomarkers is expected to provide real-time and accurate biological information for early disease diagnosis and prognosis, which is critical to the effective disease treatment and is also important in personalized medicine. As an innovative single entity analysis method, nanopore sensing is a pioneering single-molecule detection technique that is widely used in analytical bioanalytical fields. In this review, we overview the recent progress of nanopore biomarker detection as new approaches to disease diagnosis. In highlighted studies, nanopore was focusing on detecting biomarkers of different categories of communicable and noncommunicable diseases, such as pandemic Covid-19, AIDS, cancers, neurologic diseases, etc. Various sensitive and selective nanopore detecting strategies for different types of biomarkers are summarized. In addition, the challenges, opportunities, and direction for future development of nanopore-based biomarker sensors are also discussed.
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Affiliation(s)
- Xiaohan Chen
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing School, University of Chinese Academy of Science, Chongqing, 400714, China
| | - Shuo Zhou
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing School, University of Chinese Academy of Science, Chongqing, 400714, China
| | - Yunjiao Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing School, University of Chinese Academy of Science, Chongqing, 400714, China
| | - Ling Zheng
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing School, University of Chinese Academy of Science, Chongqing, 400714, China
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Sarah Guan
- Hinsdale Central High School, Hinsdale, IL 60521, USA
| | - Deqiang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing School, University of Chinese Academy of Science, Chongqing, 400714, China
| | - Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing School, University of Chinese Academy of Science, Chongqing, 400714, China
- Chongqing Key Laboratory of Intelligent Medicine Engineering for Hepatopancreatobiliary Diseases, University of Chinese Academy of Sciences, Chongqing 401147, China
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, 60616, USA
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4
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Wang Z, Hu R, Zhu R, Lu W, Wei G, Zhao J, Gu ZY, Zhao Q. Metal-Organic Cage as Single-Molecule Carrier for Solid-State Nanopore Analysis. SMALL METHODS 2022; 6:e2200743. [PMID: 36216776 DOI: 10.1002/smtd.202200743] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/19/2022] [Indexed: 06/16/2023]
Abstract
The ability to detect biomolecules at the single-molecule level is at the forefront of biological research, precision medicine, and early diagnosis. Recently, solid-state nanopore sensors have emerged as a promising technique for label-free and precise diagnosis assay. However, insufficient sensitivity and selectivity for small analytes are a great challenge for clinical diagnosis applications via solid-state nanopores. Here, for the first time, a metal-organic cage, PCC-57, is employed as a carrier to increase the sensitivity and selectivity of solid-state nanopores based on the intrinsic interaction of the nanocage with biomolecules. Firstly, it is found that the carrier itself is undetectable unless bound with the target analytes and used oligonucleotides as linkers to attach PCC-57 and target analytes. Secondly, two small analytes, oligonucleotide conjugated angiopep-2 and polyphosphoric acid, are successfully distinguished using the molecular carrier. Finally, selectivity of nanopore detection is achieved by attaching PCC-57 to oligonucleotide-tailed aptamers, and the human alpha-thrombin sample is successfully detected. It is believed that the highly designable metal-organic cage could serve as a rich carrier repository for a variety of biomolecules, facilitating single-molecule screening of clinically relevant biomolecules based on solid-state nanopores in the future.
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Affiliation(s)
- Zhan Wang
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, Electron Microscopy Laboratory, School of Physics, Peking University, Beijing, 100871, China
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Rui Hu
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, Electron Microscopy Laboratory, School of Physics, Peking University, Beijing, 100871, China
| | - Rui Zhu
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, Electron Microscopy Laboratory, School of Physics, Peking University, Beijing, 100871, China
| | - Wenlong Lu
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, Electron Microscopy Laboratory, School of Physics, Peking University, Beijing, 100871, China
| | - Guanghao Wei
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, Electron Microscopy Laboratory, School of Physics, Peking University, Beijing, 100871, China
| | - Jing Zhao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China
| | - Zhi-Yuan Gu
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Qing Zhao
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, Electron Microscopy Laboratory, School of Physics, Peking University, Beijing, 100871, China
- Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu, 226010, China
- Collaborative Innovation Center of Quantum Matter, Beijing, 100084, China
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5
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Li S, Zeng S, Wen C, Zhang Z, Hjort K, Zhang SL. Docking and Activity of DNA Polymerase on Solid-State Nanopores. ACS Sens 2022; 7:1476-1483. [PMID: 35537188 PMCID: PMC9150166 DOI: 10.1021/acssensors.2c00216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Integration of motor enzymes with biological nanopores has enabled commercial DNA sequencing technology; yet studies of the similar principle applying to solid-state nanopores are limited. Here, we demonstrate the real-life monitoring of phi29 DNA polymerase (DNAP) docking onto truncated-pyramidal nanopore (TPP) arrays through both electrical and optical readout. To achieve effective docking, atomic layer deposition of hafnium oxide is employed to reduce the narrowest pore opening size of original silicon (Si) TPPs to sub-10 nm. On a single TPP with pore opening size comparable to DNAP, ionic current measurements show that a polymerase-DNA complex can temporally dock onto the TPP with a certain docking orientation, while the majority become translocation events. On 5-by-5 TPP arrays, a label-free optical detection method using Ca2+ sensitive dye, are employed to detect the docking dynamics of DNAP. The results show that this label-free detection strategy is capable of accessing the docking events of DNAP on TPP arrays. Finally, we examine the activity of docked DNAP by performing on-site rolling circle amplification to synthesize single-stranded DNA (ssDNA), which serves as a proof-of-concept demonstration of utilizing this docking scheme for emerging nanopore sensing applications.
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Affiliation(s)
- Shiyu Li
- Department of Electrical Engineering, Division of Solid-State Electronics, Uppsala University, SE-751 03 Uppsala, Sweden
| | - Shuangshuang Zeng
- Department of Electrical Engineering, Division of Solid-State Electronics, Uppsala University, SE-751 03 Uppsala, Sweden
| | - Chenyu Wen
- Department of Electrical Engineering, Division of Solid-State Electronics, Uppsala University, SE-751 03 Uppsala, Sweden
| | - Zhen Zhang
- Department of Electrical Engineering, Division of Solid-State Electronics, Uppsala University, SE-751 03 Uppsala, Sweden
| | - Klas Hjort
- Department of Material Science and Engineering, Division of Microsystem Technology, Uppsala University, SE-751 21 Uppsala, Sweden
| | - Shi-Li Zhang
- Department of Electrical Engineering, Division of Solid-State Electronics, Uppsala University, SE-751 03 Uppsala, Sweden
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6
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Effect of Solvent Viscosity on the Driven Translocation of Charged Polymers through Nanopores. CHINESE JOURNAL OF POLYMER SCIENCE 2022. [DOI: 10.1007/s10118-022-2696-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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7
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Carlsen A, Tabard-Cossa V. Mapping shifts in nanopore signal to changes in protein and protein-DNA conformation. Proteomics 2021; 22:e2100068. [PMID: 34845853 DOI: 10.1002/pmic.202100068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/28/2021] [Accepted: 11/12/2021] [Indexed: 11/08/2022]
Abstract
Solid-state nanopores have been used extensively in biomolecular studies involving DNA and proteins. However, the interpretation of signals generated by the translocation of proteins or protein-DNA complexes remains challenging. Here, we investigate the behavior of monovalent streptavidin and the complex it forms with short biotinylated DNA over a range of nanopore sizes, salts, and voltages. We describe a simple geometric model that is broadly applicable and employ it to explain observed variations in conductance blockage and dwell time with experimental conditions. The general approach developed here underscores the value of nanopore-based protein analysis and represents progress toward the interpretation of complex translocation signals.
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Affiliation(s)
- Autumn Carlsen
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
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8
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Wang Z, Lv TY, Shi ZB, Yang SS, Gu ZY. Two-dimensional materials as solid-state nanopores for chemical sensing. Dalton Trans 2021; 50:13608-13619. [PMID: 34518861 DOI: 10.1039/d1dt02206g] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Solid-state nanopores as a versatile alternative to biological nanopores have grown tremendously over the last two decades. They exhibit unique characteristics including mechanical robustness, thermal and chemical stability, easy modifications and so on. Moreover, the pore size of a solid-state nanopore could be accurately controlled from sub-nanometers to hundreds of nanometers based on the experimental requirements, presenting better adaptability than biological nanopores. Two-dimensional (2D) materials with single layer thicknesses and highly ordered structures have great potential as solid-state nanopores. In this perspective, we introduced three kinds of substrate-supported 2D material solid-state nanopores, including graphene, MoS2 and MOF nanosheets, which exhibited big advantages compared to traditional solid-state nanopores and other biological counterparts. Besides, we suggested the fabrication and modulation of 2D material solid-state nanopores. We also discussed the applications of 2D materials as solid-state nanopores for ion transportation, DNA sequencing and biomolecule detection.
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Affiliation(s)
- Zhan Wang
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
| | - Tian-Yi Lv
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
| | - Zi-Bo Shi
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
| | - Shi-Shu Yang
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
- Henan Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, 453007, P. R. China.
| | - Zhi-Yuan Gu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
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9
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Zhang J, Zhang L, Li Z, Zhang Q, Li Y, Ying Y, Fu Y. Nanoconfinement Effect for Signal Amplification in Electrochemical Analysis and Sensing. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2101665. [PMID: 34278716 DOI: 10.1002/smll.202101665] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 06/07/2021] [Indexed: 06/13/2023]
Abstract
Owing to the urgent need for electrochemical analysis and sensing of trace target molecules in various fields such as medical diagnosis, agriculture and food safety, and environmental monitoring, signal amplification is key to promoting analysis and sensing performance. The nanoconfinement effect, derived from nanoconfined spaces and interfaces with sizes approaching those of target molecules, has witnessed rapid development for ultra-sensitive analyzing and sensing. In this review, the two main types of nanoconfinement systems - confined nanochannels and planes - are assessed and recent progress is highlighted. The merits of each nanoconfinement system, the nanoconfinement effect mechanisms, and applications for electrochemical analysis and sensing are summarized and discussed. This review aims to help deepen the understanding of nanoconfinement devices and their effects in order to develop new analysis and sensing applications for researchers in various fields.
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Affiliation(s)
- Jie Zhang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, P.R. China
| | - Lin Zhang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, P.R. China
| | - Zhishang Li
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, P.R. China
| | - Qi Zhang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, P.R. China
| | - Yanbin Li
- Department of Biological and Agricultural Engineering, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Yibin Ying
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, P.R. China
| | - Yingchun Fu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, P.R. China
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10
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Si W, Yang H, Wu G, Zhang Y, Sha J. Velocity control of protein translocation through a nanopore by tuning the fraction of benzenoid residues. NANOSCALE 2021; 13:15352-15361. [PMID: 34498657 DOI: 10.1039/d1nr04492c] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Protein sequencing is essential to unveil the mechanism of cellular processes that govern the function of living organisms, and which play a crucial role in the field of drug design and molecular diagnostics. Nanopores have been proved to be effective tools in single molecule sensing, but the fast translocation speed of a peptide through a nanopore is one of the major obstacles that hinders the development of nanopore-based protein sequencing. In this work, by using molecular dynamics simulations (MDS) it is found that the peptide containing more hydrophobic residues permeates slower through a molybdenum disulfide nanopore, which originates from the strong interaction between the membrane surface and the hydrophobic residues. The binding affinity is remarkable especially for benzenoid residues as they contain a hydrophobic aromatic ring that is composed of relatively non-polar C-C and C-H bonds. By tuning the fraction of benzenoid residues of the peptide, the velocity of the protein translocation through the nanopore is well controlled. The peptide with all the hydrophobic residues being benzenoid residues is found to translocate through the nanopore almost ten times slower than the one without any benzenoid residues, which is beneficial for gathering adequate information for precise 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.
| | - Haojie Yang
- 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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11
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Zhan L, Zhang Y, Si W, Sha J, Chen Y. Detection and Separation of Single-Stranded DNA Fragments Using Solid-State Nanopores. J Phys Chem Lett 2021; 12:6469-6477. [PMID: 34240883 DOI: 10.1021/acs.jpclett.1c01163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Many biological assays require effectively and sensitively sorting DNA fragments. Here, we demonstrate a solid-state nanopore platform for label-free detection and separation of short single-stranded DNA (ssDNA) fragments (<100 nt), based on their length-dependent translocation behaviors. Our experimental data show that each sized pore has a passable length threshold. The negative charged ssDNA fragments with length smaller than the threshold can be electrically facilitated driven through the correspondingly sized nanopore along the direction of electric field. In addition, the passable length threshold increases with the pore size enlarging. As a result, this phenomenon is able to be applicable for the controllable selectivity of ssDNA by tuning nanopore size, and the selectivity limitation is up to 30nt. Numerical simulation results indicate the translocation direction of ssDNA is governed by the competition of electroosmosis and electrophoresis effects on the ssDNA and offer the relationship between passable length threshold and pore size.
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Affiliation(s)
- Lijian Zhan
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Yin Zhang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Wei Si
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Yunfei Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
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12
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Affiliation(s)
- Mengjie Cui
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University Linyi Shandong 276005 China
| | - Yaxian Ge
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University Linyi Shandong 276005 China
| | - Xiao Zhuge
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University Linyi Shandong 276005 China
| | - Xin Zhou
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University Linyi Shandong 276005 China
| | - Dongmei Xi
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University Linyi Shandong 276005 China
| | - Shusheng Zhang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University Linyi Shandong 276005 China
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13
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Pal S, Ramkumar B, Jugade S, Rao A, Naik A, Chakraborty B, Varma MM. Effect of single nanoparticle-nanopore interaction strength on ionic current modulation. SENSORS AND ACTUATORS. B, CHEMICAL 2020; 325:128785. [PMID: 34321714 PMCID: PMC8312308 DOI: 10.1016/j.snb.2020.128785] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Solid-state nanopores are rapidly emerging as promising platforms for developing various single molecule sensing applications. The modulation of ionic current through the pore due to translocation of the target molecule has been the dominant measurement modality in nanopore sensors. Here, we focus on the dwell time, which is the duration taken by the target molecule or particle to traverse the pore and study its dependence on the strength of interaction of the target with the pore using single gold nanoparticles (NPs) as targets interacting with a silicon nitride (SiN) nanopore. The strength of interaction, which in our case is electrostatic in nature, can be controlled by coating the nanoparticles with charged polymers. We report on an operating regime of this nanopore sensor, characterized by attractive interactions between the nanoparticle and the pore, where the dwell time is exponentially sensitive to the target-pore interaction. We used negatively and positively charged gold nanoparticles to control the strength of their interaction with the Silicon Nitride pore which is negatively charged. Our experiments revealed how this modulation of the electrostatic force greatly affects the dwell time. Positively charged NPs with strong attractive interactions with the pore resulted in increase of dwell times by 2-3 orders of magnitude, from 0.4 ms to 75.3 ms. This extreme sensitivity of the dwell time on the strength of interaction between a target and nanopore can be exploited in emerging nanopore sensor applications.
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Affiliation(s)
- Sohini Pal
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - B. Ramkumar
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Sanket Jugade
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, United States
| | - Akshay Naik
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Banani Chakraborty
- Department of Chemical Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Manoj M. Varma
- Centre for Nano Science and Engineering, Indian Institute of Science, Bangalore 560012, India
- Corresponding author. (M.M. Varma)
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14
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Zhang Y, Zhao J, Kan Y, Ji R, Pan J, Huang W, Xu Z, Si W, Sha J. Concentration effects on capture rate and translocation configuration of nanopore-based DNA detection. Electrophoresis 2020; 41:1523-1528. [PMID: 32529653 DOI: 10.1002/elps.202000016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 01/21/2023]
Abstract
Nanopore is a kind of powerful tool to detect single molecules and investigate fundamental biological processes. In biological cells or real detection systems, concentration of DNA molecules is various. Here, we report an experimental study of the effects of DNA concentration on capture rate and translocation configuration with different sized nanopores and applied voltages. Three classes of DNA translocation configurations have been observed including linear translocation, folded translocation, and cotranslocation. In the case of relatively large sized nanopore or high applied voltage, considerable cotranslocation events have been detected. The percentage of cotranslocation events also increases with DNA concentration, which leads to the relationship between capture rate and DNA concentration deviates from linearity. Therefore, in order to reflect the number of translocation molecules accurately, the capture rate should be corrected by double-counting cotranslocation events. These results will provide a valuable reference for the design of nanopore sensors.
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Affiliation(s)
- Yin Zhang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, P. R. China
| | - Jiabin Zhao
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, P. R. China
| | - Yajing Kan
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, P. R. China
| | - Rui Ji
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, P. R. China
| | - Jianqiang Pan
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, P. R. China
| | - Weichi Huang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, P. R. China
| | - Zheng Xu
- Key Laboratory for Micro/Nano Technology and System of Liaoning Province, Dalian University of Technology, Dalian, P. R. China
| | - Wei Si
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, P. R. China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing, P. R. China
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15
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Ma T, Janot JM, Balme S. Dynamics of long hyaluronic acid chains through conical nanochannels for characterizing enzyme reactions in confined spaces. NANOSCALE 2020; 12:7231-7239. [PMID: 32195519 DOI: 10.1039/d0nr00645a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This research reports the transport behaviors of long flexible polymers (hyaluronic acid) through long conical track-etched nanochannels with and without grafted enzymes. The impacts of the channel diameter and the polymer regimes in solution (dilute and semi-dilute) have been investigated. Without enzymes, the experimental results can be well explained by the analytical models of the scaling law of de Gennes. Then, the corresponding enzymes (hyaluronidase) were grafted inside the channel. When enzymes are located at the base side, polymers get degraded at the entrance and the degraded products are detected. When enzymes are grafted at the tip side, the extension of translocation duration due to the binding of substrate-enzyme is observed. This is for the first time that the enzymatic degradation reactions are characterized in situ at the single molecule level by nanopore technology.
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Affiliation(s)
- Tianji Ma
- Institut Européen des Membranes, UMR5635 UM ENSCM CNRS, Place Eugène Bataillon, 34095 Montpellier cedex 5, France.
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16
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Affiliation(s)
- Si-Min Lu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yue-Yi Peng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
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17
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Wang S, Liang L, Tang J, Cai Y, Zhao C, Fang S, Wang H, Weng T, Wang L, Wang D. Label-free single-molecule identification of telomere G-quadruplexes with a solid-state nanopore sensor. RSC Adv 2020; 10:27215-27224. [PMID: 35515777 PMCID: PMC9055465 DOI: 10.1039/d0ra05083k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 07/06/2020] [Indexed: 12/14/2022] Open
Abstract
Telomere sequences can spontaneously form G-quadruplexes (G4) in the presence of some cations. In view of their relevance to genetic processes and potential as therapeutic-targets, hitherto, a wealth of conventional techniques have been reported for interrogation of G4 conformation diversity and corresponding folding kinetics, most of which are limited in precision and sensitivity. This work introduces a label-free solid-state nanopore (SSN) approach for the determination of inter-, intra- and tandem molecular G4 with distinct base permutation in various cation buffers with a tailored aperture and meanwhile captures the single-molecule G4 folding process. SSN translocation properties elucidated that both inter- and intramolecular G4 generated higher current blockage with longer duration than flexible homopolymer nucleotide, and intramolecular G4 are structurally more stable with higher event frequency and longer blockage time than intermolecular ones; base arrangement played weak role in translocation behaviors; the same sequences with one, two and three G4 skeletons displayed an increase in current blockage and a gradual extension in dwell time with the increase of molecule size recorded in the same nanopore. We observed the conformation change of single-molecule G4 which indicated the existence of folding/unfolding equilibration in nanopore, and real-time test suggested a gradual formation of G4 with time. Our results could provide a continued and improved understanding of the underlying relevance of structural stability and G4 folding process by utilizing SSN platform which exhibits strategic potential advances over the other methods with high spatial and temporal resolution. Nanopore detection of single-molecule G-quadruplexes.![]()
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18
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Li Q, Ying YL, Hu YX, Liu SC, Long YT. Monitoring nanobubble nucleation at early-stage within a sub-9 nm solid-state nanopore. Electrophoresis 2019; 41:959-965. [PMID: 31652002 DOI: 10.1002/elps.201900305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/04/2019] [Accepted: 10/19/2019] [Indexed: 12/14/2022]
Abstract
Nanobubble nucleation study is important for understanding the dynamic behavior of nanobubble growth, which is instructive for the nanobubble applications. Benefiting from nanopore fabrication, herein, we fabricated a sub-9 nm SiNX nanopore with the comparable size to nanobubbles at early-stage. The confined nanopore interface serves as a generator for producing nanobubbles by the chemical reaction between NaBH4 and H2 O and as an ultra-sensitive sensor for monitoring the H2 nanobubble nucleation process. By carrying out the NaBH4 concentration-dependent experiments, we found the life-time of nanobubbles decreased 250 times and the frequency of nanobubble generation increased 38 times with the NaBH4 concentration increasing from 6 to 100 mM. The long-time equilibrium between gas molecules inward flux and outward flux could prolong the life-time of nanobubbles to hundreds of milliseconds at low NaBH4 concentration. The raw current trace depicted that the transient accumulation and dissolution of cavity occurred during all the life-time of nanobubbles. Therefore, the sub-9 nm SiNX nanopore shows a strong ability for real-time monitoring the nanobubble nucleation at early-stage with high temporal and spatial resolution. This work provides a guide to study the dynamic and stochastic characteristics of nanobubbles.
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Affiliation(s)
- Qiao Li
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, P. R. China
| | - Yi-Lun Ying
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, P. R. China.,State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, P. R. China
| | - Yong-Xu Hu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, P. R. China
| | - Shao-Chuang Liu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, P. R. China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, P. R. China
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19
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Fragasso A, Pud S, Dekker C. 1/f noise in solid-state nanopores is governed by access and surface regions. NANOTECHNOLOGY 2019; 30:395202. [PMID: 31247592 DOI: 10.1088/1361-6528/ab2d35] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The performance of solid-state nanopores as promising biosensors is severely hampered by low-frequency 1/f noise in the through-pore ionic current recordings. Here, we develop a model for the 1/f noise in such nanopores, that, unlike previous reports, accounts for contributions from both the pore-cylinder, pore-surface, and access regions. To test our model, we present measurements of the open-pore current noise through solid-state nanopores of different diameters (1-50 nm). To describe the observed trends, it appears essential to include the access resistance in the modeling of the 1/f noise. We attribute a different Hooge constant for the charge carrier fluctuations occurring in the bulk electrolyte and at the pore surface. The model reported here can be used to accurately analyze different contributions to the nanopore low-frequency noise, rendering it a powerful tool for characterizing and comparing different membrane materials in terms of their 1/f noise properties.
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Affiliation(s)
- Alessio Fragasso
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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20
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21
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Gao R, Lin Y, Ying YL, Long YT. Nanopore-based sensing interface for single molecule electrochemistry. Sci China Chem 2019. [DOI: 10.1007/s11426-019-9509-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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22
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Li Q, Ying YL, Liu SC, Lin Y, Long YT. Detection of Single Proteins with a General Nanopore Sensor. ACS Sens 2019; 4:1185-1189. [PMID: 30860364 DOI: 10.1021/acssensors.9b00228] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Single protein sensing based on solid-state nanopores is promising but challenging, because the fast translocation velocity of a protein is beyond the bandwidth of nanopore instruments. To decelerate the translocation speed, here, we employed a common protein cross-link interaction to achieve a general and robust nanopore sensing platform for single-molecule detection of protein. Benefiting from the EDC/NHS coupling interaction between nanopore and proteins, a 10-fold decrease in speed has been achieved. The clearly distinguishable current signatures further reveal that the anisotropic translocation of a protein, which are horizontal, vertical, and flipping transit inside nanopore confinement. This strategy provides a general platform for rapid detection of proteins as well as exploring fundamental protein dynamics at the single-molecule level.
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Affiliation(s)
- Qiao Li
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Shao-Chuang Liu
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yao Lin
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
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23
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Liu S, Li Q, Ying Y, Long Y. Detection of structured single‐strand DNA via solid‐state nanopore. Electrophoresis 2019; 40:2112-2116. [DOI: 10.1002/elps.201900096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 03/21/2019] [Accepted: 03/23/2019] [Indexed: 01/13/2023]
Affiliation(s)
- Shao‐Chuang Liu
- Key Laboratory for Advanced Materials School of Chemistry and Molecular Engineering East East China University of Science and Technology Shanghai P. R. China
| | - Qiao Li
- Key Laboratory for Advanced Materials School of Chemistry and Molecular Engineering East East China University of Science and Technology Shanghai P. R. China
| | - Yi‐Lun Ying
- Key Laboratory for Advanced Materials School of Chemistry and Molecular Engineering East East China University of Science and Technology Shanghai P. R. China
| | - Yi‐Tao Long
- Key Laboratory for Advanced Materials School of Chemistry and Molecular Engineering East East China University of Science and Technology Shanghai P. R. China
- School of Chemistry and Chemical Engineering Nanjing University Nanjing P. R. China
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24
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Si W, Yang H, Sha J, Zhang Y, Chen Y. Discrimination of single-stranded DNA homopolymers by sieving out G-quadruplex using tiny solid-state nanopores. Electrophoresis 2019; 40:2117-2124. [PMID: 30779188 DOI: 10.1002/elps.201800537] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 01/28/2019] [Accepted: 02/13/2019] [Indexed: 12/19/2022]
Abstract
Nanopore sensor has been developed as a promising technology for DNA sequencing at the single-base resolution. However, the discrimination of homopolymers composed of guanines from other nucleotides has not been clearly revealed due to the easily formed G-quadruplex in aqueous buffers. In this work, we report that a tiny silicon nitride nanopore was used to sieve out G tetramers to make sure only homopolymers composed of guanines could translocate through the nanopore, then the 20-nucleotide long ssDNA homopolymers could be identified and differentiated. It is found that the size of the nucleotide plays a major role in affecting the current blockade as well as the dwell time while DNA is translocating through the nanopore. By the comparison of translocation behavior of ssDNA homopolymers composed of nucleotides with different volumes, it is found that smaller nucleotides can lead to higher translocation speed and lower current blockage, which is also found and validated for the 105-nucleotide long homopolymers. The studies performed in this work will improve our understanding of nanopore-based DNA sequencing at single-base level.
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Affiliation(s)
- Wei Si
- School of Mechanical Engineering, Southeast University, Nanjing, P. R. China.,Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, P. R. China
| | - Haojie Yang
- School of Mechanical Engineering, Southeast University, Nanjing, P. R. China.,Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, P. R. China
| | - Jingjie Sha
- School of Mechanical Engineering, Southeast University, Nanjing, P. R. China.,Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, P. R. China
| | - Yin Zhang
- School of Mechanical Engineering, Southeast University, Nanjing, P. R. China.,Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, P. R. China
| | - Yunfei Chen
- School of Mechanical Engineering, Southeast University, Nanjing, P. R. China.,Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, P. R. China
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25
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Luan B, Zhou R. Atomic-Scale Fluidic Diodes Based on Triangular Nanopores in Bilayer Hexagonal Boron Nitride. NANO LETTERS 2019; 19:977-982. [PMID: 30628792 DOI: 10.1021/acs.nanolett.8b04208] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Nanofluidic diodes based on nanochannels have been studied theoretically and experimentally for applications such as biosensors and logic gates. However, when analyzing attoliter-scale samples or enabling high-density integration of lab-on-a-chip devices, it is beneficial to miniaturize the size of a nanofluidic channel. Using molecular dynamics simulations, we investigate conductance of nanopores in bilayer hexagonal boron nitride (h-BN). Remarkably, we found that triangular nanopores possess excellent rectifications of ionic currents while hexagonal ones do not. It is worth highlighting that the pore length is only about 0.7 nm, which is about the atomic limit for a bipolar diode. We determined scaling relations between ionic currents I and pore sizes L for small nanopores, that are I ∼ L1 in a forward biasing voltage and I ∼ L2 in a reverse biasing voltage. Simulation results qualitatively agree with analytical ones derived from the one-dimensional Poisson-Nerst-Planck equations.
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Affiliation(s)
- Binquan Luan
- Computational Biological Center , IBM Thomas J. Watson Research , Yorktown Heights , New York 10598 , United States
| | - Ruhong Zhou
- Computational Biological Center , IBM Thomas J. Watson Research , Yorktown Heights , New York 10598 , United States
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26
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Si W, Liu C, Sha J, Zhang Y, Chen Y. Computational modeling of ionic currents through difform graphene nanopores with consistent cross-sectional areas. Phys Chem Chem Phys 2019; 21:26166-26174. [DOI: 10.1039/c9cp05459f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Unveiling the mystery of ion transport behavior in nanopores with consistent cross-sectional areas shows that this behavior is highly related to the geometry and hydrophobicity of the nanopores.
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Affiliation(s)
- Wei Si
- School of Mechanical Engineering
- Southeast University
- Nanjing 211189
- China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments
| | - Chenhan Liu
- School of Mechanical Engineering
- Southeast University
- Nanjing 211189
- China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments
| | - Jingjie Sha
- School of Mechanical Engineering
- Southeast University
- Nanjing 211189
- China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments
| | - Yin Zhang
- School of Mechanical Engineering
- Southeast University
- Nanjing 211189
- China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments
| | - Yunfei Chen
- School of Mechanical Engineering
- Southeast University
- Nanjing 211189
- China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments
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27
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Yang J, Wang YQ, Li MY, Ying YL, Long YT. Direct Sensing of Single Native RNA with a Single-Biomolecule Interface of Aerolysin Nanopore. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14940-14945. [PMID: 30462509 DOI: 10.1021/acs.langmuir.8b03264] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
RNA sensing is of vital significance to advance our comprehension of gene expression and to further benefit medical diagnostics. Taking advantage of the excellent sensing capability of the aerolysin nanopore as a single-biomolecule interface, we for the first time achieved the direct characterization of single native RNA of Poly(A)4 and Poly(U)4. Poly(A)4 induces ∼10% larger blockade current amplitude than Poly(U)4. The statistical duration of Poly(A)4 is 18.83 ± 1.08 ms, which is 100 times longer than that of Poly(U)4. Our results demonstrated that the capture of RNA homopolymers is restricted by the biased diffusion. The translocation of RNA needs to overcome a lower free-energy barrier than that of DNA. Moreover, the strong RNA-aerolysin interaction is attributed to the hydroxyl in pentose, which prolongs the translocation time. This study opens an avenue for aerolysin nanopores to directly achieve RNA sensing, including discrimination of RNA epigenetic modification and selective detection of miRNA.
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Affiliation(s)
- Jie Yang
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , P. R. China
| | - Ya-Qian Wang
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , P. R. China
| | - Meng-Yin Li
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , P. R. China
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , P. R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , P. R. China
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28
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Zhang Y, Liu X, Zhao Y, Yu JK, Reisner W, Dunbar WB. Single Molecule DNA Resensing Using a Two-Pore Device. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1801890. [PMID: 30334362 DOI: 10.1002/smll.201801890] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 09/21/2018] [Indexed: 06/08/2023]
Abstract
A nanofluidic device is presented that, enables independent sensing and resensing of a single DNA molecule translocating through two nanopores with sub-micrometer spacing. The device concept is based upon integrating a thin nitride membrane with microchannels etched in borosilicate glass. Pores, coupled to each microchannel, are connected via a fluid-filled half-space on the device backside, enabling translocation of molecules across each pore in sequence. Critically, this approach allows for independent application of control voltage and measurement of trans-pore ionic current at each of the two pores, leading to 1) controlled assessment of molecular time of flight, 2) voltage-tuned selective molecule recapture, and 3) ability to acquire two correlated translocation signatures for each molecule analyzed. Finally, the rare cocapture of a single chain threading simultaneously through each of the two pores is reported.
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Affiliation(s)
- Yuning Zhang
- Department of Physics, McGill University, Montreal, QC, H3A 2T8, Canada
| | - Xu Liu
- Two Pore Guys, Inc., 2155 Delaware Ave #225, Santa Cruz, CA, 95060, USA
| | - Yanan Zhao
- Two Pore Guys, Inc., 2155 Delaware Ave #225, Santa Cruz, CA, 95060, USA
| | - Jen-Kan Yu
- Two Pore Guys, Inc., 2155 Delaware Ave #225, Santa Cruz, CA, 95060, USA
| | - Walter Reisner
- Department of Physics, McGill University, Montreal, QC, H3A 2T8, Canada
| | - William B Dunbar
- Two Pore Guys, Inc., 2155 Delaware Ave #225, Santa Cruz, CA, 95060, USA
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