1
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Punia B, Chaudhury S. Microscopic Mechanism of Macromolecular Crowder-Assisted DNA Capture and Translocation through Biological Nanopores. J Phys Chem B 2023. [PMID: 37294938 DOI: 10.1021/acs.jpcb.3c02792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Biological nanopore sensors are widely used for genetic sequencing as nucleic acids and other molecules translocate through them across membranes. Recent studies have shown that the transport of these polymers through nanopores is strongly influenced by macromolecular bulk crowders. By using poly(ethylene glycol) (PEG) molecules as crowders, experiments have shown an increase in the capture rates and translocation times of polymers through an α-hemolysin (αHL) nanopore, which provides high-throughput signals and accurate sensing. A clear molecular-level understanding of how the presence of PEGs offers such desirable outcomes in nanopore sensing is still missing. In this work, we present a new theoretical approach to probe the effect of PEG crowders on DNA capture and translocation through the αHL nanopore. We develop an exactly solvable discrete-state stochastic model based on the cooperative partitioning of individual polycationic PEGs within the cavity of the αHL nanopore. It is argued that the apparent electrostatic interactions between the DNA and PEGs control all of the dynamic processes. Our analytical predictions find excellent agreements with existing experiments, thereby strongly supporting our theory.
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Affiliation(s)
- Bhawakshi Punia
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Srabanti Chaudhury
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
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2
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Li M, Chen S, Wang Y, Zhang S, Song D, Tian R, Geng J, Wang L. Label-free high-precise nanopore detection of endopeptidase activity of anthrax lethal factor regulated by diverse conditions. Biosens Bioelectron 2023; 219:114800. [PMID: 36274430 DOI: 10.1016/j.bios.2022.114800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/24/2022] [Accepted: 10/08/2022] [Indexed: 11/19/2022]
Abstract
Endopeptidase activity of anthrax lethal factor (aLF) prevents the destroy of anthracis spore intracellularly by host macrophages, meanwhile disables the signaling pathways extracellularly that leads to host lethality. Hence, inhibitory of this activity is expected to be an alternative option to cure anthrax infection. Herein, we fabricated a nanopore platform via transmembrane pore construction in vitro, which allows precise mimics, monitoring of intercellular proteinic transport and enables the quantitative detection of aLF endopeptidase activity towards MAPKK signaling protein at single molecule level. Next, we inhibited the aLF activity via screening approaches of protein-metal ion acquisition and other condition controlment (proton/hydroxide strength, adapted temperature, ionizing irradiation), which were identified by nanopore electrokinetic study. Upon the results, we found that Ca2+, Mg2+, Mn2+, Ni2+ collaborating with Zn2+ promote aLF activity efficiently. In contrary, Cd2+, Co2+, Cu2+ have great inhibitory effect. Result further revealed that, the speed of aLF endopeptidase activity with different ions functions as the nanopore signal frequency in linear manner, which enables evident distinction of those divalent ions using this proteinase assay. We also found the higher strength of the proton or hydroxide, the higher the inhibitory to aLF activity. Besides, adapted temperature and γ-ray also play integral roles in inhibiting this activity. Our results lay experimental basis for accurate detection of aLF activity, meanwhile provide new direction to screening novel stimuli-responsive inhibitors specific to aLF.
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Affiliation(s)
- Minghan Li
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China; Department of Laboratory Medicine, State Key Laboratory of Biotherapy, Med-X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Shanchuan Chen
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, 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 Sciences, Chongqing, 400714, China
| | - Shaoxia Zhang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China; School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China
| | - Dandan Song
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China; School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China
| | - Rong Tian
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, Med-X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China.
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3
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Zheng W, Saliba JG, Wei X, Shu Q, Pierson LM, Mao L, Liu C, Lyon CJ, Li CZ, Wimley WC, Hu TY. Nanopore-based disease diagnosis using pathogen-derived tryptic peptides from serum. NANO TODAY 2022; 45:101515. [PMID: 37034182 PMCID: PMC10081497 DOI: 10.1016/j.nantod.2022.101515] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Nanopore sensors have shown great utility in nucleic acid detection and sequencing approaches. Recent studies also indicate that current signatures produced by peptide-nanopore interactions can distinguish high purity peptide mixtures, but the utility of nanopore sensors in clinical applications still needs to be explored due to the inherent complexity of clinical specimens. To fill this gap between research and clinical nanopore applications, we describe a methodology to select peptide biomarkers suitable for use in an immunoprecipitation-coupled nanopore (IP-NP) assay, based on their pathogen specificity, antigenicity, charge, water solubility and ability to produce a characteristic nanopore interaction signature. Using tuberculosis as a proof-of-principle example in a disease that can be challenging to diagnose, we demonstrate that a peptide identified by this approach produced high-affinity antibodies and yielded a characteristic peptide signature that was detectable over a broad linear range, to detect and quantify a pathogen-derived peptide from digested human serum samples with high sensitivity and specificity. This nanopore signal distinguished serum from a TB case, non-disease controls, and from a TB-case after extended anti-TB treatment. We believe this assay approach should be readily adaptable to other infectious and chronic diseases that can be diagnosed by peptide biomarkers.
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Affiliation(s)
- Wenshu Zheng
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, LA, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Julian G. Saliba
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, LA, USA
- Department of Biomedical Engineering, Tulane University School of Science & Engineering, New Orleans, LA, USA
| | - Xiaojun Wei
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
| | - Qingbo Shu
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, LA, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Lane M. Pierson
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, LA, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Liyan Mao
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, LA, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Chang Liu
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
| | - Christopher J. Lyon
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, LA, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Chen-Zhong Li
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, LA, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - William C. Wimley
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Tony Ye Hu
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, LA, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
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4
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Abstract
Evolution has found countless ways to transport material across cells and cellular compartments separated by membranes. Protein assemblies are the cornerstone for the formation of channels and pores that enable this regulated passage of molecules in and out of cells, contributing to maintaining most of the fundamental processes that sustain living organisms. As in several other occasions, we have borrowed from the natural properties of these biological systems to push technology forward and have been able to hijack these nano-scale proteinaceous pores to learn about the physical and chemical features of molecules passing through them. Today, a large repertoire of biological pores is exploited as molecular sensors for characterizing biomolecules that are relevant for the advancement of life sciences and application to medicine. Although the technology has quickly matured to enable nucleic acid sensing with transformative implications for genomics, biological pores stand as some of the most promising candidates to drive the next developments in single-molecule proteomics.
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Affiliation(s)
- Simon Finn Mayer
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Chan Cao
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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5
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Niu H, Li MY, Ying YL, Long YT. An engineered third electrostatic constriction of aerolysin to manipulate heterogeneously charged peptide transport. Chem Sci 2022; 13:2456-2461. [PMID: 35310483 PMCID: PMC8864703 DOI: 10.1039/d1sc06459b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/02/2022] [Indexed: 12/27/2022] Open
Abstract
Reading the primary sequence directly using nanopores remains challenging due to the complex building blocks of 20 proteinogenic amino acids and the corresponding sophisticated structures. Compared to the uniformly negatively charged polynucleotides, biological nanopores hardly provide effective ionic current responses to all heterogeneously charged peptides under nearly physiological pH conditions. Herein, we precisely design a N226Q/S228K mutant aerolysin which creates a new electrostatic constriction named R3 in-between two natural sensing regions for controlling the capture and translocation of heterogeneously charged peptides. At nearly physiological pH, the decoration of positive charges at this constriction gives a large velocity of electroosmotic flow (EOF), leading to a maximum 8-fold increase in frequency for the heterogeneously charged peptides with the net charge from +1 to −3. Even the duration time of the negatively charged peptide Aβ35-25D4 in N226Q/S228K AeL also rises from 0.07 ± 0.01 ms to 0.63 ± 0.01 ms after introducing the third electrostatic constriction. Therefore, the N226Q/S228K aerolysin nanopore with three electrostatic constrictions realizes the dual goals of both capturing and decelerating heterogeneously charged peptides without labelling, even for the folded peptides. An engineered aerolysin nanopore captures all types of peptides despite the charges and folded structure, which facilitate the achievement of nanopore protein sequencing.![]()
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Affiliation(s)
- Hongyan Niu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Meng-Ying Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
- Chemistry and Biomedicine Innovation Center, 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
- Chemistry and Biomedicine Innovation Center, 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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Bhatti H, Jawed R, Ali I, Iqbal K, Han Y, Lu Z, Liu Q. Recent advances in biological nanopores for nanopore sequencing, sensing and comparison of functional variations in MspA mutants. RSC Adv 2021; 11:28996-29014. [PMID: 35478559 PMCID: PMC9038099 DOI: 10.1039/d1ra02364k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 08/09/2021] [Indexed: 12/14/2022] Open
Abstract
Biological nanopores are revolutionizing human health by the great myriad of detection and diagnostic skills. Their nano-confined area and ingenious shape are suitable to investigate a diverse range of molecules that were difficult to identify with the previous techniques. Additionally, high throughput and label-free detection of target analytes instigated the exploration of new bacterial channel proteins such as Fragaceatoxin C (FraC), Cytolysin A (ClyA), Ferric hydroxamate uptake component A (FhuA) and Curli specific gene G (CsgG) along with the former ones, like α-hemolysin (αHL), Mycobacterium smegmatis porin A (MspA), aerolysin, bacteriophage phi 29 and Outer membrane porin G (OmpG). Herein, we discuss some well-known biological nanopores but emphasize on MspA and compare the effects of site-directed mutagenesis on the detection ability of its mutants in view of the surface charge distribution, voltage threshold and pore-analyte interaction. We also discuss illustrious and latest advances in biological nanopores for past 2-3 years due to limited space. Last but not the least, we elucidate our perspective for selecting a biological nanopore and propose some future directions to design a customized nanopore that would be suitable for DNA sequencing and sensing of other nontrivial molecules in question.
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Affiliation(s)
- Huma Bhatti
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
| | - Rohil Jawed
- School of Life Science and Technology, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China
| | - Irshad Ali
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
| | - Khurshid Iqbal
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
| | - Yan Han
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
| | - Quanjun Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
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7
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Wei X, Zhang Z, Wang X, Lenhart B, Gambarini R, Gray J, Liu C. Insight into the effects of electrochemical factors on host-guest interaction induced signature events in a biological nanopore. NANOTECHNOLOGY AND PRECISION ENGINEERING 2021; 3:2-8. [PMID: 33786424 PMCID: PMC8006565 DOI: 10.1016/j.npe.2019.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The signature events caused by host-guest interactions in the nanopore system can be used as a novel and characteristic signal in quantitative detection and analysis of various molecules. However, the effect of several electrochemical factors on the host-guest interactions in nanopore still remains unknown. Here, we systematically studied host-guest interactions, especially oscillation of DNA-azide adamantane@cucurbit[6] in α-Hemolysin nanopore under varying pH, concentration of electrolytes and counterions (Li+, Na+, K+). Our results indicate correlations between the change of pH and the duration of the oscillation signal. In addition, the asymmetric electrolyte concentration and the charge of the counterions affects the frequency of signature events in oscillation signals, and even the integrity of the protein nanopore. This study provides insight into the design of a future biosensing platform based on signature oscillation signals of the host-guest interaction within a nanopore.
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Affiliation(s)
- Xiaojun Wei
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA.,Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
| | - Zehui Zhang
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA
| | - Xiaoqin Wang
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
| | - Brian Lenhart
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
| | - Roberto Gambarini
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA
| | - Jonathan Gray
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA
| | - Chang Liu
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA.,Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, USA
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8
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Li MY, Ying YL, Li S, Wang YQ, Wu XY, Long YT. Unveiling the Heterogenous Dephosphorylation of DNA Using an Aerolysin Nanopore. ACS NANO 2020; 14:12571-12578. [PMID: 32806044 DOI: 10.1021/acsnano.0c03215] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The simultaneous occurrence of multiple heterogeneous DNA phosphorylation statuses, which include 5' end phosphorylation, 5' end dephosphorylation, 3' end phosphorylation, and 3' end dephosphorylation, is crucial for regulating numerous cellular processes. Although there are many methods for detecting a single type of DNA phosphorylation, the direct and simultaneous identification of DNA phosphorylation/dephosphorylation on the 5' and/or 3' ends remains a challenge, let alone the unveiling of the heterogeneous catalysis processes of related phosphatases and kinases. Taking advantage of the charge-sensitive aerolysin nanopore interface, herein, an orientation-dependent sensing strategy is developed to enhance phosphorylation-site-dependent interaction with the nanopore sensing interface, enabling the direct and simultaneous electric identification of four heterogeneous phosphorylation statuses of a single DNA. By using this strategy, we can directly evaluate the heterogeneous dephosphorylation process of alkaline phosphatase (ALP) at the single-molecule level. Our results demonstrate that the ALP in fetal bovine serum preferentially catalyzes the 3' phosphate rather than both ends. The quantification of endogenous ALP activity in fetal bovine serum could reach the submilli-IU/L level. Our aerolysin measurements provide a direct look at the heterogeneous phosphorylation status of DNA, allowing the unveiling of the dynamic single-molecule functions of kinase and phosphatase.
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Affiliation(s)
- Meng-Yin Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
- Chemistry and Biomedicine Innovation Center, 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
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, P.R. China
| | - Shuang Li
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China
| | - Ya-Qian Wang
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China
| | - Xue-Yuan Wu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, 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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9
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Li X, Guo Z, Zheng X. Voltammetrically Measuring pH of Strong Basic Solution on Au Electrode Modified with Ag
3
PO
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Shell@Ag Core Nanoparticles. ChemistrySelect 2020. [DOI: 10.1002/slct.201904139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Xinni Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi ProvinceSchool of Chemistry and Chemical EngineeringShaanxi Normal University Xi'an 710062 PR China
| | - Zhihui Guo
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi ProvinceSchool of Chemistry and Chemical EngineeringShaanxi Normal University Xi'an 710062 PR China
| | - Xingwang Zheng
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi ProvinceSchool of Chemistry and Chemical EngineeringShaanxi Normal University Xi'an 710062 PR China
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10
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Yao F, Peng X, Su Z, Tian L, Guo Y, Kang XF. Crowding-Induced DNA Translocation through a Protein Nanopore. Anal Chem 2020; 92:3827-3833. [PMID: 32048508 DOI: 10.1021/acs.analchem.9b05249] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A crowded cellular environment is highly associated with many significant biological processes. However, the effect of molecular crowding on the translocation behavior of DNA through a pore has not been explored. Here, we use nanopore single-molecule analytical technique to quantify the thermodynamics and kinetics of DNA transport under heterogeneous cosolute PEGs. The results demonstrate that the frequency of the translocation event exhibits a nonmonotonic dependence on the crowding agent size, while both the event frequency and translocation time increase monotonically with increasing crowder concentration. In the presence of PEGs, the rate of DNA capture into the nanopore elevates 118.27-fold, and at the same time the translocation velocity decreases from 20 to 120 μs/base. Interestingly, the impact of PEG 4k on the DNA-nanopore interaction is the most notable, with up to ΔΔG = 16.27 kJ mol-1 change in free energy and 764.50-fold increase in the binding constant at concentration of 40% (w/v). The molecular crowding effect will has broad applications in nanopore biosensing and nanopore DNA sequencing in which the strategy to capture analyte and to control the transport is urgently required.
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Affiliation(s)
- Fujun Yao
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China
| | - Xiao Peng
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China
| | - Zhuoqun Su
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China
| | - Lei Tian
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China
| | - Yanli Guo
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China
| | - Xiao-Feng Kang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an 710069, P. R. China
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11
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Yuan B, Li S, Ying YL, Long YT. The analysis of single cysteine molecules with an aerolysin nanopore. Analyst 2020; 145:1179-1183. [DOI: 10.1039/c9an01965k] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Biological nanopore technology has the advantages of high selectivity and high reproducibility for characterizing single biomolecules.
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Affiliation(s)
- Bo Yuan
- School of Chemistry & Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- P.R. China
- School of Chemistry and Chemical Engineering
| | - Shuang Li
- School of Chemistry & Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- P.R. China
| | - Yi-Lun Ying
- School of Chemistry & Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- P.R. China
- School of Chemistry and Chemical Engineering
| | - Yi-Tao Long
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210023
- P.R. China
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12
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Wu X, Li M, Ying Y, Long Y. The Effects of Tetramethylammonium Cation on Oligonucleotide Analysis with Aerolysin Nanopore. ChemElectroChem 2019. [DOI: 10.1002/celc.201901376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Xue‐Yuan Wu
- School of Chemistry & Molecular EngineeringEast China University of Science and Technology 130 Meilong Road Shanghai 200237 P.R. China
| | - Meng‐Yin Li
- School of Chemistry & Molecular EngineeringEast China University of Science and Technology 130 Meilong Road Shanghai 200237 P.R. China
| | - Yi‐Lun Ying
- School of Chemistry & Molecular EngineeringEast China University of Science and Technology 130 Meilong Road Shanghai 200237 P.R. China
- School of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 P. R. China 163 Xianlin Road, Qixia District, Nanjing, Jiangsu Province
| | - Yi‐Tao Long
- School of Chemistry & Molecular EngineeringEast China University of Science and Technology 130 Meilong Road Shanghai 200237 P.R. China
- School of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 P. R. China 163 Xianlin Road, Qixia District, Nanjing, Jiangsu Province
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13
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Misawa N, Osaki T, Takeuchi S. Membrane protein-based biosensors. J R Soc Interface 2019; 15:rsif.2017.0952. [PMID: 29669891 DOI: 10.1098/rsif.2017.0952] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/19/2018] [Indexed: 01/09/2023] Open
Abstract
This review highlights recent development of biosensors that use the functions of membrane proteins. Membrane proteins are essential components of biological membranes and have a central role in detection of various environmental stimuli such as olfaction and gustation. A number of studies have attempted for development of biosensors using the sensing property of these membrane proteins. Their specificity to target molecules is particularly attractive as it is significantly superior to that of traditional human-made sensors. In this review, we classified the membrane protein-based biosensors into two platforms: the lipid bilayer-based platform and the cell-based platform. On lipid bilayer platforms, the membrane proteins are embedded in a lipid bilayer that bridges between the protein and a sensor device. On cell-based platforms, the membrane proteins are expressed in a cultured cell, which is then integrated in a sensor device. For both platforms we introduce the fundamental information and the recent progress in the development of the biosensors, and remark on the outlook for practical biosensing applications.
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Affiliation(s)
- Nobuo Misawa
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu, Kawasaki 213-0012, Japan
| | - Toshihisa Osaki
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu, Kawasaki 213-0012, Japan.,Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8505, Japan
| | - Shoji Takeuchi
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu, Kawasaki 213-0012, Japan .,Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8505, Japan
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14
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Li MY, Wang YQ, Ying YL, Long YT. Revealing the transient conformations of a single flavin adenine dinucleotide using an aerolysin nanopore. Chem Sci 2019; 10:10400-10404. [PMID: 32110330 PMCID: PMC6988595 DOI: 10.1039/c9sc03163d] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 09/20/2019] [Indexed: 12/13/2022] Open
Abstract
Flavin adenine dinucleotide (FAD) as a cofactor is involved in numerous important metabolic pathways where the biological function is intrinsically related to its transient conformations. The confined space of enzymes requires FAD set in its specific intermediate conformation. However, conventional methods only detect stable conformations of FAD molecules, while transient intermediates are hidden in ensemble measurements. There still exists a challenge to uncover the transient conformation of each FAD molecule, which hinders the understanding of the structure-activity relationship of the FAD mechanism. Here, we employ the electrochemically confined space of an aerolysin nanopore to directly characterize a series of transient conformations of every individual FAD. Based on distinguishable current blockages, the "stack", "open", and four quasi-stacked FADs are clearly determined in solution, which is further confirmed by temperature-dependent experiments and mutant aerolysin assay. Combined with molecular dynamics simulations, we achieved a direct correlation between the residual current ratio (I/I 0) and FAD backbone angle. These results would facilitate further understanding of the structure-activity relationship in the flavoprotein.
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Affiliation(s)
- Meng-Yin Li
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , 210023 , Nanjing , P. R. China . .,School of Chemistry and Molecule Engineering , East China University of Science and Technology , 200237 , Shanghai , P. R. China
| | - Ya-Qian Wang
- School of Chemistry and Molecule Engineering , East China University of Science and Technology , 200237 , Shanghai , P. R. China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , 210023 , Nanjing , P. R. China .
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , 210023 , Nanjing , P. R. China .
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15
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Li MY, Wang YQ, Lu Y, Ying YL, Long YT. Single Molecule Study of Hydrogen Bond Interactions Between Single Oligonucleotide and Aerolysin Sensing Interface. Front Chem 2019; 7:528. [PMID: 31417894 PMCID: PMC6684785 DOI: 10.3389/fchem.2019.00528] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 07/11/2019] [Indexed: 01/06/2023] Open
Abstract
The aerolysin nanopore displays a charming sensing capability for single oligonucleotide discrimination. When reading from the electrochemical signal, stronger interaction between the aerolysin nanopore and oligonucleotide represent prolonged duration time, thereby amplifying the hidden but intrinsic signal thus improving the sensitivity. In order to further understand and optimize the performance of the aerolysin nanopore, we focus on the investigation of the hydrogen bond interaction between nanopore, and analytes. Taking advantage of site-direct mutagenesis, single residue is replaced. According to whole protein sequence screening, the region near K238 is one of the key sensing regions. Such a positively charged amino acid is then mutagenized into cysteine and tyrosine denoted as K238C, and K238Y. As (dA)4 traverses the pores, K238C dramatically produces a six times longer duration time than the WT aerolysin nanopore at the voltage of +120 mV. However, K238Y shortens the dwell time which suggests the acceleration of the translocation causing poor sensitivity. Referring to our previous findings in K238G, and K238F, our results suggest that the hydrogen bond does not dominate the dynamic translocation process, but enhances the interaction between pores and analytes confined in such nanopore space. These insights give detailed information for the rational design of the sensing mechanism of the aerolysin nanopore, thereby providing further understanding for the weak interactions between biomolecules and the confined space for nanopore sensing.
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Affiliation(s)
- Meng-Yin Li
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Ya-Qian Wang
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Yao Lu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Yi-Lun Ying
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China.,State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Yi-Tao Long
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China.,State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
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16
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Cressiot B, Ouldali H, Pastoriza-Gallego M, Bacri L, Van der Goot FG, Pelta J. Aerolysin, a Powerful Protein Sensor for Fundamental Studies and Development of Upcoming Applications. ACS Sens 2019; 4:530-548. [PMID: 30747518 DOI: 10.1021/acssensors.8b01636] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The nanopore electrical approach is a breakthrough in single molecular level detection of particles as small as ions, and complex as biomolecules. This technique can be used for molecule analysis and characterization as well as for the understanding of confined medium dynamics in chemical or biological reactions. Altogether, the information obtained from these kinds of experiments will allow us to address challenges in a variety of biological fields. The sensing, design, and manufacture of nanopores is crucial to realize these objectives. For some time now, aerolysin, a pore forming toxin, and its mutants have shown high potential in real time analytical chemistry, size discrimination of neutral polymers, oligosaccharides, oligonucleotides and peptides at monomeric resolution, sequence identification, chemical modification on DNA, potential biomarkers detection, and protein folding analysis. This review focuses on the results obtained with aerolysin nanopores on the fields of chemistry, biology, physics, and biotechnology. We discuss and compare as well the results obtained with other protein channel sensors.
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Affiliation(s)
- Benjamin Cressiot
- LAMBE, Université
Evry, Université de Cergy-Pontoise, CNRS, CEA, Université
Paris-Saclay, 91025, Evry, France
| | - Hadjer Ouldali
- LAMBE, Université
Cergy-Pontoise, Université d’Evry, CNRS, CEA, Université
Paris-Seine, 95000, Cergy, France
| | - Manuela Pastoriza-Gallego
- LAMBE, Université
Cergy-Pontoise, Université d’Evry, CNRS, CEA, Université
Paris-Seine, 95000, Cergy, France
| | - Laurent Bacri
- LAMBE, Université
Evry, Université de Cergy-Pontoise, CNRS, CEA, Université
Paris-Saclay, 91025, Evry, France
| | | | - Juan Pelta
- LAMBE, Université
Evry, Université de Cergy-Pontoise, CNRS, CEA, Université
Paris-Saclay, 91025, Evry, France
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17
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Ma X, Miao P. Silver nanoparticle@DNA tetrahedron-based colorimetric detection of HIV-related DNA with cascade strand displacement amplification. J Mater Chem B 2019; 7:2608-2612. [PMID: 32254992 DOI: 10.1039/c9tb00274j] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
DNA tetrahedron-modified silver nanoparticles (AgNPs) were achieved via amino-silver chemistry for the first time and were applied as a colorimetric biosensor for detecting HIV-related DNA. Target DNA initiated strand displacement polymerization and nicking endonuclease-aided cycles were involved to link DNA tetrahedron-modified AgNPs, reporting colorimetric responses. This developed method showed excellent specificity and sensitivity. A wide linear range from 1 to 15 000 nM was achieved with a limit of detection of 0.84 nM. Moreover, it was successfully applied to determine DNA in blood serum samples.
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Affiliation(s)
- Xiaoyi Ma
- University of Science and Technology of China, Hefei 230026, China.
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18
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Sui XJ, Li MY, Ying YL, Yan BY, Wang HF, Zhou JL, Gu Z, Long YT. Aerolysin Nanopore Identification of Single Nucleotides Using the AdaBoost Model. JOURNAL OF ANALYSIS AND TESTING 2019. [DOI: 10.1007/s41664-019-00088-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Nawaz H, Tian W, Zhang J, Jia R, Yang T, Yu J, Zhang J. Visual and Precise Detection of pH Values under Extreme Acidic and Strong Basic Environments by Cellulose-Based Superior Sensor. Anal Chem 2019; 91:3085-3092. [PMID: 30648395 DOI: 10.1021/acs.analchem.8b05554] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Precise determination of pH values with an instrument-free mode is challenging and practical in industry processes, life science, and environmental monitoring. Here, taking advantage of the intramolecular charge transfer process, we construct a cellulose-based superior pH sensor, Phen-MDI-CA, which contains a highly sensitive, pH-responsive, and extended conjugation structure by combining phenanthroline moiety as a chromophore with urea group as a bridge. The resultant Phen-MDI-CA can precisely and visually determine pH values under extreme acidic and strong basic environments, depending on the different colors. In visible light mode, Phen-MDI-CA can readily discriminate the pH values of 14.0, 13.0, 12.0, and 11.0 and distinguish pH 2.0 from 1.0 by the naked eye. In fluorescent mode, Phen-MDI-CA can recognize more accurate pH values of pH 11.6-13.2 at a 0.2-0.4 pH interval by the high-contrasting color change. After addition of pH-irresponsive dyes as the reference, the corresponding ratiometric systems exhibit different colors at a 0.2-0.4 pH interval during the pH values of 11.0-14.0 and 1.0-2.0. Benefiting from the excellent formability, the Phen-MDI-CA was readily fabricated into pH test strips by coating method. To our knowledge, this is the first study to monitor extreme acidity and strong basicity in such precise pH values with an instrument-free mode.
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Affiliation(s)
- Haq Nawaz
- CAS Key Laboratory of Engineering Plastics, CAS Research/Education Center for Excellence in Molecular Sciences , Institute of Chemistry, Chinese Academy of Sciences (CAS) , Beijing 100190 , China
| | - Weiguo Tian
- CAS Key Laboratory of Engineering Plastics, CAS Research/Education Center for Excellence in Molecular Sciences , Institute of Chemistry, Chinese Academy of Sciences (CAS) , Beijing 100190 , China
| | - Jinming Zhang
- CAS Key Laboratory of Engineering Plastics, CAS Research/Education Center for Excellence in Molecular Sciences , Institute of Chemistry, Chinese Academy of Sciences (CAS) , Beijing 100190 , China
| | - Ruonan Jia
- CAS Key Laboratory of Engineering Plastics, CAS Research/Education Center for Excellence in Molecular Sciences , Institute of Chemistry, Chinese Academy of Sciences (CAS) , Beijing 100190 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Tiantian Yang
- CAS Key Laboratory of Engineering Plastics, CAS Research/Education Center for Excellence in Molecular Sciences , Institute of Chemistry, Chinese Academy of Sciences (CAS) , Beijing 100190 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Jian Yu
- CAS Key Laboratory of Engineering Plastics, CAS Research/Education Center for Excellence in Molecular Sciences , Institute of Chemistry, Chinese Academy of Sciences (CAS) , Beijing 100190 , China
| | - Jun Zhang
- CAS Key Laboratory of Engineering Plastics, CAS Research/Education Center for Excellence in Molecular Sciences , Institute of Chemistry, Chinese Academy of Sciences (CAS) , Beijing 100190 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
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20
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Hu ZL, Li MY, Liu SC, Ying YL, Long YT. A lithium-ion-active aerolysin nanopore for effectively trapping long single-stranded DNA. Chem Sci 2019; 10:354-358. [PMID: 30746084 PMCID: PMC6334748 DOI: 10.1039/c8sc03927e] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/12/2018] [Indexed: 12/15/2022] Open
Abstract
Wild-type aerolysin (AeL) nanopores allow direct single nucleotide discrimination of very short oligonucleotides (≤10 nt) without labelling, which shows great potential for DNA sensing. To achieve real applications, one major obstacle of AeL is its poor capture ability of long single-stranded DNA (ssDNA, >10 nt). Here, we have proposed a novel and robust strategy for the electrostatic focusing of long ssDNA into a lithium-chloride (LiCl)-active AeL. By using this method, for the first time we have demonstrated AeL detection of ssDNA longer than 100 nt. Due to screening more negative charges, LiCl improves AeL capture ability of long ssDNA (i.e. 60 nt) by 2.63- to 10.23-fold compared to KCl. Further calculations and molecular dynamics simulations revealed that strong binding between Li+ and the negatively charged residue neutralized the AeL, leading to a reduction in the energy barrier for ssDNA capture. These findings facilitate the future high-throughput applications of AeL in genetic and epigenetic diagnostics.
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Affiliation(s)
- Zheng-Li Hu
- Key Laboratory for Advanced Materials , School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China . ; Tel: +86-21-64252339
| | - 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 . ; Tel: +86-21-64252339
| | - Shao-Chuang Liu
- Key Laboratory for Advanced Materials , School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China . ; Tel: +86-21-64252339
| | - 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 . ; Tel: +86-21-64252339
| | - 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 . ; Tel: +86-21-64252339
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21
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Wang Y, Gu LQ, Tian K. The aerolysin nanopore: from peptidomic to genomic applications. NANOSCALE 2018; 10:13857-13866. [PMID: 29998253 PMCID: PMC6157726 DOI: 10.1039/c8nr04255a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The aerolysin pore (ARP) is a newly emerging nanopore that has been extensively used for peptide and protein sensing. Recently, several groups have explored the application of ARP in detecting genetic and epigenetic markers. This brief review summarizes the current applications of ARP, progressing from peptidomic to genomic detection; the recently reported site-directed mutagenesis of ARP; and new genomic DNA sensing approaches, and their advantages and disadvantages. This review will also discuss the perspectives and future applications of ARP for nucleic acid sequencing and biomolecule sensing.
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Affiliation(s)
- Yong Wang
- Virginia G. Piper Biodesign Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
| | - Li-Qun Gu
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211, USA.
| | - Kai Tian
- Department of Bioengineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211, USA.
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22
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Mapping the sensing spots of aerolysin for single oligonucleotides analysis. Nat Commun 2018; 9:2823. [PMID: 30026547 PMCID: PMC6053387 DOI: 10.1038/s41467-018-05108-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 06/05/2018] [Indexed: 12/05/2022] Open
Abstract
Nanopore sensing is a powerful single-molecule method for DNA and protein sequencing. Recent studies have demonstrated that aerolysin exhibits a high sensitivity for single-molecule detection. However, the lack of the atomic resolution structure of aerolysin pore has hindered the understanding of its sensing capabilities. Herein, we integrate nanopore experimental results and molecular simulations based on a recent pore structural model to precisely map the sensing spots of this toxin for ssDNA translocation. Rationally probing ssDNA length and composition upon pore translocation provides new important insights for molecular determinants of the aerolysin nanopore. Computational and experimental results reveal two critical sensing spots (R220, K238) generating two constriction points along the pore lumen. Taking advantage of the sensing spots, all four nucleobases, cytosine methylation and oxidation of guanine can be clearly identified in a mixture sample. The results provide evidence for the potential of aerolysin as a nanosensor for DNA sequencing. Nanopores are an emerging powerful single-molecule method of DNA sequencing. Here the authors map the structure of aerolysin for use as a nanopore and show detection of modified and unmodified nucleobases.
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23
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Wang YQ, Li MY, Qiu H, Cao C, Wang MB, Wu XY, Huang J, Ying YL, Long YT. Identification of Essential Sensitive Regions of the Aerolysin Nanopore for Single Oligonucleotide Analysis. Anal Chem 2018; 90:7790-7794. [PMID: 29882404 DOI: 10.1021/acs.analchem.8b01473] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The aerolysin nanopore channel is one of the confined spaces for single molecule analysis which displays high spatial and temporal resolution for the discrimination of single nucleotides, identification of DNA base modification, and analyzing the structural transition of DNAs. However, to overcome the challenge of achieving the ultimate goal of the widespread real analytical application, it is urgent to probe the sensing regions of the aerolysin to further improve the sensitivity. In this paper, we explore the sensing regions of the aerolysin nanopore by a series of well-designed mutant nanopore experiments combined with molecular dynamics simulations-based electrostatic analysis. The positively charged lumen-exposed Lys-238, identified as one of the key sensing sites due to the presence of a deep valley in the electrostatic potentials, was replaced by different charged and sized amino acids. The results show that the translocation time of oligonucleotides through the nanopore can be readily modulated by the choice of the target amino acid at the 238 site. In particular, a 7-fold slower translocation at a voltage bias of +120 mV is observed with respect to the wild-type aerolysin, which provides a high resolution for methylated cytosine discrimination. We further determine that both the electrostatic properties and geometrical structure of the aerolysin nanopore are crucial to its sensing ability. These insights open ways for rationally designing the sensing mechanism of the aerolysin nanopore, thus providing a novel paradigm for nanopore sensing.
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Affiliation(s)
- 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
| | - Hu Qiu
- State Key Laboratory of Mechanics and Control of Mechanical Structures , Nanjing University of Aeronautics and Astronautics , Nanjing , 210016 , P. R. China
| | - Chan Cao
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China
| | - Ming-Bo Wang
- School of Pharmacy , East China University of Science and Technology , Shanghai , 200237 , P. R. China
| | - Xue-Yuan Wu
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China
| | - Jin Huang
- School of Pharmacy , 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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24
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Li S, Cao C, Yang J, Long YT. Detection of Peptides with Different Charges and Lengths by Using the Aerolysin Nanopore. ChemElectroChem 2018. [DOI: 10.1002/celc.201800288] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Shuang Li
- Key Laboratory for Advanced Materials School of Chemistry & Molecular Engineering; East China University of Science and Technology; 130 Meilong Road Shanghai 200237 P.R. China
| | - Chan Cao
- Key Laboratory for Advanced Materials School of Chemistry & Molecular Engineering; East China University of Science and Technology; 130 Meilong Road Shanghai 200237 P.R. China
| | - Jie Yang
- Key Laboratory for Advanced Materials School of Chemistry & Molecular Engineering; East China University of Science and Technology; 130 Meilong Road 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; 130 Meilong Road Shanghai 200237 P.R. China
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25
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Wang YQ, Cao C, Ying YL, Li S, Wang MB, Huang J, Long YT. Rationally Designed Sensing Selectivity and Sensitivity of an Aerolysin Nanopore via Site-Directed Mutagenesis. ACS Sens 2018; 3:779-783. [PMID: 29619834 DOI: 10.1021/acssensors.8b00021] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Selectivity and sensitivity are two key parameters utilized to describe the performance of a sensor. In order to investigate selectivity and sensitivity of the aerolysin nanosensor, we manipulated its surface charge at different locations via single site-directed mutagenesis. To study the selectivity, we replaced the positively charged R220 at the entrance of the pore with negatively charged glutamic acid, resulting in barely no current blockages for sensing negatively charged oligonucleotides. For the sensitivity, we substituted the positively charged lumen-exposed amino acid K238 located at trans-ward third of the β-barrel stem with glutamic acid. This leads to a surprisingly longer duration time at +140 mV, which is about 20 times slower in translocation speed for Poly(dA)4 compared to that of wild-type aerolysin, indicating the stronger pore-analyte interactions and enhanced sensitivity. Therefore, it is both feasible and understandable to rationally design confined biological nanosensors for single molecule detection with high selectivity and sensitivity.
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Affiliation(s)
- 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
| | - Chan Cao
- 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
| | - Shuang Li
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Ming-Bo Wang
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Jin Huang
- School of Pharmacy, 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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26
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Borghei YS, Hosseini M, Ganjali MR, Hosseinkhani S. A novel BRCA1 gene deletion detection in human breast carcinoma MCF-7 cells through FRET between quantum dots and silver nanoclusters. J Pharm Biomed Anal 2018; 152:81-88. [DOI: 10.1016/j.jpba.2018.01.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/31/2017] [Accepted: 01/08/2018] [Indexed: 02/01/2023]
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27
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Hu ZL, Li ZY, Ying YL, Zhang J, Cao C, Long YT, Tian H. Real-Time and Accurate Identification of Single Oligonucleotide Photoisomers via an Aerolysin Nanopore. Anal Chem 2018. [PMID: 29516718 DOI: 10.1021/acs.analchem.8b00096] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Identification of the configuration for the photoresponsive oligonucleotide plays an important role in the ingenious design of DNA nanomolecules and nanodevices. Due to the limited resolution and sensitivity of present methods, it remains a challenge to determine the accurate configuration of photoresponsive oligonucleotides, much less a precise description of their photoconversion process. Here, we used an aerolysin (AeL) nanopore-based confined space for real-time determination and quantification of the absolute cis/ trans configuration of each azobenzene-modified oligonucleotide (Azo-ODN) with a single molecule resolution. The two completely separated current distributions with narrow peak widths at half height (<0.62 pA) are assigned to cis/ trans-Azo-ODN isomers, respectively. Due to the high current sensitivity, each isomer of Azo-ODN could be undoubtedly identified, which gives the accurate photostationary conversion values of 82.7% for trans-to- cis under UV irradiation and 82.5% for cis-to- trans under vis irradiation. Further real-time kinetic evaluation reveals that the photoresponsive rate constants of Azo-ODN from trans-to- cis and cis-to -trans are 0.43 and 0.20 min-1, respectively. This study will promote the sophisticated design of photoresponsive ODN to achieve an efficient and applicable photocontrollable process.
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Affiliation(s)
- Zheng-Li Hu
- Key Laboratory for Advanced Materials and School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China
| | - Zi-Yuan Li
- Key Laboratory for Advanced Materials and 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 and School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China
| | - Junji Zhang
- Key Laboratory for Advanced Materials and School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China
| | - Chan Cao
- Key Laboratory for Advanced Materials and 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 and School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China
| | - He Tian
- Key Laboratory for Advanced Materials and School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China
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