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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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Wang X, Stevens KC, Ting JM, Marras AE, Rezvan G, Wei X, Taheri-Qazvini N, Tirrell MV, Liu C. Translocation Behaviors of Synthetic Polyelectrolytes through Alpha-Hemolysin (α-HL) and Mycobacterium smegmatis Porin A (MspA) Nanopores. JOURNAL OF THE ELECTROCHEMICAL SOCIETY 2022; 169:057510. [PMID: 35599744 PMCID: PMC9121822 DOI: 10.1149/1945-7111/ac6c55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
DNAs have been used as probes for nanopore sensing of noncharged biomacromolecules due to its negative phosphate backbone. Inspired by this, we explored the potential of diblock synthetic polyelectrolytes as more flexible and inexpensive nanopore sensing probes by investigating translocation behaviors of PEO-b-PSS and PEO-b-PVBTMA through commonly used alpha-hemolysin (α-HL) and Mycobacterium smegmatis porin A (MspA) nanopores. Translocation recordings in different configurations of pore orientation and testing voltage indicated efficient PEO-b-PSS translocations through α-HL and PEO-b-PVBTMA translocations through MspA. This work provides insight into synthetic polyelectrolyte-based probes to expand probe selection and flexibility for nanopore sensing.
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Affiliation(s)
- Xiaoqin Wang
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Kaden C. Stevens
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Jeffrey M. Ting
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Alexander E. Marras
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Gelareh Rezvan
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Xiaojun Wei
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, USA
- Biomedical Engineering Program, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Nader Taheri-Qazvini
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, USA
- Biomedical Engineering Program, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Matthew V. Tirrell
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Chang Liu
- Department of Chemical Engineering, University of South Carolina, Columbia, South Carolina 29208, USA
- Biomedical Engineering Program, University of South Carolina, Columbia, South Carolina 29208, USA
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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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4
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Nanodevices for Biological and Medical Applications: Development of Single-Molecule Electrical Measurement Method. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12031539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A comprehensive detection of a wide variety of diagnostic markers is required for the realization of personalized medicine. As a sensor to realize such personalized medicine, a single molecule electrical measurement method using nanodevices is currently attracting interest for its comprehensive simultaneous detection of various target markers for use in biological and medical application. Single-molecule electrical measurement using nanodevices, such as nanopore, nanogap, or nanopipette devices, has the following features:; high sensitivity, low-cost, high-throughput detection, easy-portability, low-cost availability by mass production technologies, and the possibility of integration of various functions and multiple sensors. In this review, I focus on the medical applications of single- molecule electrical measurement using nanodevices. This review provides information on the current status and future prospects of nanodevice-based single-molecule electrical measurement technology, which is making a full-scale contribution to realizing personalized medicine in the future. Future prospects include some discussion on of the current issues on the expansion of the application requirements for single-mole-cule measurement.
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Nanoparticle-assisted detection of nucleic acids in a polymeric nanopore with a large pore size. Biosens Bioelectron 2021; 196:113697. [PMID: 34649096 PMCID: PMC8643331 DOI: 10.1016/j.bios.2021.113697] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/03/2021] [Accepted: 10/07/2021] [Indexed: 01/17/2023]
Abstract
Rapid and accurate detection of nucleic acids is of paramount importance in many fields, including medical diagnosis, gene therapy and virus identification. In this work, by taking advantage of two DNA hybridization probes, one of which was immobilized on the surface of gold nanoparticles, while the other was free in solution, detection of short length nucleic acids was successfully achieved using a large size (20 nm tip diameter) polyethylene terephythalate (PET) nanopore. The sensor was sensitive and selective: DNA samples with concentrations at as low as 0.5 nM could be detected within minutes and the number of mismatches can be discerned from the translocation frequency. Furthermore, the nanopore can be repeatedly used many times. Our developed large-size nanopore sensing platform offers the potential for fieldable/point-of-care diagnostic applications.
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Chen X, Zhang Y, Guan X. Simultaneous detection of multiple proteases using a non-array nanopore platform. NANOSCALE 2021; 13:13658-13664. [PMID: 34477641 PMCID: PMC8485758 DOI: 10.1039/d1nr04085e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Multiplexing methods which are capable of measurement of multiple analytes in a single assay are of great importance in many fields. The conventional strategy for simultaneous detection of multiple species is to construct a sensor array. Herein, we report an innovative multiplex multi-analyte detection platform in a non-array format for protease measurement. By monitoring protease degradation of a single peptide substrate containing two cleavage sites for a disintegrin and metalloproteinase 10 (ADAM10) and a disintegrin and metalloproteinase 10 (ADAM17) in a single nanopore, simultaneous detection and quantification of these two model proteases in mixture samples could satisfactorily be accomplished. Our developed multiplexing sensing platform has the potential to be coupled with the traditional sensor array to further improve the multiplexing capability of the sensor, which may find useful applications in clinical diagnosis and prognosis.
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Affiliation(s)
- Xiaohan Chen
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA.
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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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Chen X, Zhang Y, Arora P, Guan X. Nanopore Stochastic Sensing Based on Non-covalent Interactions. Anal Chem 2021; 93:10974-10981. [PMID: 34319076 DOI: 10.1021/acs.analchem.1c02102] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A variety of species could be detected by using nanopores engineered with various recognition sites based upon non-covalent interactions, including electrostatic, aromatic, and hydrophobic interactions. The existence of these engineered non-covalent bonding sites was supported by the single-channel recording technique. The advantage of the non-covalent interaction-based sensing strategy was that the recognition site of the engineered nanopore was not specific for a particular molecule but instead selective for a class of species (e.g., cationic, anionic, aromatic, and hydrophobic). Since different species produce current modulations with quite different signatures represented by amplitude, residence time, and even characteristic voltage-dependence curve, the non-covalent interaction-based nanopore sensor could not only differentiate individual molecules in the same category but also enable differentiation between species with similar structures or molecular weights. Hence, our developed non-covalent interaction-based nanopore sensing strategy may find useful application in the detection of molecules of medical and/or environmental importance.
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Affiliation(s)
- Xiaohan Chen
- Department of Chemistry, Illinois Institute of Technology, 3101 S. Dearborn Street, Chicago, Illinois 60616, United States
| | - Youwen Zhang
- Department of Chemistry, Illinois Institute of Technology, 3101 S. Dearborn Street, Chicago, Illinois 60616, United States
| | - Pearl Arora
- Department of Chemistry, Illinois Institute of Technology, 3101 S. Dearborn Street, Chicago, Illinois 60616, United States
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, 3101 S. Dearborn Street, Chicago, Illinois 60616, United States
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9
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Hu Z, Huo M, Ying Y, Long Y. Biological Nanopore Approach for Single‐Molecule Protein Sequencing. Angew Chem Int Ed Engl 2021; 60:14738-14749. [DOI: 10.1002/anie.202013462] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Indexed: 12/21/2022]
Affiliation(s)
- Zheng‐Li Hu
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
| | - Ming‐Zhu Huo
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue 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 163 Xianlin Avenue Nanjing 210023 P. R. China
- Chemistry and Biomedicine Innovation Center Nanjing University 163 Xianlin Avenue 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 163 Xianlin Avenue Nanjing 210023 P. R. China
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10
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Hu Z, Huo M, Ying Y, Long Y. Biological Nanopore Approach for Single‐Molecule Protein Sequencing. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202013462] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Zheng‐Li Hu
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue Nanjing 210023 P. R. China
| | - Ming‐Zhu Huo
- State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University 163 Xianlin Avenue 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 163 Xianlin Avenue Nanjing 210023 P. R. China
- Chemistry and Biomedicine Innovation Center Nanjing University 163 Xianlin Avenue 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 163 Xianlin Avenue Nanjing 210023 P. R. China
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Yan H, Zhang Z, Weng T, Zhu L, Zhang P, Wang D, Liu Q. Recognition of Bimolecular Logic Operation Pattern Based on a Solid-State Nanopore. SENSORS (BASEL, SWITZERLAND) 2020; 21:s21010033. [PMID: 33374742 PMCID: PMC7793508 DOI: 10.3390/s21010033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 05/17/2023]
Abstract
Nanopores have a unique advantage for detecting biomolecules in a label-free fashion, such as DNA that can be synthesized into specific structures to perform computations. This method has been considered for the detection of diseased molecules. Here, we propose a novel marker molecule detection method based on DNA logic gate by deciphering a variable DNA tetrahedron structure using a nanopore. We designed two types of probes containing a tetrahedron and a single-strand DNA tail which paired with different parts of the target molecule. In the presence of the target, the two probes formed a double tetrahedron structure. As translocation of the single and the double tetrahedron structures under bias voltage produced different blockage signals, the events could be assigned into four different operations, i.e., (0, 0), (0, 1), (1, 0), (1, 1), according to the predefined structure by logic gate. The pattern signal produced by the AND operation is obviously different from the signal of the other three operations. This pattern recognition method has been differentiated from simple detection methods based on DNA self-assembly and nanopore technologies.
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Affiliation(s)
- Han Yan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, China; (H.Y.); (Z.Z.); (L.Z.)
| | - Zhen Zhang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, China; (H.Y.); (Z.Z.); (L.Z.)
| | - Ting Weng
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (T.W.); (P.Z.); (D.W.)
| | - Libo Zhu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, China; (H.Y.); (Z.Z.); (L.Z.)
| | - Pang Zhang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (T.W.); (P.Z.); (D.W.)
| | - Deqiang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (T.W.); (P.Z.); (D.W.)
| | - Quanjun Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, China; (H.Y.); (Z.Z.); (L.Z.)
- Correspondence:
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12
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Zhang Y, Chen X, Yuan S, Wang L, Guan X. Joint Entropy-Assisted Graphene Oxide-Based Multiplexing Biosensing Platform for Simultaneous Detection of Multiple Proteases. Anal Chem 2020; 92:15042-15049. [PMID: 33118812 DOI: 10.1021/acs.analchem.0c03007] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Due to the limited clinical utility of individual biomarkers, there is growing recognition of the need for combining multiple biomarkers as a panel to improve the accuracy and efficacy of disease diagnosis and prognosis. The conventional method to detect multiple analyte species is to construct a sensor array, which consists of an array of individual selective probes for different species. In this work, by using cancer biomarker matrix metalloproteinases (MMPs) and a disintegrin and metalloproteinases (ADAMs) as model analytes and functionalized nanographene oxide (nGO) as a sensing element, we developed a multiplexing fluorescence sensor in a nonarray format for simultaneous measurement of the activities of multiple proteases. The constructed nGO-based biosensor was rapid, sensitive, and selective and was also utilized for the successful profiling of ADAMs/MMPs in simulated serum samples. Furthermore, we showed that joint entropy and programming could be utilized to guide experiment design, especially in terms of the selection of a subset of proteases from the entire MMPs/ADAMs family as an appropriate biomarker panel. Our developed nGO-based multiplex sensing platform should find useful application in early cancer detection and diagnosis.
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Affiliation(s)
- Youwen Zhang
- Department of Chemistry, Illinois Institute of Technology, 3101 South Dearborn Street, Chicago, Illinois 60616, United States
| | - Xiaohan Chen
- Department of Chemistry, Illinois Institute of Technology, 3101 South Dearborn Street, Chicago, Illinois 60616, United States
| | - Shaoqing Yuan
- Amazon, 2121 Seventh Avenue, Seattle, Washington 98121, United States
| | - 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
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, 3101 South Dearborn Street, Chicago, Illinois 60616, United States
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13
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Wang Y, Zhang Y, Chen X, Guan X, Wang L. Analysis with biological nanopore: On-pore, off-pore strategies and application in biological fluids. Talanta 2020; 223:121684. [PMID: 33303138 DOI: 10.1016/j.talanta.2020.121684] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 10/23/2022]
Abstract
Inspired from ion channels in biology, nanopores have been developed as promising analytical tools. In principle, nanopores provide crucial information from the observation and analysis of ionic current modulations caused by the interaction between target analytes and fluidic pores. In this respect, the biological, chemical and physical parameters of the nanopore regime need to be well-understood and regulated for intermolecular interaction. Because of well-defined molecular structures, biological nanopores consequently are of a focal point, allowing precise interaction analysis at single-molecule level. In this overview, two analytical strategies are summarized and discussed accordingly, upon the challenges arising in case-dependent analysis using biological nanopores. One kind of strategies relies on modification, functionalization and engineering on nanopore confined interface to improve molecular recognition sites (on-pore strategies); The other kind of highlighted strategies concerns to measurement of various chemistry/biochemistry based interactions triggered by employed molecular agents or probes (off-pore strategies). In particularly, a few recent paradigms using these strategies for practical application of accurate analysis of biomarkers in biological fluids are illustrated. To end, the challenging and future outlook of using analytical tools by means of biological nanopores are depicted.
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Affiliation(s)
- 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
| | - Youwen Zhang
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Xiaohan Chen
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, 60616, USA.
| | - 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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14
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Zhang Y, Chen X, Wang C, Roozbahani GM, Chang HC, Guan X. Chemically functionalized conical PET nanopore for protein detection at the single-molecule level. Biosens Bioelectron 2020; 165:112289. [PMID: 32729470 DOI: 10.1016/j.bios.2020.112289] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/04/2020] [Accepted: 05/10/2020] [Indexed: 12/18/2022]
Abstract
Proteins are essential for all living organisms, and perform a wide variety of functions in the cell and human body, including structural, mechanical, biochemical, and signaling. Since proteins can serve as valuable biomarkers for health status and diseases states, and enable personalized medicine, sensitive and rapid detection of proteins is of paramount importance. Herein, we report a chemically functionalized conical shaped poly-(ethylene terephthalate) nanopore (PET nanopore) as a stochastic sensing element for detection of proteins at the single-molecule level. We demonstrate that the PET nanopore sensor is not only sensitive and selective, but also can differentiate proteins rapidly, offering the potential for label-free protein detection and characterization. Our developed PET nanopore sensing strategy not only provides a general platform for exploring fundamental protein dynamics and rapid detection of proteins at the single-molecule level, but also opens new avenues toward advanced deeper understanding of enzymes, development of more efficient biosensing technologies, and constructing novel biomimetic nanopore systems.
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Affiliation(s)
- Youwen Zhang
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL, 60616, USA
| | - Xiaohan Chen
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL, 60616, USA
| | - Ceming Wang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Golbarg M Roozbahani
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL, 60616, USA
| | - Hsueh-Chia Chang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL, 60616, USA.
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15
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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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Roozbahani GM, Zhang Y, Chen X, Soflaee MH, Guan X. Enzymatic reaction-based nanopore detection of zinc ions. Analyst 2019; 144:7432-7436. [PMID: 31691699 DOI: 10.1039/c9an01784d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report a label-free nanopore sensor for the detection of Zn2+ ions. By taking advantage of the cleavage of a substrate peptide by zinc-dependent enzymes, nanomolar concentrations of Zn2+ ions could be detected within minutes. Furthermore, structurally similar transition metals such as Ni2+, Co2+, Hg2+, Cu2+, and Cd2+ did not interfere with their detection. The enzymatic reaction-based nanopore sensing strategy developed in this work may find potential applications in environmental monitoring and medical diagnosis.
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