1
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Sauciuc A, Whittaker J, Tadema M, Tych K, Guskov A, Maglia G. Blobs form during the single-file transport of proteins across nanopores. Proc Natl Acad Sci U S A 2024; 121:e2405018121. [PMID: 39264741 PMCID: PMC11420176 DOI: 10.1073/pnas.2405018121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 08/05/2024] [Indexed: 09/14/2024] Open
Abstract
The transport of biopolymers across nanopores is an important biological process currently under investigation for the rapid analysis of DNA and proteins. While the transport of DNA is generally understood, methods to induce unfolded protein translocation have only recently been discovered (Yu et al., 2023, Sauciuc et al., 2023). Here, we found that during electroosmotically driven translocation of polypeptides, blob-like structures typically form inside nanopores, often obstructing their transport and preventing addressing individual amino acids. This is in contrast with the electrophoretic transport of DNA, where the formation of such structures has not been reported. Comparisons between different nanopore sizes and shapes and modifications by different surface chemistries allowed formulating a mechanism for blob formation. We also show that single-file transport can be achieved by using 1) nanopores that have an entry and an internal diameter smaller than the persistence length of the polymer, 2) nanopores with a nonsticky (i.e., nonaromatic) inner surface, and 3) moderate translocation velocities. These experiments provide a basis for understanding polypeptide transport under confinement and for improving the design and engineering of nanopores for protein analysis.
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Affiliation(s)
- Adina Sauciuc
- Chemical Biology I, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Jacob Whittaker
- Chemical Biology I, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Matthijs Tadema
- Chemical Biology I, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Katarzyna Tych
- Chemical Biology I, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Albert Guskov
- Chemical Biology I, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Giovanni Maglia
- Chemical Biology I, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
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2
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He P, Wang H, Zhu A, Zhang Z, Sha J, Ni Z, Chen Y. Detection of Intrinsically Disordered Peptides by Biological Nanopore. Chem Asian J 2024; 19:e202400389. [PMID: 38865098 DOI: 10.1002/asia.202400389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/03/2024] [Accepted: 06/11/2024] [Indexed: 06/13/2024]
Abstract
Intrinsically disordered protein regions (IDPRs) are pivotal in regulation of transcription and facilitation of signal transduction. Because of their multiple conformational states of structure, characterizing the highly flexible structures of IDPRs becomes challenging. Herein, we employed the wild-type (WT) aerolysin nanopore as a real-time biosensor for identification and monitoring of long peptides containing IDPRs. This sensor successfully identified three intrinsically disordered peptides, with the lengths up to 43 amino acids, by distinguishing the unique signatures of blockade current and duration time. The analysis of the binding constant revealed that interactions between the nanopore and peptides are critical for peptide translocation, which suggests that mechanisms beyond mere volume exclusion. Furthermore, we were able to compare the conformational stabilities of various IDPRs by examining the detailed current traces of blockade events. Our approach can detect the conformational changes of IDPR in a confined nanopore space. These insights broaden the understanding of peptide structural changes. The nanopore biosensor showed the potential to study the conformations change of IDPRs, IDPRs transmembrane interactions, and protein drug discovery.
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Affiliation(s)
- Pinyao He
- School of Mechanical Engineering, Southeast University, Nanjing, 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Haiyan Wang
- School of Mechanical Engineering, Southeast University, Nanjing, 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
- Engineering Research Center of New Light Sources Technology and Equipment, Ministry of Education, Southeast University, Nanjing, 211189, China
| | - Anqi Zhu
- School of Mechanical Engineering, Southeast University, Nanjing, 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Zhenyu Zhang
- School of Mechanical Engineering, Southeast University, Nanjing, 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Jingjie Sha
- School of Mechanical Engineering, Southeast University, Nanjing, 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Zhonghua Ni
- School of Mechanical Engineering, Southeast University, Nanjing, 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Yunfei Chen
- School of Mechanical Engineering, Southeast University, Nanjing, 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
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3
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Li M, Wang J, Zhang C, Zhao X, Xiong Y, Cao Y, Wang D, Li X, Liang X, Qing G. Single-Molecule Identification and Quantification of Steviol Glycosides with a Deep Learning-Powered Nanopore Sensor. ACS NANO 2024; 18:25155-25169. [PMID: 39189792 DOI: 10.1021/acsnano.4c07038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
Steviol glycosides (SGs) are a class of high-potency noncalorie natural sweeteners made up of a common diterpenoid core and varying glycans. Thus, the diversity of glycans in composition, linkage, and isomerism results in the tremendous structural complexity of the SG family, which poses challenges for the precise identification and leads to the fact that SGs are frequently used in mixtures and their variances in biological activity remain largely unexplored. Here we show that a wild-type aerolysin nanopore can detect and discriminate diverse SG species through the modulable electro-osmotic flow effect at varied applied voltages. At low voltages, the neutral SG molecule was drawn and stuck in the pore entrance due to an energy barrier around R220 sites. The ensuing binding events enable the identification of the majority of SG species. Increasing the voltage can break the barrier and cause translocation events, allowing for the unambiguous identification of several pairs of SGs differing by only one hydroxyl group through recognition accumulation from multiple sensing regions and sites. Based on nanopore data of 15 SGs, a deep learning-based artificial intelligence (AI) model was created to process the individual blockage events, achieving the rapid, automated, and precise single-molecule identification and quantification of SGs in real samples. This work highlights the value of nanopore sensing for precise structural analysis of complex glycans-containing glycosides, as well as the potential for sensitive and rapid quality assurance analysis of glycoside products with the use of AI.
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Affiliation(s)
- Minmin Li
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Jing Wang
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Chen Zhang
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, P. R. China
| | - Xinjia Zhao
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Yuting Xiong
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- Dalian Lingshui Bay Laboratory, Dalian 116023, P. R. China
| | - Yuchen Cao
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Dongdong Wang
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Xiaonong Li
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, P. R. China
| | - Xinmiao Liang
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Guangyan Qing
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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4
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Wiswedel R, Bui ATN, Kim J, Lee MK. Beta-Barrel Nanopores as Diagnostic Sensors: An Engineering Perspective. BIOSENSORS 2024; 14:345. [PMID: 39056622 PMCID: PMC11274599 DOI: 10.3390/bios14070345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/13/2024] [Accepted: 07/14/2024] [Indexed: 07/28/2024]
Abstract
Biological nanopores are ultrasensitive and highly attractive platforms for disease diagnostics, including the sequencing of viral and microbial genes and the detection of biomarkers and pathogens. To utilize biological nanopores as diagnostic sensors, they have been engineered through various methods resulting in the accurate and highly sensitive detection of biomarkers and disease-related biomolecules. Among diverse biological nanopores, the β-barrel-containing nanopores have advantages in nanopore engineering because of their robust structure, making them well-suited for modifications. In this review, we highlight the engineering approaches for β-barrel-containing nanopores used in single-molecule sensing for applications in early diagnosis and prognosis. In the highlighted studies, β-barrel nanopores can be modified by genetic mutation to change the structure; alter charge distributions; or add enzymes, aptamers, and protein probes to enhance sensitivity and accuracy. Furthermore, this review discusses challenges and future perspectives for advancing nanopore-based diagnostic sensors.
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Affiliation(s)
- Rani Wiswedel
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; (R.W.); (A.T.N.B.); (J.K.)
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Anh Thi Ngoc Bui
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; (R.W.); (A.T.N.B.); (J.K.)
| | - Jinhyung Kim
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; (R.W.); (A.T.N.B.); (J.K.)
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Mi-Kyung Lee
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; (R.W.); (A.T.N.B.); (J.K.)
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea
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5
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Lu W, Zhao X, Li M, Li Y, Zhang C, Xiong Y, Li J, Zhou H, Ye X, Li X, Wang J, Liang X, Qing G. Precise Structural Analysis of Neutral Glycans Using Aerolysin Mutant T240R Nanopore. ACS NANO 2024; 18:12412-12426. [PMID: 38693619 DOI: 10.1021/acsnano.4c01571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Glycans play vital roles in nearly all life processes of multicellular organisms, and understanding these activities is inseparable from elucidating the biological significance of glycans. However, glycan research has lagged behind that of DNA and protein due to the challenges posed by structural heterogeneity and isomerism (i.e., structures with equal molecular weights) the lack of high-efficiency structural analysis techniques. Nanopore technology has emerged as a sensitive single-molecule biosensor, shining a light on glycan analysis. However, a significant number of glycans are small and uncharged, making it challenging to elicit identifiable nanopore signals. Here we introduce a R-binaphthyl tag into glycans, which enhances the cation-π interaction between the derivatized glycan molecules and the nanopore interface, enabling the detection of neutral glycans with an aerolysin nanopore. This approach allows for the distinction of di-, tri-, and tetrasaccharides with monosaccharide resolution and has the potential for group discrimination, the monitoring of enzymatic transglycosylation reactions. Notably, the aerolysin mutant T240R achieves unambiguous identification of six disaccharide isomers, trisaccharide and tetrasaccharide linkage isomers. Molecular docking simulations reveal that multiple noncovalent interactions occur between residues R282, K238, and R240 and the glycans and R-binaphthyl tag, significantly slowing down their translocation across the nanopore. Importantly, we provide a demonstration of the kinetic translocation process of neutral glycan isomers, establishing a solid theoretical foundation for glycan nanopore analysis. The development of our technology could promote the analysis of glycan structural isomers and has the potential for nanopore-based glycan structural determination and sequencing.
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Affiliation(s)
- Wenqi Lu
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xinjia Zhao
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Minmin Li
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Yuting Li
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, P. R. China
| | - Chen Zhang
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, P. R. China
| | - Yuting Xiong
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Jiaqi Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Han Zhou
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, P. R. China
| | - Xianlong Ye
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, P. R. China
| | - Xiaonong Li
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, P. R. China
| | - Jing Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Xinmiao Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, P. R. China
| | - Guangyan Qing
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
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6
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Fan P, Cao Z, Zhang S, Wang Y, Xiao Y, Jia W, Zhang P, Huang S. Nanopore analysis of cis-diols in fruits. Nat Commun 2024; 15:1969. [PMID: 38443434 PMCID: PMC10915164 DOI: 10.1038/s41467-024-46303-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/13/2024] [Indexed: 03/07/2024] Open
Abstract
Natural fruits contain a large variety of cis-diols. However, due to the lack of a high-resolution sensor that can simultaneously identify all cis-diols without a need of complex sample pretreatment, direct and rapid analysis of fruits in a hand-held device has never been previously reported. Nanopore, a versatile single molecule sensor, can be specially engineered to perform this task. A hetero-octameric Mycobacterium smegmatis porin A (MspA) nanopore modified with a sole phenylboronic acid (PBA) adapter is prepared. This engineered MspA accurately recognizes 1,2-diphenols, alditols, α-hydroxy acids and saccharides in prune, grape, lemon, different varieties of kiwifruits and commercial juice products. Assisted with a custom machine learning program, an accuracy of 99.3% is reported and the sample pretreatment is significantly simplified. Enantiomers such as DL-malic acids can also be directly identified, enabling sensing of synthetic food additives. Though demonstrated with fruits, these results suggest wide applications of nanopore in food and drug administration uses.
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Affiliation(s)
- Pingping Fan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Zhenyuan Cao
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 210023, Nanjing, China
- Institute for the Environment and Health, Nanjing University Suzhou Campus, 215163, Suzhou, China
| | - Yunqi Xiao
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Wendong Jia
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China.
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7
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Sauciuc A, Whittaker J, Tadema M, Tych K, Guskov A, Maglia G. Unravelled proteins form blobs during translocation across nanopores. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576815. [PMID: 38328101 PMCID: PMC10849628 DOI: 10.1101/2024.01.23.576815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The electroosmotic-driven transport of unravelled proteins across nanopores is an important biological process that is now under investigation for the rapid analysis and sequencing of proteins. For this approach to work, however, it is crucial that the polymer is threaded in single file. Here we found that, contrary to the electrophoretic transport of charged polymers such as DNA, during polypeptide translocation blob-like structures typically form inside nanopores. Comparisons between different nanopore sizes, shapes and surface chemistries showed that under electroosmotic-dominated regimes single-file transport of polypeptides can be achieved using nanopores that simultaneously have an entry and an internal diameter that is smaller than the persistence length of the polymer, have a uniform non-sticky ( i . e . non-aromatic) nanopore inner surface, and using moderate translocation velocities.
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8
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Greive SJ, Bacri L, Cressiot B, Pelta J. Identification of Conformational Variants for Bradykinin Biomarker Peptides from a Biofluid Using a Nanopore and Machine Learning. ACS NANO 2024; 18:539-550. [PMID: 38134312 DOI: 10.1021/acsnano.3c08433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
There is a current need to develop methods for the sensitive detection of peptide biomarkers in complex mixtures of molecules, such as biofluids, to enable early disease detection. Moreover, to our knowledge, there is currently no detection method capable of identifying the different conformations of a peptide biomarker differing by a single amino acid. Single-molecule nanopore sensing promises to provide this level of resolution. In order to be able to identify these differences in a biofluid such as serum, it is necessary to carefully characterize electrical parameters to obtain specific signatures of each biomarker population observed. We are interested here in a family of peptide biomarkers, kinins such as bradykinin and des-Arg9 bradykinin, that are involved in many disabling pathologies (allergy, asthma, angioedema, sepsis, or cancer). We show the proof of concept for direct identification of these biomarkers in serum at the single-molecule level using a protein nanopore. Each peptide exhibits two unique electrical signatures attributed to specific conformations in bulk. The same signatures are found in serum, allowing their discrimination and identification in a complex mixture such as biofluid. To extend the utility of our experimental results, we developed a principal component analysis approach to define the most relevant electrical parameters for their identification. Finally, we used semisupervised classification to assign each event type to a specific biomarker at physiological serum concentration. In the future, single-molecule scale analysis of peptide biomarkers using a powerful nanopore coupled with machine learning will facilitate the identification and quantification of other clinically relevant biomarkers from biofluids.
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Affiliation(s)
| | - Laurent Bacri
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
| | - Benjamin Cressiot
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, F-95000 Cergy, France
| | - Juan Pelta
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, F-95000 Cergy, France
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9
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Lucas FLR, Finol-Urdaneta RK, Van Thillo T, McArthur JR, van der Heide NJ, Maglia G, Dedecker P, Strauss O, Wloka C. Evidence of Cytolysin A nanopore incorporation in mammalian cells assessed by a graphical user interface. NANOSCALE 2023; 15:16914-16923. [PMID: 37853831 DOI: 10.1039/d3nr01977b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Technologies capable of assessing cellular metabolites with high precision and temporal resolution are currently limited. Recent developments in the field of nanopore sensors allow the non-stochastic quantification of metabolites, where a nanopore is acting as an electrical transducer for selective substrate binding proteins (SBPs). Here we show that incorporation of the pore-forming toxin Cytolysin A (ClyA) into the plasma membrane of Chinese hamster ovary cells (CHO-K1) results in the appearance of single-channel conductance amenable to multiplexed automated patch-clamp (APC) electrophysiology. In CHO-K1 cells, SBPs modify the ionic current flowing though ClyA nanopores, thus demonstrating its potential for metabolite sensing of living cells. Moreover, we developed a graphical user interface for the analysis of the complex signals resulting from multiplexed APC recordings. This system lays the foundation to bridge the gap between recent advances in the nanopore field (e.g., proteomic and transcriptomic) and potential cellular applications.
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Affiliation(s)
| | - Rocio K Finol-Urdaneta
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.
- Electrophysiology Facility for Cell Phenotyping and Drug Discovery, Wollongong, NSW 2522, Australia
- Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Toon Van Thillo
- Lab for Nanobiology, Department of Chemistry, KU Leuven, Belgium.
| | - Jeffrey R McArthur
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.
- Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Nieck Jordy van der Heide
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747 AG, Groningen, The Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747 AG, Groningen, The Netherlands
| | - Peter Dedecker
- Lab for Nanobiology, Department of Chemistry, KU Leuven, Belgium.
| | - Olaf Strauss
- Experimental Ophthalmology, Department of Ophthalmology, Charité - Universitätsmedizin Berlin, A Corporate Member of Freie Universität, Humboldt-University, The Berlin Institute of Health, Berlin, Germany.
| | - Carsten Wloka
- Experimental Ophthalmology, Department of Ophthalmology, Charité - Universitätsmedizin Berlin, A Corporate Member of Freie Universität, Humboldt-University, The Berlin Institute of Health, Berlin, Germany.
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10
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Wei X, Penkauskas T, Reiner JE, Kennard C, Uline MJ, Wang Q, Li S, Aksimentiev A, Robertson JW, Liu C. Engineering Biological Nanopore Approaches toward Protein Sequencing. ACS NANO 2023; 17:16369-16395. [PMID: 37490313 PMCID: PMC10676712 DOI: 10.1021/acsnano.3c05628] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Biotechnological innovations have vastly improved the capacity to perform large-scale protein studies, while the methods we have for identifying and quantifying individual proteins are still inadequate to perform protein sequencing at the single-molecule level. Nanopore-inspired systems devoted to understanding how single molecules behave have been extensively developed for applications in genome sequencing. These nanopore systems are emerging as prominent tools for protein identification, detection, and analysis, suggesting realistic prospects for novel protein sequencing. This review summarizes recent advances in biological nanopore sensors toward protein sequencing, from the identification of individual amino acids to the controlled translocation of peptides and proteins, with attention focused on device and algorithm development and the delineation of molecular mechanisms with the aid of simulations. Specifically, the review aims to offer recommendations for the advancement of nanopore-based protein sequencing from an engineering perspective, highlighting the need for collaborative efforts across multiple disciplines. These efforts should include chemical conjugation, protein engineering, molecular simulation, machine-learning-assisted identification, and electronic device fabrication to enable practical implementation in real-world scenarios.
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Affiliation(s)
- Xiaojun Wei
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, United States
| | - Tadas Penkauskas
- Biophysics and Biomedical Measurement Group, Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, United States
- School of Engineering, Brown University, Providence, RI 02912, United States
| | - Joseph E. Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, VA 23284, United States
| | - Celeste Kennard
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
| | - Mark J. Uline
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, United States
| | - Qian Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States
| | - Sheng Li
- School of Data Science, University of Virginia, Charlottesville, VA 22903, United States
| | - Aleksei Aksimentiev
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Joseph W.F. Robertson
- Biophysics and Biomedical Measurement Group, Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, United States
| | - Chang Liu
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, United States
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11
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Abraham Versloot R, Arias-Orozco P, Tadema MJ, Rudolfus Lucas FL, Zhao X, Marrink SJ, Kuipers OP, Maglia G. Seeing the Invisibles: Detection of Peptide Enantiomers, Diastereomers, and Isobaric Ring Formation in Lanthipeptides Using Nanopores. J Am Chem Soc 2023; 145:18355-18365. [PMID: 37579582 PMCID: PMC10450680 DOI: 10.1021/jacs.3c04076] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Indexed: 08/16/2023]
Abstract
Mass spectrometry (MS) is widely used in proteomic analysis but cannot differentiate between molecules with the same mass-to-charge ratio. Nanopore technology might provide an alternative method for the rapid and cost-effective analysis and sequencing of proteins. In this study, we demonstrate that nanopore currents can distinguish between diastereomeric and enantiomeric differences in l- and d-peptides, not observed by conventional MS analysis, down to individual d-amino acids in small opioid peptides. Molecular dynamics simulations suggest that similar to chiral chromatography the resolution likely arises from multiple chiral interactions during peptide transport across the nanopore. Additionally, we used nanopore recordings to rapidly assess 4- and 11-amino acid ring formation in lanthipeptides, a process used in the synthesis of pharmaceutical peptides. The cyclization step requires distinguishing between constitutional isomers, which have identical MS signals and typically involve numerous tedious experiments to confirm. Hence, nanopore technology offers new possibilities for the rapid and cost-effective analysis of peptides, including those that cannot be easily differentiated by mass spectrometry.
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Affiliation(s)
| | - Patricia Arias-Orozco
- Groningen Biomolecular Sciences and
Biotechnology Institute, University of Groningen, 9747AG Groningen, Netherlands
| | - Matthijs Jonathan Tadema
- Groningen Biomolecular Sciences and
Biotechnology Institute, University of Groningen, 9747AG Groningen, Netherlands
| | | | - Xinghong Zhao
- Groningen Biomolecular Sciences and
Biotechnology Institute, University of Groningen, 9747AG Groningen, Netherlands
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences and
Biotechnology Institute, University of Groningen, 9747AG Groningen, Netherlands
| | - Oscar Paul Kuipers
- Groningen Biomolecular Sciences and
Biotechnology Institute, University of Groningen, 9747AG Groningen, Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and
Biotechnology Institute, University of Groningen, 9747AG Groningen, Netherlands
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12
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Samineni L, Acharya B, Behera H, Oh H, Kumar M, Chowdhury R. Protein engineering of pores for separation, sensing, and sequencing. Cell Syst 2023; 14:676-691. [PMID: 37591205 DOI: 10.1016/j.cels.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/13/2023] [Accepted: 07/19/2023] [Indexed: 08/19/2023]
Abstract
Proteins are critical to cellular function and survival. They are complex molecules with precise structures and chemistries, which allow them to serve diverse functions for maintaining overall cell homeostasis. Since the discovery of the first enzyme in 1833, a gamut of advanced experimental and computational tools has been developed and deployed for understanding protein structure and function. Recent studies have demonstrated the ability to redesign/alter natural proteins for applications in industrial processes of interest and to make customized, novel synthetic proteins in the laboratory through protein engineering. We comprehensively review the successes in engineering pore-forming proteins and correlate the amino acid-level biochemistry of different pore modification strategies to the intended applications limited to nucleotide/peptide sequencing, single-molecule sensing, and precise molecular separations.
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Affiliation(s)
- Laxmicharan Samineni
- Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Bibek Acharya
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA
| | - Harekrushna Behera
- Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Hyeonji Oh
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Manish Kumar
- Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX 78712, USA; McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Ratul Chowdhury
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA.
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13
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Yu L, Kang X, Li F, Mehrafrooz B, Makhamreh A, Fallahi A, Foster JC, Aksimentiev A, Chen M, Wanunu M. Unidirectional single-file transport of full-length proteins through a nanopore. Nat Biotechnol 2023; 41:1130-1139. [PMID: 36624148 PMCID: PMC10329728 DOI: 10.1038/s41587-022-01598-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 11/02/2022] [Indexed: 01/10/2023]
Abstract
The electrical current blockade of a peptide or protein threading through a nanopore can be used as a fingerprint of the molecule in biosensor applications. However, threading of full-length proteins has only been achieved using enzymatic unfolding and translocation. Here we describe an enzyme-free approach for unidirectional, slow transport of full-length proteins through nanopores. We show that the combination of a chemically resistant biological nanopore, α-hemolysin (narrowest part is ~1.4 nm in diameter), and a high concentration guanidinium chloride buffer enables unidirectional, single-file protein transport propelled by an electroosmotic effect. We show that the mean protein translocation velocity depends linearly on the applied voltage and translocation times depend linearly on length, resembling the translocation dynamics of ssDNA. Using a supervised machine-learning classifier, we demonstrate that single-translocation events contain sufficient information to distinguish their threading orientation and identity with accuracies larger than 90%. Capture rates of protein are increased substantially when either a genetically encoded charged peptide tail or a DNA tag is added to a protein.
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Affiliation(s)
- Luning Yu
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Xinqi Kang
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Fanjun Li
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, MA, USA
| | - Behzad Mehrafrooz
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Amr Makhamreh
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Ali Fallahi
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Joshua C Foster
- Molecular and Cellular Biology Program, University of Massachusetts at Amherst, Amherst, MA, USA
| | - Aleksei Aksimentiev
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Min Chen
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, MA, USA
- Molecular and Cellular Biology Program, University of Massachusetts at Amherst, Amherst, MA, USA
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, MA, USA.
- Department of Bioengineering, Northeastern University, Boston, MA, USA.
- Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA.
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14
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Straathof S, Di Muccio G, Yelleswarapu M, Alzate Banguero M, Wloka C, van der Heide NJ, Chinappi M, Maglia G. Protein Sizing with 15 nm Conical Biological Nanopore YaxAB. ACS NANO 2023; 17:13685-13699. [PMID: 37458334 PMCID: PMC10373527 DOI: 10.1021/acsnano.3c02847] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Nanopores are promising single-molecule tools for the electrical identification and sequencing of biomolecules. However, the characterization of proteins, especially in real-time and in complex biological samples, is complicated by the sheer variety of sizes and shapes in the proteome. Here, we introduce a large biological nanopore, YaxAB for folded protein analysis. The 15 nm cis-opening and a 3.5 nm trans-constriction describe a conical shape that allows the characterization of a wide range of proteins. Molecular dynamics showed proteins are captured by the electroosmotic flow, and the overall resistance is largely dominated by the narrow trans constriction region of the nanopore. Conveniently, proteins in the 35-125 kDa range remain trapped within the conical lumen of the nanopore for a time that can be tuned by the external bias. Contrary to cylindrical nanopores, in YaxAB, the current blockade decreases with the size of the trapped protein, as smaller proteins penetrate deeper into the constriction region than larger proteins do. These characteristics are especially useful for characterizing large proteins, as shown for pentameric C-reactive protein (125 kDa), a widely used health indicator, which showed a signal that could be identified in the background of other serum proteins.
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Affiliation(s)
- Sabine Straathof
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Giovanni Di Muccio
- Department of Industrial Engineering, University of Rome Tor Vergata, Via del Politecnico 1, 00133 Rome, Italy
| | - Maaruthy Yelleswarapu
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Melissa Alzate Banguero
- Department of Industrial Engineering, University of Rome Tor Vergata, Via del Politecnico 1, 00133 Rome, Italy
| | - Carsten Wloka
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
- Experimental Ophthalmology, Department of Ophthalmology, Charité - Universitätsmedizin Berlin, A Corporate Member of Freie Universität, Humboldt-University, The Berlin Institute of Health, Berlin 10178, Germany
| | - Nieck Jordy van der Heide
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Mauro Chinappi
- Department of Industrial Engineering, University of Rome Tor Vergata, Via del Politecnico 1, 00133 Rome, Italy
| | - Giovanni Maglia
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
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15
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Zhang S, Wang Y, Song D, Guan S, Zhou D, Gong L, Liang L, Guan X, Wang L. Nanopore discrimination and sensitive plasma detection of multiple natriuretic peptides: The representative biomarker of human heart failure. Biosens Bioelectron 2023; 231:115299. [PMID: 37054600 PMCID: PMC10147535 DOI: 10.1016/j.bios.2023.115299] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/02/2023] [Accepted: 04/05/2023] [Indexed: 04/15/2023]
Abstract
Natriuretic peptides can relieve cardiovascular stress and closely related to heart failure. Besides, these peptides also have preferable interactions of binding to cellular protein receptors, and subsequently mediate various physiology actions. Hence, detection of these circulating biomarkers could be evaluated as a predictor ("Gold standard") for rapid, early diagnosis and risk stratification in heart failure. Herein, we proposed a measurement to discriminate multiple natriuretic peptides via the peptide-protein nanopore interaction. The nanopore single-molecular kinetics revealed that the strength of peptide-protein interactions was in the order of ANP > CNP > BNP, which was demonstrated by the simulated peptide structures using SWISS-MODEL. More importantly, the peptide-protein interaction analyzing also allowed us to measure the peptide linear analogs and structure damage in peptide by single-chemical bond breakup. Finally, we presented an ultra-sensitive detection of plasma natriuretic peptide using asymmetric electrolyte assay, obtaining a detection limit of ∼770 fM for BNP. At approximately, it is 1597 times lower than that of using symmetric assay (∼1.23 nM), 8 times lower than normal human level (∼6 pM), and 13 times lower than the diagnostic values (∼10.09 pM) complied in the guideline of European Society of Cardiology. That said, the designed nanopore sensor is benefit for natriuretic peptides measurement at single molecule level and demonstrates its potential for heart failure diagnosis.
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Affiliation(s)
- Shaoxia Zhang
- School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China; Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences & 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 School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Dandan Song
- School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China; Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences & Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Sarah Guan
- Hinsdale Central High School, Hinsdale, IL, 60521, USA
| | - Daming Zhou
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences & Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Linyu Gong
- School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China
| | - Liyuan Liang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences & Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - 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 School, University of Chinese Academy of Sciences, Chongqing, 400714, China.
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16
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Liu M, Li J, Tan CS. Unlocking the Power of Nanopores: Recent Advances in Biosensing Applications and Analog Front-End. BIOSENSORS 2023; 13:598. [PMID: 37366963 DOI: 10.3390/bios13060598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/24/2023] [Accepted: 05/29/2023] [Indexed: 06/28/2023]
Abstract
The biomedical field has always fostered innovation and the development of various new technologies. Beginning in the last century, demand for picoampere-level current detection in biomedicine has increased, leading to continuous breakthroughs in biosensor technology. Among emerging biomedical sensing technologies, nanopore sensing has shown great potential. This paper reviews nanopore sensing applications, such as chiral molecules, DNA sequencing, and protein sequencing. However, the ionic current for different molecules differs significantly, and the detection bandwidths vary as well. Therefore, this article focuses on current sensing circuits, and introduces the latest design schemes and circuit structures of different feedback components of transimpedance amplifiers mainly used in nanopore DNA sequencing.
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Affiliation(s)
- Miao Liu
- Medical College, Tianjin University, Tianjin 300072, China
| | - Junyang Li
- Medical College, Tianjin University, Tianjin 300072, China
| | - Cherie S Tan
- Medical College, Tianjin University, Tianjin 300072, China
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17
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Stierlen A, Greive SJ, Bacri L, Manivet P, Cressiot B, Pelta J. Nanopore Discrimination of Coagulation Biomarker Derivatives and Characterization of a Post-Translational Modification. ACS CENTRAL SCIENCE 2023; 9:228-238. [PMID: 36844502 PMCID: PMC9951287 DOI: 10.1021/acscentsci.2c01256] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Indexed: 06/18/2023]
Abstract
One of the most important health challenges is the early and ongoing detection of disease for prevention, as well as personalized treatment management. Development of new sensitive analytical point-of-care tests are, therefore, necessary for direct biomarker detection from biofluids as critical tools to address the healthcare needs of an aging global population. Coagulation disorders associated with stroke, heart attack, or cancer are defined by an increased level of the fibrinopeptide A (FPA) biomarker, among others. This biomarker exists in more than one form: it can be post-translationally modified with a phosphate and also cleaved to form shorter peptides. Current assays are long and have difficulties in discriminating between these derivatives; hence, this is an underutilized biomarker for routine clinical practice. We use nanopore sensing to identify FPA, the phosphorylated FPA, and two derivatives. Each of these peptides is characterized by unique electrical signals for both dwell time and blockade level. We also show that the phosphorylated form of FPA can adopt two different conformations, each of which have different values for each electrical parameter. We were able to use these parameters to discriminate these peptides from a mix, thereby opening the way for the potential development of new point-of-care tests.
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Affiliation(s)
- Aïcha Stierlen
- LAMBE,
CNRS, CY Cergy Paris Université, 95033 Cergy, France
| | | | - Laurent Bacri
- LAMBE,
CNRS, Univ Evry, Université Paris-Saclay, 91025 Evry-Courcouronnes, France
| | - Philippe Manivet
- Centre
de Ressources Biologiques Biobank Lariboisière (BB-0033-00064), DMU BioGem, AP-HP, 75475 Paris, France
- Université
Paris Cité, Inserm, NeuroDiderot, F-75019 Paris, France
| | | | - Juan Pelta
- LAMBE,
CNRS, CY Cergy Paris Université, 95033 Cergy, France
- LAMBE,
CNRS, Univ Evry, Université Paris-Saclay, 91025 Evry-Courcouronnes, France
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