1
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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:e202400389. [PMID: 38865098 DOI: 10.1002/asia.202400389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [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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2
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Xu W, Ma C, Wang G, Fu F, Sha J. Trapping and recapturing single DNA molecules with pore-cavity-pore device. NANOTECHNOLOGY 2024; 35:335302. [PMID: 38772350 DOI: 10.1088/1361-6528/ad4e3d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Accepted: 05/21/2024] [Indexed: 05/23/2024]
Abstract
Single-molecule detection technology is a technique capable of detecting molecules at the single-molecule level, characterized by high sensitivity, high resolution, and high specificity. Nanopore technology, as one of the single-molecule detection tools, is widely used to study the structure and function of biomolecules. In this study, we constructed a small-sized nanopore with a pore-cavity-pore structure, which can achieve a higher reverse capture rate. Through simulation, we investigated the electrical potential distribution of the nanopore with a pore-cavity-pore structure and analyzed the influence of pore size on the potential distribution. Accordingly, different pore sizes can be designed based on the radius of gyration of the target biomolecules, restricting their escape paths inside the chamber. In the future, nanopores with a pore-cavity-pore structure based on two-dimensional thin film materials are expected to be applied in single-molecule detection research, which provides new insights for various detection needs.
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Affiliation(s)
- Wei Xu
- Jiangsu Key Laboratory for Design and Manufacture for Micro/Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, People's Republic of China
| | - Chaofan Ma
- Jiangsu Key Laboratory for Design and Manufacture for Micro/Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, People's Republic of China
| | - Gang Wang
- Jiangsu Key Laboratory for Design and Manufacture for Micro/Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, People's Republic of China
| | - Fangzhou Fu
- Jiangsu Key Laboratory for Design and Manufacture for Micro/Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, People's Republic of China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture for Micro/Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, People's Republic of China
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3
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Liu W, Ma C, Wang H, Sha J. Conformation Influence of DNA on the Detection Signal through Solid-State Nanopores. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:9622-9629. [PMID: 38652583 DOI: 10.1021/acs.langmuir.4c00401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
The detection and identification of nanoscale molecules are crucial, but traditional technology comes with a high cost and requires skilled operators. Solid-state nanopores are new powerful tools for discerning the three-dimensional shape and size of molecules, enabling the translation of molecular structural information into electric signals. Here, DNA molecules with different shapes were designed to explore the effects of electroosmotic forces (EOF), electrophoretic forces (EPF), and volume exclusion on electric signals within solid-state nanopores. Our results revealed that the electroosmotic force was the main driving force for single-stranded DNA (ssDNA), whereas double-stranded DNA (dsDNA) was primarily dominated by electrophoretic forces in nanopores. Moreover, dsDNA caused greater amplitude signals and moved faster through the nanopore due to its larger diameter and carrying more charges. Furthermore, at the same charge level and amount of bases, circular dsDNA exhibited a tighter structure compared to brush DNA, resulting in a shorter length. Consequently, circular dsDNA caused higher current-blocking amplitudes and faster passage speeds. The characterization approach based on nanopores allows researchers to get molecular information about size and shape in real time. These findings suggest that nanopore detection has the potential to streamline nanoscale characterization and analysis, potentially reducing both the cost and complexity.
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Affiliation(s)
- Wei Liu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Chaofan Ma
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Haiyan Wang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
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4
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Rao YF, Sun LZ, Luo MB. Na +-Mg 2+ ion effects on conformation and translocation dynamics of single-stranded RNA: Cooperation and competition. Int J Biol Macromol 2024; 267:131273. [PMID: 38569994 DOI: 10.1016/j.ijbiomac.2024.131273] [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: 02/04/2024] [Revised: 03/20/2024] [Accepted: 03/28/2024] [Indexed: 04/05/2024]
Abstract
The nanopore-based translocation of a single-stranded RNA (ssRNA) in mixed salt solution has garnered increasing interest for its biological and technological significance. However, it is challenging to comprehensively understand the effects of the mixed ion species on the translocation dynamics due to their cooperation and competition, which can be directly reflected by the ion screening and neutralizing effects, respectively. In this study, Langevin dynamics simulation is employed to investigate the properties of ssRNA conformation and translocation in mixed Na+-Mg2+ ion environments. Simulation results reveal that the ion screening effect dominates the change in the ssRNA conformational size, the ion neutralizing effect controls the capture rate of the ssRNA by the nanopore, and both of them take charge of the different changes in translocation time of the ssRNA under various mixed ion environments. Under high Na+ ion concentration, as Mg2+ concentration increases, the ion neutralizing effect strengthens, weakening the driving force inside the nanopore, leading to longer translocation time. Conversely, at low Na+ concentration, an increase in Mg2+ concentration enhances the ion screening effect, aiding in faster translocation. Furthermore, these simulation results will be explained by quantitative analysis, advancing a deeper understanding of the complicated effects of the mixed Na+-Mg2+ ions.
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Affiliation(s)
- Yi-Fan Rao
- School of Physics, Zhejiang University, Hangzhou 310027, China; Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
| | - Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
| | - Meng-Bo Luo
- School of Physics, Zhejiang University, Hangzhou 310027, China.
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5
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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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6
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Liu LZ, Liu L, Shi ZH, Bian XL, Si ZR, Wang QQ, Xiang Y, Zhang Y. Amphibian pore-forming protein βγ-CAT drives extracellular nutrient scavenging under cell nutrient deficiency. iScience 2023; 26:106598. [PMID: 37128610 PMCID: PMC10148134 DOI: 10.1016/j.isci.2023.106598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 02/22/2023] [Accepted: 03/30/2023] [Indexed: 05/03/2023] Open
Abstract
Nutrient acquisition is essential for animal cells. βγ-CAT is a pore-forming protein (PFP) and trefoil factor complex assembled under tight regulation identified in toad Bombina maxima. Here, we reported that B. maxima cells secreted βγ-CAT under glucose, glutamine, and pyruvate deficiency to scavenge extracellular proteins for their nutrient supply and survival. AMPK signaling positively regulated the expression and secretion of βγ-CAT. The PFP complex selectively bound extracellular proteins and promoted proteins uptake through endolysosomal pathways. Elevated intracellular amino acids, enhanced ATP production, and eventually prolonged cell survival were observed in the presence of βγ-CAT and extracellular proteins. Liposome assays indicated that high concentration of ATP negatively regulated the opening of βγ-CAT channels. Collectively, these results uncovered that βγ-CAT is an essential element in cell nutrient scavenging under cell nutrient deficiency by driving vesicular uptake of extracellular proteins, providing a new paradigm for PFPs in cell nutrient acquisition and metabolic flexibility.
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Affiliation(s)
- Ling-Zhen Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Engineering Laboratory of Peptides of the Chinese Academy of Sciences, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Long Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Engineering Laboratory of Peptides of the Chinese Academy of Sciences, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Human Aging Research Institute (HARI) and School of Life Sciences, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Zhi-Hong Shi
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Engineering Laboratory of Peptides of the Chinese Academy of Sciences, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Xian-Ling Bian
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Engineering Laboratory of Peptides of the Chinese Academy of Sciences, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- School of Life Science, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Zi-Ru Si
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Engineering Laboratory of Peptides of the Chinese Academy of Sciences, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- School of Life Science, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Qi-Quan Wang
- Human Aging Research Institute (HARI) and School of Life Sciences, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Yang Xiang
- Human Aging Research Institute (HARI) and School of Life Sciences, Nanchang University, Nanchang, Jiangxi 330031, China
- Corresponding author
| | - Yun Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Engineering Laboratory of Peptides of the Chinese Academy of Sciences, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Corresponding author
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7
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Kang X, Wu C, Alibakhshi MA, Liu X, Yu L, Walt DR, Wanunu M. Nanopore-Based Fingerprint Immunoassay Based on Rolling Circle Amplification and DNA Fragmentation. ACS NANO 2023; 17:5412-5420. [PMID: 36877993 PMCID: PMC10629239 DOI: 10.1021/acsnano.2c09889] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
In recent years, nanopore-based sequencers have become robust tools with unique advantages for genomics applications. However, progress toward applying nanopores as highly sensitive, quantitative diagnostic tools has been impeded by several challenges. One major limitation is the insufficient sensitivity of nanopores in detecting disease biomarkers, which are typically present at pM or lower concentrations in biological fluids, while a second limitation is the general absence of unique nanopore signals for different analytes. To bridge this gap, we have developed a strategy for nanopore-based biomarker detection that utilizes immunocapture, isothermal rolling circle amplification, and sequence-specific fragmentation of the product to release multiple DNA reporter molecules for nanopore detection. These DNA fragment reporters produce sets of nanopore signals that form distinctive fingerprints, or clusters. This fingerprint signature therefore allows the identification and quantification of biomarker analytes. As a proof of concept, we quantify human epididymis protein 4 (HE4) at low pM levels in a few hours. Future improvement of this method by integration with a nanopore array and microfluidics-based chemistry can further reduce the limit of detection, allow multiplexed biomarker detection, and further reduce the footprint and cost of existing laboratory and point-of-care devices.
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Affiliation(s)
- Xinqi Kang
- Departments
of Bioengineering, Physics, and Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Connie Wu
- Department
of Pathology, Brigham and Women’s Hospital, Harvard Medical School and Wyss Institute for Biologically Inspired
Engineering at Harvard University, Boston, Massachusetts 02115, United States
| | - Mohammad Amin Alibakhshi
- Departments
of Bioengineering, Physics, and Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Xingyan Liu
- Departments
of Bioengineering, Physics, and Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Luning Yu
- Departments
of Bioengineering, Physics, and Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - David R. Walt
- Department
of Pathology, Brigham and Women’s Hospital, Harvard Medical School and Wyss Institute for Biologically Inspired
Engineering at Harvard University, Boston, Massachusetts 02115, United States
| | - Meni Wanunu
- Departments
of Bioengineering, Physics, and Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
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8
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Jeong KB, Kim JS, Dhanasekar NN, Lee MK, Chi SW. Application of nanopore sensors for biomolecular interactions and drug discovery. Chem Asian J 2022; 17:e202200679. [PMID: 35929410 DOI: 10.1002/asia.202200679] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/04/2022] [Indexed: 11/07/2022]
Abstract
Biomolecular interactions, including protein-protein, protein-nucleic acid, and protein/nucleic acid-ligand interactions, play crucial roles in various cellular signaling and biological processes, and offer attractive therapeutic targets in numerous human diseases. Currently, drug discovery is limited by the low efficiency and high cost of conventional ensemble-averaging-based techniques for biomolecular interaction analysis and high-throughput drug screening. Nanopores are an emerging technology for single-molecule sensing of biomolecules. Owing to the robust advantages of single-molecule sensing, nanopore sensors have contributed tremendously to nucleic acid sequencing and disease diagnostics. In this minireview, we summarize the recent developments and outlooks in single-molecule sensing of various biomolecular interactions for drug discovery applications using biological and solid-state nanopore sensors.
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Affiliation(s)
- Ki-Baek Jeong
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, 34141, Daejeon, Republic of Korea
- Critical Diseases Diagnostics Convergence Research Center, KRIBB, 34141, Daejeon, Republic of Korea
| | - Jin-Sik Kim
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, 34141, Daejeon, Republic of Korea
- Critical Diseases Diagnostics Convergence Research Center, KRIBB, 34141, Daejeon, Republic of Korea
| | - Naresh Niranjan Dhanasekar
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, 34141, Daejeon, Republic of Korea
| | - Mi-Kyung Lee
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, 34141, Daejeon, Republic of Korea
- Critical Diseases Diagnostics Convergence Research Center, KRIBB, 34141, Daejeon, Republic of Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, 34113, Daejeon, Republic of Korea
| | - Seung-Wook Chi
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, 34141, Daejeon, Republic of Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, 34113, Daejeon, Republic of Korea
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Zhu J, Bošković F, Keyser UF. Split G-Quadruplexes Enhance Nanopore Signals for Simultaneous Identification of Multiple Nucleic Acids. NANO LETTERS 2022; 22:4993-4998. [PMID: 35730196 PMCID: PMC9228402 DOI: 10.1021/acs.nanolett.2c01764] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/28/2022] [Indexed: 05/22/2023]
Abstract
Assembly of DNA structures based on hybridization like split G-quadruplex (GQ) have great potential for the base-pair specific identification of nucleic acid targets. Herein, we combine multiple split G-quadruplex (GQ) assemblies on designed DNA nanostructures (carrier) with a solid-state nanopore sensing platform. The split GQ probes recognize various nucleic acid sequences in a parallel assay that is based on glass nanopore analysis of molecular structures. Specifically, we split a GQ into two asymmetric parts extended with sequences complementary to the target. The longer G-segment is in solution, and the shorter one is on a DNA carrier. If the target is present, the two separate GQ parts will be brought together to facilitate the split GQ formation and enhance the nanopore signal. We demonstrated detection of multiple target sequences from different viruses with low crosstalk. Given the programmability of this DNA based nanopore sensing platform, it is promising in biosensing.
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10
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Shi HQ, Ma Y, Wang YH, Fang F, Wu ZY. Current pulse signature of native kanamycin aptamer and its implication for molecular interactions on a single protein nanopore sensing interface. Biosens Bioelectron 2022; 201:113966. [PMID: 35016110 DOI: 10.1016/j.bios.2022.113966] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/30/2021] [Accepted: 01/03/2022] [Indexed: 11/02/2022]
Abstract
Due to the pore size limitation of single α-hemolysin (α-HL) nanopore sensing interface, ssDNA with secondary conformations can only pass through the nanopore after unzipping as linear ssDNA. For hairpin DNA, a tail with 15-50 bases was usually added to the stem terminal (5' or 3') to facilitate the capture rate and unzipping process, and the typical translocation signal behaves as a square wave with a short dip at the end of the pulse. In this work, the pulse signal of native kanamycin aptamer, a hairpin DNA without the added long tail, was investigated with the single nanopore sensing interface, and different current pulse pattern was observed. The pulse signal exhibited two precise current levels with significantly extended duration of the second, and both duration of the two levels correlate to the interaction of the aptamer to kanamycin. Moreover, the pulse signal not only reveals the selectivity of the aptamer to its target, but also sensitive to the loop sequence change of the aptamer. This work shows that a single nanopore sensing interface could be used as a unique alternative means for interaction investigation of hairpin DNA aptamer without labeling or adding the extra-long tail.
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Affiliation(s)
- Hui-Qing Shi
- Research Center for Analytical Sciences, Chemistry Department, College of Sciences, Northeastern University, Shenyang, 110819, China
| | - Yao Ma
- Research Center for Analytical Sciences, Chemistry Department, College of Sciences, Northeastern University, Shenyang, 110819, China
| | - Yu-Hang Wang
- Research Center for Analytical Sciences, Chemistry Department, College of Sciences, Northeastern University, Shenyang, 110819, China
| | - Fang Fang
- Research Center for Analytical Sciences, Chemistry Department, College of Sciences, Northeastern University, Shenyang, 110819, China
| | - Zhi-Yong Wu
- Research Center for Analytical Sciences, Chemistry Department, College of Sciences, Northeastern University, Shenyang, 110819, China.
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11
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Xi D, Cui M, Zhou X, Zhuge X, Ge Y, Wang Y, Zhang S. Nanopore-Based Single-Molecule Investigation of DNA Sequences with Potential to Form i-Motif Structures. ACS Sens 2021; 6:2691-2699. [PMID: 34237940 DOI: 10.1021/acssensors.1c00712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
i-Motifs are DNA secondary structures present in cytosine-rich sequences. These structures are formed in regulatory regions of the human genome and play key regulatory roles. The investigation of sequences capable of forming i-motif structures at the single-molecule level is highly important. In this study, we used α-hemolysin nanopores to systematically study a series of DNA sequences at the nanometer scale by providing structure-dependent signature current signals to gain in-sights into the i-motif DNA sequence and structural stability. Increasing the length of the cytosine tract in a range of 3-10 nucleobases resulted in a longer translocation time through the pore, indicating improved stability. Changing the loop sequence and length in the sequences did not affect the formation of the i-motif structure but changed its stability. Importantly, the application of all-atom molecular dynamics simulations revealed the structural morphology of all sequences. Based on these results, we postulated a folding rule for i-motif formation, suggesting that thousands of cytosine-rich sequences in the human genome might fold into i-motif structures. Many of these were found in locations where structure formation is likely to play regulatory roles. These findings provide insights into the application of nanopores as a powerful tool for discovering potential i-motif-forming sequences and lay a foundation for future studies exploring the biological roles of i-motifs.
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Affiliation(s)
- Dongmei Xi
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Life Sciences, Linyi University, Linyi 276005, P. R. China
| | - Mengjie Cui
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Xin Zhou
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Xiao Zhuge
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Yaxian Ge
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Ying Wang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Life Sciences, Linyi University, Linyi 276005, P. R. China
| | - Shusheng Zhang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
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Affiliation(s)
- Mengjie Cui
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University Linyi Shandong 276005 China
| | - Yaxian Ge
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University Linyi Shandong 276005 China
| | - Xiao Zhuge
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University Linyi Shandong 276005 China
| | - Xin Zhou
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University Linyi Shandong 276005 China
| | - Dongmei Xi
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University Linyi Shandong 276005 China
| | - Shusheng Zhang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University Linyi Shandong 276005 China
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13
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Oh S, Lee MK, Chi SW. Single-molecule analysis of interaction between p53TAD and MDM2 using aerolysin nanopores. Chem Sci 2021; 12:5883-5891. [PMID: 34168813 PMCID: PMC8179679 DOI: 10.1039/d1sc00386k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/19/2021] [Indexed: 12/12/2022] Open
Abstract
Protein-protein interactions (PPIs) are regarded as important, but undruggable targets. Intrinsically disordered p53 transactivation domain (p53TAD) mediates PPI with mouse double minute 2 (MDM2), which is an attractive anticancer target for therapeutic intervention. Here, using aerolysin nanopores, we probed the p53TAD peptide/MDM2 interaction and its modulation by small-molecule PPI inhibitors or p53TAD phosphorylation. Although the p53TAD peptide showed short-lived (<100 ms) translocation, the protein complex induced the characteristic extraordinarily long-lived (0.1 s ∼ tens of min) current blockage, indicating that the MDM2 recruitment by p53TAD peptide almost fully occludes the pore. Simultaneously, the protein complex formation substantially reduced the event frequency of short-lived peptide translocation. Notably, the addition of small-molecule PPI inhibitors, Nutlin-3 and AMG232, or Thr18 phosphorylation of p53TAD peptide, were able to diminish the extraordinarily long-lived events and restore the short-lived translocation of the peptide rescued from the complex. Taken together, our results elucidate a novel mechanism of single-molecule sensing for analyzing PPIs and their inhibitors using aerolysin nanopores. This novel methodology may contribute to remarkable improvements in drug discovery targeted against undruggable PPIs.
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Affiliation(s)
- Sohee Oh
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology Daejeon 34141 Republic of Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology Daejeon 34113 Republic of Korea
| | - Mi-Kyung Lee
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology Daejeon 34141 Republic of Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology Daejeon 34113 Republic of Korea
| | - Seung-Wook Chi
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology Daejeon 34141 Republic of Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology Daejeon 34113 Republic of Korea
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Deng C, Liu L, Liu L, Wang Q, Guo X, Lee W, Li S, Zhang Y. A secreted pore‐forming protein modulates cellular endolysosomes to augment antigen presentation. FASEB J 2020; 34:13609-13625. [DOI: 10.1096/fj.202001176r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/20/2020] [Accepted: 07/27/2020] [Indexed: 01/04/2023]
Affiliation(s)
- Cheng‐Jie Deng
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province Kunming Institute of Zoology The Chinese Academy of Sciences Kunming China
- Kunming College of Life Science University of Chinese Academy of Sciences Kunming China
| | - Long Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province Kunming Institute of Zoology The Chinese Academy of Sciences Kunming China
- Kunming College of Life Science University of Chinese Academy of Sciences Kunming China
| | - Ling‐Zhen Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province Kunming Institute of Zoology The Chinese Academy of Sciences Kunming China
- Kunming College of Life Science University of Chinese Academy of Sciences Kunming China
| | - Qi‐Quan Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province Kunming Institute of Zoology The Chinese Academy of Sciences Kunming China
- Kunming College of Life Science University of Chinese Academy of Sciences Kunming China
| | - Xiao‐Long Guo
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province Kunming Institute of Zoology The Chinese Academy of Sciences Kunming China
| | - Wen‐Hui Lee
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province Kunming Institute of Zoology The Chinese Academy of Sciences Kunming China
| | - Sheng‐An Li
- Department of Pathogen Biology and Immunology Faculty of Basic Medical Science Kunming Medical University Kunming China
| | - Yun Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province Kunming Institute of Zoology The Chinese Academy of Sciences Kunming China
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
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15
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Ying YL, Wang J, Leach AR, Jiang Y, Gao R, Xu C, Edwards MA, Pendergast AD, Ren H, Weatherly CKT, Wang W, Actis P, Mao L, White HS, Long YT. Single-entity electrochemistry at confined sensing interfaces. Sci China Chem 2020. [DOI: 10.1007/s11426-020-9716-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Ji N, Shi HQ, Fang XY, Wu ZY. Exploring the interaction of G-quadruplex and porphyrin derivative by single protein nanopore sensing interface. Anal Chim Acta 2020; 1106:126-132. [DOI: 10.1016/j.aca.2020.01.053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/18/2020] [Accepted: 01/23/2020] [Indexed: 11/26/2022]
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Fang Z, Liu L, Wang Y, Xi D, Zhang S. Unambiguous Discrimination of Multiple Protein Biomarkers by Nanopore Sensing with Double-Stranded DNA-Based Probes. Anal Chem 2019; 92:1730-1737. [DOI: 10.1021/acs.analchem.9b02965] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Zhen Fang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, P.R. China
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, P.R. China
| | - Liping Liu
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, P.R. China
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, P.R. China
| | - Ying Wang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, P.R. China
| | - Dongmei Xi
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, P.R. China
| | - Shusheng Zhang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, P.R. China
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Oh S, Lee MK, Chi SW. Single-Molecule-Based Detection of Conserved Influenza A Virus RNA Promoter Using a Protein Nanopore. ACS Sens 2019; 4:2849-2853. [PMID: 31689087 DOI: 10.1021/acssensors.9b01558] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Influenza A viruses (IAVs) cause annual epidemic and severe pandemic outbreaks worldwide and result in high mortality. Despite the importance of surveillance for preventing IAV infection, the existing techniques are inefficient for ultrasensitive diagnosis in real time. In this study, we performed protein nanopore-based measurements to detect the highly conserved IAV RNA promoter at the single-molecule level. The binding of specific DNA probes to the IAV RNA promoter generated two types of characteristic nanopore signatures with single or double spikes of current blockade and substantially increased dwell times, which facilitated the discrimination of the IAV promoter from nonspecific macromolecules. Our DNA probe-mediated nanopore sensor will serve as an ultrasensitive, real-time, point-of-care diagnostic tool for highly pathogenic IAVs.
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Affiliation(s)
- Sohee Oh
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Proteome Structural Biology, KRIBB school of Biosicence, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Mi-Kyung Lee
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Seung-Wook Chi
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Proteome Structural Biology, KRIBB school of Biosicence, University of Science and Technology, Daejeon 34113, Republic of Korea
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Gao R, Lin Y, Ying YL, Long YT. Nanopore-based sensing interface for single molecule electrochemistry. Sci China Chem 2019. [DOI: 10.1007/s11426-019-9509-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Liu YM, Fang XY, Fang F, Wu ZY. Investigation of hairpin DNA and chelerythrine interaction by a single bio-nanopore sensing interface. Analyst 2019; 144:4081-4085. [PMID: 31169284 DOI: 10.1039/c9an00113a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Chelerythrine (CHE) is one of the potential drugs for cancer treatments. The interaction between hairpin DNA and CHE has been investigated by spectral and mass spectrometry methods. In this paper, the stability of hairpin DNA with different loop bases and its interaction with CHE were explored with a single α-hemolysin (α-HL) nanopore sensing interface. The results showed that the characteristic current pulses not only relate to the loop composition changes of the hairpin DNA, but also provide interaction information between CHE and the hairpin DNA molecules. The dwell time of current pulses for hairpin DNA was significantly increased (hundreds of ms) due to the addition of CHE, and two characteristic current distributions were recognized for the hairpin with T3 and C3 loops. The two characteristic current groups could be ascribed to the hairpin DNA and the ones with CHE. This study indicates that it is possible to study the interaction between single CHE and single hairpin DNA molecules by the single-nanopore sensing interface as an alternative method to conventional spectrometric methods for therapeutic mechanism and drug screening purposes.
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Affiliation(s)
- Yuan-Min Liu
- Research Center for Analytical Sciences, Chemistry Department, College of Sciences, Northeastern University, Shenyang 110819, China.
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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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Wang J, Yang J, Ying YL, Long YT. Nanopore-Based Confined Spaces for Single-Molecular Analysis. Chem Asian J 2019; 14:389-397. [PMID: 30548206 DOI: 10.1002/asia.201801648] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/09/2018] [Indexed: 11/07/2022]
Abstract
The field of nanopore sensing at the single-molecular level is in a "boom" period. Such nanopores, which are either composed of biological materials or are fabricated from solid-state substrates, offer a unique confined space that is compatible with the single-molecular scale. Under the influence of an electrical field, such single-biomolecular interfaces can read single-molecular information and, if appropriately fine-tuned, each molecule plays its individual ionic rhythm to compose a "molecular symphony". Over the past few decades, many research groups have worked on nanopore-based single-molecular sensors for a range of thrilling chemical and clinical applications. Furthermore, for the past decade, we have also focused on nanopore-based sensors. In this Minireview, we summarize the recent developments in fundamental research and applications in this area, along with data algorithms and advances in hardware, which act as infrastructure for the electrochemical analysis.
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Affiliation(s)
- Jiajun Wang
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Jie Yang
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
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Yang J, Wang YQ, Li MY, Ying YL, Long YT. Direct Sensing of Single Native RNA with a Single-Biomolecule Interface of Aerolysin Nanopore. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14940-14945. [PMID: 30462509 DOI: 10.1021/acs.langmuir.8b03264] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
RNA sensing is of vital significance to advance our comprehension of gene expression and to further benefit medical diagnostics. Taking advantage of the excellent sensing capability of the aerolysin nanopore as a single-biomolecule interface, we for the first time achieved the direct characterization of single native RNA of Poly(A)4 and Poly(U)4. Poly(A)4 induces ∼10% larger blockade current amplitude than Poly(U)4. The statistical duration of Poly(A)4 is 18.83 ± 1.08 ms, which is 100 times longer than that of Poly(U)4. Our results demonstrated that the capture of RNA homopolymers is restricted by the biased diffusion. The translocation of RNA needs to overcome a lower free-energy barrier than that of DNA. Moreover, the strong RNA-aerolysin interaction is attributed to the hydroxyl in pentose, which prolongs the translocation time. This study opens an avenue for aerolysin nanopores to directly achieve RNA sensing, including discrimination of RNA epigenetic modification and selective detection of miRNA.
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Affiliation(s)
- Jie Yang
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , P. R. China
| | - Ya-Qian Wang
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , P. R. China
| | - Meng-Yin Li
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , P. R. China
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , P. R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , P. R. China
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