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Cui R, Wang Z, Li L, Liu L, Li Z, Liu X, Chen T, Rauf A, Kang X, Guo Y. Bionic nanopore recognition receptors for single-molecule enantioselectivity studies of chiral drugs. Anal Chim Acta 2024; 1318:342960. [PMID: 39067929 DOI: 10.1016/j.aca.2024.342960] [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: 01/25/2024] [Revised: 06/09/2024] [Accepted: 07/08/2024] [Indexed: 07/30/2024]
Abstract
BACKGROUND Enantiodiscrimination of chiral drugs is critical for understanding physiological phenomena and ensuring medical safety. Although enantiomers of these drugs share identical physicochemical properties, they exhibit significant differences in pharmacodynamic, pharmacokinetic, and toxicological properties due to the differences in their three-dimensional shapes. Therefore, the development of effective methods for chiral recognition is of great significance and has been a hot topic in chemo/biological studies. RESULTS In this study, we designed a recognition receptor comprising a α-hemolysin (α-HL) nanopore and sulfobutyl ether-β-cyclodextrin (SBEβCD) for identifying the enantiomers of the antidepressant duloxetine at the single-molecule level. Chiral molecules were discriminated based on the different current blockages within the recognition receptor. The results indicated a strong interaction between R-duloxetine and the recognition receptor. By combining the experimental data and molecular docking results, we explored the recognition mechanism of the designed nanopore recognition receptor for chiral drug molecules. It was found that hydrophobic and electrostatic interactions play key roles in chiral recognition. Additionally, by comparing the binding kinetics of enantiomers to cyclodextrins in confined nanospace and bulk solution, we found that enantiomeric identification was better facilitated in the confined nanospace. Finally, the enantiomeric excess (ee) of the enantiomeric duloxetine mixture was measured using this recognized receptor. SIGNIFICANCE This strategy has the advantages of low cost, high sensitivity, and no need for additional derivative modifications, providing a new perspective on the development of chiral recognition sensors with excellent enantioselectivity in drug design, pharmaceuticals, and biological applications.
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Affiliation(s)
- Rikun Cui
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Zhenzhao Wang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Linna Li
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Lili Liu
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Zhen Li
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Xingtong Liu
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Tingting Chen
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Ayesha Rauf
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Xiaofeng Kang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Yanli Guo
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, PR China.
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2
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Yang H, Lin Y, Mo Q, Li Z, Yang F, Li X. Monitoring Enzymatic Reaction Kinetics and Activity Assays in Confined Nanospace. Anal Chem 2024. [PMID: 39024010 DOI: 10.1021/acs.analchem.4c01901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Enzyme-mediating biotransformations commonly occur in micro- and nanospace, which is crucial to maintain the essential biochemical processes and physiological functions in living systems. Probing enzyme-catalytic reactions in a biomimetic fashion remains challenging due to the lack of competent tools and methodology. Here, we show that studying enzymatic reaction kinetics can be readily achieved by a well-designed solid-state nanopore. Using tyrosine as a classical substrate, we quantitatively characterize the catalytic activity of tyrosinase (TYR) and tyrosine decarboxylase (TDC) in a nanoconfined space. Tyrosine was first immobilized in the nanopipette, wherein the active sites of tyrosine were left unoccupied. When successively exposed to TYR and TDC, a two-step cascade reaction can spontaneously take place. In this process, the surface wettability and charge of the nanopipette stemming from the catalytic products can sensitively regulate ion transport and ionic current rectification behavior, which were monitored by ionic current signal. In this biomimetic scenario, we obtained the enzymatic reaction kinetics of monophenyl oxidase that were not previously actualized in the conventional macroenvironment. Significantly, TYR showed higher enzyme activity, with a Km value of 1.59 mM, which was lower than that measured in a free and open space (with a Km of 3.01 mM). This suggests that tyrosine should be the most appropriate substrate of TYR, thus improving our understanding of tyrosine-associated biochemical reactions. This work offers an applicable technical platform to mimic enzyme-mediated biotransformations and biometabolisms.
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Affiliation(s)
- Huiping Yang
- Guangxi Key Laboratory of Pharmaceutical Precision Detection and Screening, Pharmaceutical College, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, China
- Key Laboratory of Micro-Nanoscale Bioanalysis and Drug Screening of Guangxi Education Department, Pharmaceutical College, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, China
| | - Yinning Lin
- Guangxi Key Laboratory of Pharmaceutical Precision Detection and Screening, Pharmaceutical College, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, China
- Key Laboratory of Micro-Nanoscale Bioanalysis and Drug Screening of Guangxi Education Department, Pharmaceutical College, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, China
| | - Qian Mo
- Guangxi Key Laboratory of Pharmaceutical Precision Detection and Screening, Pharmaceutical College, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, China
- Key Laboratory of Micro-Nanoscale Bioanalysis and Drug Screening of Guangxi Education Department, Pharmaceutical College, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, China
| | - Zhaoquan Li
- Guangxi Key Laboratory of Pharmaceutical Precision Detection and Screening, Pharmaceutical College, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, China
- Key Laboratory of Micro-Nanoscale Bioanalysis and Drug Screening of Guangxi Education Department, Pharmaceutical College, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, China
| | - Fan Yang
- Guangxi Key Laboratory of Pharmaceutical Precision Detection and Screening, Pharmaceutical College, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, China
- Key Laboratory of Micro-Nanoscale Bioanalysis and Drug Screening of Guangxi Education Department, Pharmaceutical College, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, China
- State Key Laboratory of Targeting Oncology, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, China
| | - Xinchun Li
- Guangxi Key Laboratory of Pharmaceutical Precision Detection and Screening, Pharmaceutical College, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, China
- Key Laboratory of Micro-Nanoscale Bioanalysis and Drug Screening of Guangxi Education Department, Pharmaceutical College, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, China
- State Key Laboratory of Targeting Oncology, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021, China
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3
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Li R, Hu Y, Sun X, Zhang Z, Chen K, Liu Q, Chen X. Intra-nanoparticle plasmonic nanogap based spatial-confinement SERS analysis of polypeptides. Talanta 2024; 273:125899. [PMID: 38484502 DOI: 10.1016/j.talanta.2024.125899] [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: 12/25/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 04/09/2024]
Abstract
Sensing and characterizing water-soluble polypeptides are essential in various biological applications. However, detecting polypeptides using Surface-Enhanced Raman Scattering (SERS) remains a challenge due to the dominance of aromatic amino acid residues and backbones in the signal, which hinders the detection of non-aromatic amino acid residues. Herein, intra-nanoparticle plasmonic nanogap were designed by etching the Ag shell in Au@AgNPs (i.e., obtaining AuAg cores) with chlorauric acid under mild conditions, at the same time forming the outermost Au shell and the void between the AuAg cores and the Au shell (AuAg@void@Au). By varying the Ag to added chloroauric acid molar ratios, we pioneered a simple, controllable, and general synthetic strategy to form interlayer-free nanoparticles with tunable Au shell thickness, achieving precise regulation of electric field enhancement within the intra-nanogap. As validation, two polypeptide molecules, bacitracin and insulin B, were successfully synchronously encapsulated and spatial-confined in the intra-nanogap for sensing. Compared with concentrated 50 nm AuNPs and Au@AgNPs as SERS substrates, our simultaneous detection method improved the sensitivity of the assay while benefiting to obtain more comprehensive characteristic peaks of polypeptides. The synthetic strategy of confining analytes while fabricating plasmonic nanostructures enables the diffusion of target molecules into the nanogap in a highly specific and sensitive manner, providing the majority of the functionality required to achieve peptide detection or sequencing without the hassle of labeling.
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Affiliation(s)
- Ruili Li
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Yuyang Hu
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Xiaotong Sun
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Zhipeng Zhang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Kecen Chen
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Qi Liu
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China.
| | - Xiaoqing Chen
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China; Xiangjiang Laboratory, Changsha 410205, China.
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4
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Ahmed SA, Liu Y, Xiong T, Zhao Y, Xie B, Pan C, Ma W, Yu P. Iontronic Sensing Based on Confined Ion Transport. Anal Chem 2024; 96:8056-8077. [PMID: 38663001 DOI: 10.1021/acs.analchem.4c01354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Affiliation(s)
- Saud Asif Ahmed
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Ying Liu
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Tianyi Xiong
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Yueru Zhao
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Boyang Xie
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Cong Pan
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Wenjie Ma
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Ping Yu
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100190, China
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5
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Xu S, Wang G, Feng Y, Zheng J, Huang L, Liu J, Jiang Y, Wang Y, Liu N. PNA-Functionalized, Silica Nanowires-Filled Glass Microtube for Ultrasensitive and Label-Free Detection of miRNA-21. Anal Chem 2024; 96:7470-7478. [PMID: 38696229 DOI: 10.1021/acs.analchem.3c05839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2024]
Abstract
MicroRNAs (miRNAs) are endogenous and noncoding single-stranded RNA molecules with a length of approximately 18-25 nucleotides, which play an undeniable role in early cancer screening. Therefore, it is very important to develop an ultrasensitive and highly specific method for detecting miRNAs. Here, we present a bottom-up assembly approach for modifying glass microtubes with silica nanowires (SiNWs) and develop a label-free sensing platform for miRNA-21 detection. The three-dimensional (3D) networks formed by SiNWs make them abundant and highly accessible sites for binding with peptide nucleic acid (PNA). As a receptor, PNA has no phosphate groups and exhibits an overall electrically neutral state, resulting in a relatively small repulsion between PNA and RNA, which can improve the hybridization efficiency. The SiNWs-filled glass microtube (SiNWs@GMT) sensor enables ultrasensitive, label-free detection of miRNA-21 with a detection limit as low as 1 aM at a detection range of 1 aM-100 nM. Noteworthy, the sensor can still detect miRNA-21 in the range of 102-108 fM in complex solutions containing 1000-fold homologous interference of miRNAs. The high anti-interference performance of the sensor enables it to specifically recognize target miRNA-21 in the presence of other miRNAs and distinguish 1-, 3-mismatch nucleotide sequences. Significantly, the sensor platform is able to detect miRNA-21 in the lysate of breast cancer cell lines (e.g., MCF-7 cells and MDA-MB-231 cells), indicating that it has good potential in the screening of early breast cancers.
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Affiliation(s)
- Shiwei Xu
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Guofeng Wang
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Yueyue Feng
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Juanjuan Zheng
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Liying Huang
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Jiahao Liu
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Yisha Jiang
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Yajun Wang
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
| | - Nannan Liu
- Key Laboratory of Carbon Materials of Zhejiang Province, Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325027, Zhejiang, P. R. China
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6
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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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7
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Yao G, Ke W, Xia B, Gao Z. Nanopore-based glycan sequencing: state of the art and future prospects. Chem Sci 2024; 15:6229-6243. [PMID: 38699252 PMCID: PMC11062086 DOI: 10.1039/d4sc01466a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 04/02/2024] [Indexed: 05/05/2024] Open
Abstract
Sequencing of biomacromolecules is a crucial cornerstone in life sciences. Glycans, one of the fundamental biomolecules, derive their physiological and pathological functions from their structures. Glycan sequencing faces challenges due to its structural complexity and current detection technology limitations. As a highly sensitive sensor, nanopores can directly convert nucleic acid sequence information into electrical signals, spearheading the revolution of third-generation nucleic acid sequencing technologies. However, their potential for deciphering complex glycans remains untapped. Initial attempts demonstrated the significant sensitivity of nanopores in glycan sensing, which provided the theoretical basis and insights for the realization of nanopore-based glycan sequencing. Here, we present three potential technical routes to employ nanopore technology in glycan sequencing for the first time. The three novel technical routes include: strand sequencing, capturing glycan chains as they translocate through nanopores; sequential hydrolysis sequencing, capturing released monosaccharides one by one; splicing sequencing, mapping signals from hydrolyzed glycan fragments to an oligosaccharide database/library. Designing suitable nanopores, enzymes, and motors, and extracting characteristic signals pose major challenges, potentially aided by artificial intelligence. It would be highly desirable to design an all-in-one high-throughput glycan sequencer instrument by integrating a sample processing unit, nanopore array, and signal acquisition system into a microfluidic device. The nanopore sequencer invention calls for intensive multidisciplinary cooperation including electrochemistry, glycochemistry, engineering, materials, enzymology, etc. Advancing glycan sequencing will promote the development of basic research and facilitate the discovery of glycan-based drugs and disease markers, fostering progress in glycoscience and even life sciences.
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Affiliation(s)
- Guangda Yao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- School of Life Science and Technology, Shanghai Tech University 201210 Shanghai China
- Lingang Laboratory 200031 Shanghai China
| | - Wenjun Ke
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Bingqing Xia
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
| | - Zhaobing Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 201203 Shanghai China
- University of Chinese Academy of Sciences 100049 Beijing China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 528400 Zhongshan China
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8
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Xu S, Wang G, Feng Y, Zheng J, Huang L, Wang Y, Liu N. Silica Nanowires-Filled Glass Microporous Sensor for the Ultrasensitive Detection of Deoxyribonucleic Acid. ACS Sens 2024; 9:2050-2056. [PMID: 38632929 DOI: 10.1021/acssensors.4c00072] [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] [Indexed: 04/19/2024]
Abstract
DNA carries genetic information and can serve as an important biomarker for the early diagnosis and assessment of the disease prognosis. Here, we propose a bottom-up assembly method for a silica nanowire-filled glass microporous (SiNWs@GMP) sensor and develop a universal sensing platform for the ultrasensitive and specific detection of DNA. The three-dimensional network structure formed by SiNWs provides them with highly abundant and accessible binding sites, allowing for the immobilization of a large amount of capture probe DNA, thereby enabling more target DNA to hybridize with the capture probe DNA to improve detection performance. Therefore, the SiNWs@GMP sensor achieves ultrasensitive detection of target DNA. In the detection range of 1 aM to 100 fM, there is a good linear relationship between the decrease rate of current signal and the concentration of target DNA, and the detection limit is as low as 1 aM. The developed SiNWs@GMP sensor can distinguish target DNA sequences that are 1-, 3-, and 5-mismatched, and specifically recognize target DNA from complex mixed solution. Furthermore, based on this excellent selectivity and specificity, we validate the universality of this sensing strategy by detecting DNA (H1N1 and H5N1) sequences associated with the avian influenza virus. By replacing the types of nucleic acid aptamers, it is expected to achieve a wide range and low detection limit sensitive detection of various biological molecules. The results indicate that the developed universal sensing platform has ultrahigh sensitivity, excellent selectivity, stability, and acceptable reproducibility, demonstrating its potential application in DNA bioanalysis.
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Affiliation(s)
- Shiwei Xu
- Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, Zhejiang 325027, P. R. China
| | - Guofeng Wang
- Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, Zhejiang 325027, P. R. China
| | - Yueyue Feng
- Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, Zhejiang 325027, P. R. China
| | - Juanjuan Zheng
- Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, Zhejiang 325027, P. R. China
| | - Liying Huang
- Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, Zhejiang 325027, P. R. China
| | - Yajun Wang
- Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, Zhejiang 325027, P. R. China
| | - Nannan Liu
- Key Lab of Biohealth Materials and Chemistry of Wenzhou, College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou, Zhejiang 325027, P. R. China
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9
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Cai S, Ren R, He J, Wang X, Zhang Z, Luo Z, Tan W, Korchev Y, Edel JB, Ivanov AP. Selective Single-Molecule Nanopore Detection of mpox A29 Protein Directly in Biofluids. NANO LETTERS 2023; 23:11438-11446. [PMID: 38051760 PMCID: PMC10755749 DOI: 10.1021/acs.nanolett.3c02709] [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: 07/20/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/07/2023]
Abstract
Single-molecule antigen detection using nanopores offers a promising alternative for accurate virus testing to contain their transmission. However, the selective and efficient identification of small viral proteins directly in human biofluids remains a challenge. Here, we report a nanopore sensing strategy based on a customized DNA molecular probe that combines an aptamer and an antibody to enhance the single-molecule detection of mpox virus (MPXV) A29 protein, a small protein with an M.W. of ca. 14 kDa. The formation of the aptamer-target-antibody sandwich structures enables efficient identification of targets when translocating through the nanopore. This technique can accurately detect A29 protein with a limit of detection of ∼11 fM and can distinguish the MPXV A29 from vaccinia virus A27 protein (a difference of only four amino acids) and Varicella Zoster Virus (VZV) protein directly in biofluids. The simplicity, high selectivity, and sensitivity of this approach have the potential to contribute to the diagnosis of viruses in point-of-care settings.
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Affiliation(s)
- Shenglin Cai
- Department
of Chemistry, Imperial College London, Molecular
Science Research Hub, White City Campus, 82 Wood Lane, London W12
0BZ, U.K.
| | - Ren Ren
- Department
of Chemistry, Imperial College London, Molecular
Science Research Hub, White City Campus, 82 Wood Lane, London W12
0BZ, U.K.
- Department
of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith
Campus, Du Cane Road, London W12 0NN, U.K.
- Nano
Life Science Institute (WPI-NanoLSI), Kanazawa
University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Jiaxuan He
- The
Key Laboratory of Zhejiang Province for Aptamers and Theranostics,
Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, People’s
Republic of China
| | - Xiaoyi Wang
- Department
of Chemistry, Imperial College London, Molecular
Science Research Hub, White City Campus, 82 Wood Lane, London W12
0BZ, U.K.
| | - Zheng Zhang
- The
Key Laboratory of Zhejiang Province for Aptamers and Theranostics,
Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, People’s
Republic of China
| | - Zhaofeng Luo
- The
Key Laboratory of Zhejiang Province for Aptamers and Theranostics,
Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, People’s
Republic of China
| | - Weihong Tan
- The
Key Laboratory of Zhejiang Province for Aptamers and Theranostics,
Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, People’s
Republic of China
| | - Yuri Korchev
- Department
of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith
Campus, Du Cane Road, London W12 0NN, U.K.
- Nano
Life Science Institute (WPI-NanoLSI), Kanazawa
University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Joshua B. Edel
- Department
of Chemistry, Imperial College London, Molecular
Science Research Hub, White City Campus, 82 Wood Lane, London W12
0BZ, U.K.
| | - Aleksandar P. Ivanov
- Department
of Chemistry, Imperial College London, Molecular
Science Research Hub, White City Campus, 82 Wood Lane, London W12
0BZ, U.K.
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10
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Liu Y, Wang X, Campolo G, Teng X, Ying L, Edel JB, Ivanov AP. Single-Molecule Detection of α-Synuclein Oligomers in Parkinson's Disease Patients Using Nanopores. ACS NANO 2023; 17:22999-23009. [PMID: 37947369 PMCID: PMC10690843 DOI: 10.1021/acsnano.3c08456] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/22/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023]
Abstract
α-Synuclein (α-Syn) is an intrinsically disordered protein whose aggregation in the brain has been significantly implicated in Parkinson's disease (PD). Beyond the brain, oligomers of α-Synuclein are also found in cerebrospinal fluid (CSF) and blood, where the analysis of these aggregates may provide diagnostic routes and enable a better understanding of disease mechanisms. However, detecting α-Syn in CSF and blood is challenging due to its heterogeneous protein size and shape, and low abundance in clinical samples. Nanopore technology offers a promising route for the detection of single proteins in solution; however, the method often lacks the necessary selectivity in complex biofluids, where multiple background biomolecules are present. We address these limitations by developing a strategy that combines nanopore-based sensing with molecular carriers that can specifically capture α-Syn oligomers with sizes of less than 20 nm. We demonstrate that α-Synuclein oligomers can be detected directly in clinical samples, with minimal sample processing, by their ion current characteristics and successfully utilize this technology to differentiate cohorts of PD patients from healthy controls. The measurements indicate that detecting α-Syn oligomers present in CSF may potentially provide valuable insights into the progression and monitoring of Parkinson's disease.
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Affiliation(s)
- Yaxian Liu
- Department
of Chemistry, Imperial College London, Molecular
Sciences Research Hub, London W12 0BZ, United
Kingdom
| | - Xiaoyi Wang
- Department
of Chemistry, Imperial College London, Molecular
Sciences Research Hub, London W12 0BZ, United
Kingdom
| | - Giulia Campolo
- Department
of Chemistry, Imperial College London, Molecular
Sciences Research Hub, London W12 0BZ, United
Kingdom
| | - Xiangyu Teng
- Department
of Chemistry, Imperial College London, Molecular
Sciences Research Hub, London W12 0BZ, United
Kingdom
| | - Liming Ying
- National
Heart and Lung Institute, Imperial College
London, Molecular Sciences Research Hub, London W12 0BZ, United Kingdom
| | - Joshua B. Edel
- Department
of Chemistry, Imperial College London, Molecular
Sciences Research Hub, London W12 0BZ, United
Kingdom
| | - Aleksandar P. Ivanov
- Department
of Chemistry, Imperial College London, Molecular
Sciences Research Hub, London W12 0BZ, United
Kingdom
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11
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Ren R, Cai S, Fang X, Wang X, Zhang Z, Damiani M, Hudlerova C, Rosa A, Hope J, Cook NJ, Gorelkin P, Erofeev A, Novak P, Badhan A, Crone M, Freemont P, Taylor GP, Tang L, Edwards C, Shevchuk A, Cherepanov P, Luo Z, Tan W, Korchev Y, Ivanov AP, Edel JB. Multiplexed detection of viral antigen and RNA using nanopore sensing and encoded molecular probes. Nat Commun 2023; 14:7362. [PMID: 37963924 PMCID: PMC10646045 DOI: 10.1038/s41467-023-43004-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 10/27/2023] [Indexed: 11/16/2023] Open
Abstract
We report on single-molecule nanopore sensing combined with position-encoded DNA molecular probes, with chemistry tuned to simultaneously identify various antigen proteins and multiple RNA gene fragments of SARS-CoV-2 with high sensitivity and selectivity. We show that this sensing strategy can directly detect spike (S) and nucleocapsid (N) proteins in unprocessed human saliva. Moreover, our approach enables the identification of RNA fragments from patient samples using nasal/throat swabs, enabling the identification of critical mutations such as D614G, G446S, or Y144del among viral variants. In particular, it can detect and discriminate between SARS-CoV-2 lineages of wild-type B.1.1.7 (Alpha), B.1.617.2 (Delta), and B.1.1.539 (Omicron) within a single measurement without the need for nucleic acid sequencing. The sensing strategy of the molecular probes is easily adaptable to other viral targets and diseases and can be expanded depending on the application required.
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Affiliation(s)
- Ren Ren
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 82 Wood Lane, London, W12 0BZ, UK
- Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK
| | - Shenglin Cai
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 82 Wood Lane, London, W12 0BZ, UK.
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Xiaona Fang
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China
| | - Xiaoyi Wang
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 82 Wood Lane, London, W12 0BZ, UK
| | - Zheng Zhang
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China
| | - Micol Damiani
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 82 Wood Lane, London, W12 0BZ, UK
| | - Charlotte Hudlerova
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 82 Wood Lane, London, W12 0BZ, UK
| | - Annachiara Rosa
- The Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
- Wolfson Education Centre, Faculty of Medicine, Imperial College London, London, UK
| | - Joshua Hope
- The Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Nicola J Cook
- The Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Peter Gorelkin
- National University of Science and Technology "MISIS", Leninskiy Prospect 4, 119991, Moscow, Russian Federation
| | - Alexander Erofeev
- National University of Science and Technology "MISIS", Leninskiy Prospect 4, 119991, Moscow, Russian Federation
| | - Pavel Novak
- ICAPPIC Limited, The Fisheries, Mentmore Terrace, London, E8 3PN, UK
| | - Anjna Badhan
- Molecular Diagnostic Unit, Section of Virology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Michael Crone
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Paul Freemont
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Graham P Taylor
- Molecular Diagnostic Unit, Section of Virology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Longhua Tang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, International Research Center for Advanced Photonics, Zhejiang University, 310027, Hangzhou, China
| | - Christopher Edwards
- Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK
- ICAPPIC Limited, The Fisheries, Mentmore Terrace, London, E8 3PN, UK
| | - Andrew Shevchuk
- Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK
| | - Peter Cherepanov
- The Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
- Molecular Diagnostic Unit, Section of Virology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Zhaofeng Luo
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China
| | - Weihong Tan
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China.
| | - Yuri Korchev
- Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Aleksandar P Ivanov
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 82 Wood Lane, London, W12 0BZ, UK.
| | - Joshua B Edel
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 82 Wood Lane, London, W12 0BZ, UK.
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12
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Martin-Baniandres P, Lan WH, Board S, Romero-Ruiz M, Garcia-Manyes S, Qing Y, Bayley H. Enzyme-less nanopore detection of post-translational modifications within long polypeptides. NATURE NANOTECHNOLOGY 2023; 18:1335-1340. [PMID: 37500774 PMCID: PMC10656283 DOI: 10.1038/s41565-023-01462-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 06/15/2023] [Indexed: 07/29/2023]
Abstract
Means to analyse cellular proteins and their millions of variants at the single-molecule level would uncover substantial information previously unknown to biology. Nanopore technology, which underpins long-read DNA and RNA sequencing, holds potential for full-length proteoform identification. We use electro-osmosis in an engineered charge-selective nanopore for the non-enzymatic capture, unfolding and translocation of individual polypeptides of more than 1,200 residues. Unlabelled thioredoxin polyproteins undergo transport through the nanopore, with directional co-translocational unfolding occurring unit by unit from either the C or N terminus. Chaotropic reagents at non-denaturing concentrations accelerate the analysis. By monitoring the ionic current flowing through the nanopore, we locate post-translational modifications deep within the polypeptide chains, laying the groundwork for compiling inventories of the proteoforms in cells and tissues.
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Affiliation(s)
| | - Wei-Hsuan Lan
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Stephanie Board
- Department of Physics, Randall Centre for Cell and Molecular Biophysics and London Centre for Nanotechnology, King's College London, London, UK
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK
| | | | - Sergi Garcia-Manyes
- Department of Physics, Randall Centre for Cell and Molecular Biophysics and London Centre for Nanotechnology, King's College London, London, UK
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK
| | - Yujia Qing
- Department of Chemistry, University of Oxford, Oxford, UK.
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, Oxford, UK.
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