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1
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Iesu L, Sai M, Torbeev V, Kieffer B, Pelta J, Cressiot B. Single-molecule nanopore sensing of proline cis/ trans amide isomers. Chem Sci 2025:d5sc01156f. [PMID: 40321189 PMCID: PMC12045290 DOI: 10.1039/d5sc01156f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2025] [Accepted: 04/23/2025] [Indexed: 05/08/2025] Open
Abstract
Molecules known as stereoisomers possess identical numbers and types of atoms, which are oriented differently in space. Cis-trans isomerization of proline, a distinctive case of stereoisomerism in peptides and proteins, includes the rearrangement of chemical groups around an acyl-proline amide bond that bears the partial double bond character. Many cellular processes are affected by cis-trans proline isomerization and associated conformational protein interconversions. This work explored the conformer ratio of natural and chemically modified prolines using the aerolysin pore as a nanosensor. Despite the well-known involvement of proline in protein folding, stability, and aggregation, the highly demanding discrimination of cis and trans isomers of the Xaa-Pro peptide bond has not so far been reported at a single-molecule level using an electrical detection with a nanopore. For a proline-rich 19 amino acid residue fragment of the Dynamin 2 protein, one of the subfamilies of GTP-binding proteins, the third proline in the sequence was substituted by two stereoisomeric 4-fluoroprolines. The nanopore experiments were able to sense the influence of fluorination in shifting the cis/trans conformers' equilibrium compared to the natural proline: for 4-(R)-fluoroproline, the trans amide isomer is more favored, while the opposite shift was observed for 4-(S)-fluoroproline. NMR spectroscopy was used to validate the nanopore results. Overall, our findings demonstrate the high sensitivity of single-molecule nanopore sensing as an analytical tool for stereoisomer identification within peptides.
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Affiliation(s)
- Luca Iesu
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE 95000 Cergy France
| | - Mariam Sai
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U 1258, University of Strasbourg 67400 Illkirch France
| | - Vladimir Torbeev
- École Supérieure de Biotechnologie de Strasbourg (ESBS), CNRS UMR 7242 Biotechnology and Cellular Signalling, University of Strasbourg 67400 Illkirch France
| | - Bruno Kieffer
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U 1258, University of Strasbourg 67400 Illkirch France
| | - Juan Pelta
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE 91025 Evry-Courcouronnes France
| | - Benjamin Cressiot
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE 95000 Cergy France
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2
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Miyagi M, Yamaji M, Kurokawa N, Yohda M, Kawano R. Redesign of Translocon EXP2 Nanopore for Detecting Peptide Fragments. SMALL METHODS 2025; 9:e2401562. [PMID: 39905884 PMCID: PMC12020339 DOI: 10.1002/smtd.202401562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2024] [Revised: 12/27/2024] [Indexed: 02/06/2025]
Abstract
Nanopore sensing is a rapid, label-free technique that enables single-molecule detection and is successfully applied to nucleic acid sequencing. Extending this technology to the detection and sequencing of peptides and proteins is a key area of interest. However, the complex structures and diverse charge distributions of peptides and proteins present challenges for extensive detection using existing nanopores. In this study, the focus is on the EXP2 nanopore derived from the malaria parasite Plasmodium falciparum to address these challenges. Previously, it is characterized wild-type EXP2 (WT-EXP2) nanopores and demonstrated their ability to detect polypeptides, although intrinsic electrical noise from the pore posed difficulties for accurate detection. To overcome these limitations, several EXP2 nanopore mutants are designed, including EXP2ΔD231, EXP2NC, and EXP2NC K42D/S46F, to reduce electrical noise and improve peptide detection accuracy. The EXP2ΔD231 mutant reduced electrical noise by more than 50% compared to WT-EXP2 and improved the discrimination accuracy of oligoarginine peptides. In addition, the EXP2ΔD231 detected and discriminated eight different peptides, ranging in molecular weight from small to large, that are previously challenging to detect using a single nanopore type. These results suggest that engineered EXP2 nanopores could serve as effective tools for peptide and protein detection and sequencing, contributing to the broader application of nanopore technology in biochemical and clinical research.
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Affiliation(s)
- Mitsuki Miyagi
- Department of Biotechnology and Life ScienceTokyo University of Agriculture and TechnologyTokyo184‐8588Japan
| | - Misa Yamaji
- Department of Biotechnology and Life ScienceTokyo University of Agriculture and TechnologyTokyo184‐8588Japan
| | - Nina Kurokawa
- Department of Biotechnology and Life ScienceTokyo University of Agriculture and TechnologyTokyo184‐8588Japan
| | - Masafumi Yohda
- Department of Biotechnology and Life ScienceTokyo University of Agriculture and TechnologyTokyo184‐8588Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life ScienceTokyo University of Agriculture and TechnologyTokyo184‐8588Japan
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3
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Gao F, Wang JH, Ma H, Xia B, Wen L, Long YT, Ying YL. Identification of Oligosaccharide Isomers Using Electrostatically Asymmetric OmpF Nanopore. Angew Chem Int Ed Engl 2025; 64:e202422118. [PMID: 39856493 DOI: 10.1002/anie.202422118] [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: 11/13/2024] [Revised: 01/09/2025] [Accepted: 01/22/2025] [Indexed: 01/27/2025]
Abstract
Glycans, unlike uniformly charged DNA and compositionally diverse peptides, are typically uncharged and possess rich stereoisomeric diversity in the glycosidic bonds between two monosaccharide units. These unique features, including charge heterogeneity and structural complexity, pose significant challenges for accurate analysis. Herein, we developed a novel single-molecule oligosaccharide sensor, OmpF nanopore. The natural electroosmotic flow within OmpF generates a robust driving force for unlabeled neutral oligosaccharides, enabling detection at a concentration as low as 6.4 μM. Furthermore, the asymmetric constriction zone of OmpF was employed to construct a stereoselective recognition site, enabling sensitive identification of glycosidic bond differences in cell lysate samples. With the assistance of machine learning algorithms, the OmpF nanopore achieved a recognition accuracy of 99.9 % for tetrasaccharides differing in only one glycosidic bond was achieved. This nanopore sensor provides a highly sensitive analytical tool with a broad dynamic range. It enables chiral recognition of oligosaccharides at low concentrations and is suitable for analysing both low-abundance and practical samples.
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Affiliation(s)
- Fan Gao
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Jia-Hong Wang
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Hui Ma
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Bingqing Xia
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Liuqing Wen
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yi-Tao Long
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Yi-Lun Ying
- Molecular Sensing and Imaging Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, 210023, P. R. China
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4
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Yao G, Xia B, Wei F, Wang J, Yang Y, Ma S, Ke W, Li T, Cheng X, Wen L, Long YT, Gao Z. Glycan Sequencing Based on Glycosidase-Assisted Nanopore Sensing. J Am Chem Soc 2025; 147:1721-1731. [PMID: 39745005 DOI: 10.1021/jacs.4c12940] [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: 01/16/2025]
Abstract
Nanopores are promising sensors for glycan analysis with the accurate identification of complex glycans laying the foundation for nanopore-based sequencing. However, their applicability toward continuous glycan sequencing has not yet been demonstrated. Here, we present a proof-of-concept of glycan sequencing by combining nanopore technology with glycosidase-hydrolyzing reactions. By continuously monitoring the changes in the characteristic current generated by the translocation of glycan hydrolysis products through a nanopore, the glycan sequence can be accurately identified based on the specificity of glycosidases. With machine learning, we improved the sequencing accuracy to over 98%, allowing for the reliable determination of consecutive building blocks and glycosidic linkages of glycan chains while reducing the need for operator expertise. This approach was validated on real glycan samples, with accuracy calibrated using hydrophilic interaction chromatography-high-performance liquid chromatography (HILIC-HPLC) and mass spectrometry (MS). We achieved the sequencing of ten consecutive units in natural glycan chains, which provided the first evidence for the feasibility of a nanopore-glycosidase-compatible system in glycan sequencing. Compared to traditional methods, this strategy enhances sequencing efficiency by over 5-fold. Additionally, we introduced the concept of 'inverse sequencing', which focuses on electrical signal changes rather than monosaccharide identification. This eliminates the reliance on glycan fingerprint libraries typically required in putative 'forward hydrolysis' strategies. When the challenges in both 'forward and inverse hydrolysis sequencing strategies' are addressed, this approach will pave the way for establishing a glycan sequencing technology at a single-molecule level.
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Affiliation(s)
- Guangda Yao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
- Lingang Laboratory, Shanghai 200031, China
| | - Bingqing Xia
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangyu Wei
- University of Chinese Academy of Sciences, Beijing 100049, China
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jiahong Wang
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yuting Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shengzhou Ma
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjun Ke
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tiehai Li
- University of Chinese Academy of Sciences, Beijing 100049, China
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xi Cheng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou 330106, China
| | - Liuqing Wen
- University of Chinese Academy of Sciences, Beijing 100049, China
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yi-Tao Long
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zhaobing Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
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5
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Jia W, Ouyang Y, Zhang S, Zhang P, Huang S. Nanopore Identification of L-, D-Lactic Acids, D-Glucose and Gluconic Acid in the Serum of Human and Animals. SMALL METHODS 2025; 9:e2400664. [PMID: 38864527 DOI: 10.1002/smtd.202400664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 05/30/2024] [Indexed: 06/13/2024]
Abstract
DL-Lactic acid and D-glucose are important human health indicators. Their aberrant levels in body fluids may indicate a variety of human pathological conditions, suggesting an urgent need of daily monitoring. However, simultaneous and rapid analysis of DL-lactic acid and D-glucose using a sole but simple sensing system has never been reported. Here, an engineered Mycobacterium smegmatis porin A (MspA) nanopore is used to simultaneously identify DL-lactic acid and D-glucose. Highly distinguishable nanopore event features are reported. Assisted with a custom machine learning algorithm, direct identification of DL-lactic acid and D-glucose is performed with human serum, demonstrating its sensing reliability against complex and heterogeneous samples. This sensing strategy is further applied in the analysis of different animal serum samples, according to which gluconic acid is further identified. The serum samples from different animals report distinguishable levels of DL-lactic acid, D-glucose and gluconic acid, suggesting its potential applications in agricultural science and breeding industry. This sensing strategy is generally direct, rapid, economic and requires only ≈µL of input serum, suitable for point of care testing (POCT) applications.
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Affiliation(s)
- Wendong Jia
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Yusheng Ouyang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
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6
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Sun Y, Mi Z, Chen X, Li JJ, Lu J, Shan X, Lu X, Du Y. Identification of nine mammal monosaccharides by solid-state nanopores. Sci Rep 2024; 14:32000. [PMID: 39738399 PMCID: PMC11686368 DOI: 10.1038/s41598-024-83690-z] [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: 11/06/2024] [Accepted: 12/16/2024] [Indexed: 01/02/2025] Open
Abstract
Glycans, nucleic acids and proteins are three major classes of natural biopolymers. The extremely high diversity of isomerization makes structural elucidation of glycans the most challenging job among three classes. In the past few years, the single molecule sensing technique based on nanopores has achieved great success in sequencing of DNA. Inspired by this, it is potential to sequence glycans in the similar manner. Herein, SiNx nanopores were used to identify nine common monosaccharides in mammals. Each monosaccharide showed characteristic blockage current, which roughly increased with the increase of its molecular weight. In order to distinguish nine monosaccharides, several machine learning models were trained and tested, of which the highest F1 value was 1. These results illustrated that nine common monosaccharides in mammals could be clearly identified and discriminate by our method combining solid-state nanopores and machine learning. As far as we know, this is the first report that monosaccharides can be sensed and distinguished by solid-state nanopores. Our work showed the great potential of solid-state nanopores in glycan sequencing, and would lay the foundation for solid-state nanopore-based glycan sequencing.
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Affiliation(s)
- Yunze Sun
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhuang Mi
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Xiaoyu Chen
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jian-Jun Li
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China.
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Jun Lu
- Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Xinyan Shan
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Xinghua Lu
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Yuguang Du
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China.
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, Beijing, 100190, China.
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7
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Liu W, Zhu Q, Yang CN, Fu YH, Zhang JC, Li MY, Yang ZL, Xin KL, Ma J, Winterhalter M, Ying YL, Long YT. Single-molecule sensing inside stereo- and regio-defined hetero-nanopores. NATURE NANOTECHNOLOGY 2024; 19:1693-1701. [PMID: 39164412 DOI: 10.1038/s41565-024-01721-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 06/17/2024] [Indexed: 08/22/2024]
Abstract
Heteromeric pore-forming proteins often contain recognition patterns or stereospecific selection filters. However, the construction of heteromeric pore-forming proteins for single-molecule sensing is challenging due to the uncontrollability of producing position isomers and difficulties in purification of regio-defined products. To overcome these preparation obstacles, we present an in situ strategy involving single-molecule chemical modification of a heptameric pore-forming protein to build a stereo- and regio-specific heteromeric nanopore (hetero-nanopore) with a subunit stoichiometric ratio of 3:4. The steric hindrance inherent in the homo-nanopore of K238C aerolysin directs the stereo- and regio-selective modification of maleimide derivatives. Our method utilizes real-time ionic current recording to facilitate controlled voltage manipulation for stoichiometric modification and position-based side-isomer removal. Single-molecule experiments and all-atom molecular dynamics simulations revealed that the hetero-nanopore features an asymmetric stereo- and regio-defined residue structure. The hetero-nanopore produced was characterized by mass spectrometry and single-particle cryogenic electron microscopy. In a proof-of-concept single-molecule sensing experiment, the hetero-nanopore exhibited 95% accuracy for label-free discrimination of four peptide stereoisomers with single-amino-acid structural and chiral differences in the mixtures. The customized hetero-nanopores could advance single-molecule sensing.
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Affiliation(s)
- Wei Liu
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Molecular Sensing and Imaging Center, Nanjing University, Nanjing, China
| | - Qiang Zhu
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Chao-Nan Yang
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Molecular Sensing and Imaging Center, Nanjing University, Nanjing, China
| | - Ying-Huan Fu
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Molecular Sensing and Imaging Center, Nanjing University, Nanjing, China
| | - Ji-Chang Zhang
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Molecular Sensing and Imaging Center, Nanjing University, Nanjing, China
| | - Meng-Yin Li
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Molecular Sensing and Imaging Center, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, China
| | - Zhong-Lin Yang
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Kai-Li Xin
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Molecular Sensing and Imaging Center, Nanjing University, Nanjing, China
| | - Jing Ma
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | | | - Yi-Lun Ying
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China.
- Molecular Sensing and Imaging Center, Nanjing University, Nanjing, China.
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, China.
| | - Yi-Tao Long
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Molecular Sensing and Imaging Center, Nanjing University, Nanjing, China
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8
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Zhang Y, Hu C, Liu R, He S, Yang J, Yao W, Li Y, Guo X. Protein nanopore-based sensors for public health analyte detection. J Mater Chem B 2024; 12:9845-9862. [PMID: 39258387 DOI: 10.1039/d4tb01149j] [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: 09/12/2024]
Abstract
High-throughput and label-free protein nanopore-based sensors are extensively used in DNA sequencing, single-protein analysis, molecular sensing and chemical catalysis with single channel recording. These technologies show great potential for identifying various harmful substances linked to public health by addressing the limitations of current portability and the speed of existing techniques. In this review, we provide an overview of the fundamental principles of nanopore sensing, with a focus on chemical modification and genetic engineering strategies aimed at enhancing the detection sensitivity and identification accuracy of protein nanopores. The engineered protein nanopores enable direct sensing, while the introduction of aptamers and substrates enables indirect sensing, translating the physical structure and chemical properties of analytes into readable signals. These scientific discoveries and engineering efforts have provided new prospects for detecting and monitoring trace hazardous substances.
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Affiliation(s)
- Yanhua Zhang
- Dongguan Key Laboratory of Public Health Laboratory Science, School of Public Health, Guangdong Medical University, Dongguan 523808, China.
| | - Chan Hu
- Dongguan Key Laboratory of Public Health Laboratory Science, School of Public Health, Guangdong Medical University, Dongguan 523808, China.
| | - Ronghui Liu
- School of Microelectronics, Southern University of Science and Technology, Shenzhen 518055, People's Republic of China.
| | - Shujun He
- Dongguan Key Laboratory of Public Health Laboratory Science, School of Public Health, Guangdong Medical University, Dongguan 523808, China.
| | - Jie Yang
- Dongguan Key Laboratory of Public Health Laboratory Science, School of Public Health, Guangdong Medical University, Dongguan 523808, China.
| | - Wen Yao
- Dongguan Key Laboratory of Public Health Laboratory Science, School of Public Health, Guangdong Medical University, Dongguan 523808, China.
| | - Yi Li
- School of Microelectronics, Southern University of Science and Technology, Shenzhen 518055, People's Republic of China.
| | - Xinrong Guo
- Dongguan Key Laboratory of Public Health Laboratory Science, School of Public Health, Guangdong Medical University, Dongguan 523808, China.
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9
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Ouyang Y, Wang K, Jia W, Zhang P, Huang S. Simultaneous Identification of Vitamins B1, B3, B5, and B6 by an Engineered Nanopore. NANO LETTERS 2024; 24:11944-11953. [PMID: 39269011 DOI: 10.1021/acs.nanolett.4c03329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/15/2024]
Abstract
Vitamin Bs, a group of water-soluble compounds, are essential nutrients for almost all living organisms. However, due to their structural heterogeneity, rapid and simultaneous analysis of multiple vitamin Bs is still challenging. In this paper, it is discovered that a hetero-octameric Mycobacterium smegmatis porin A (MspA) nanopore containing a sole nickel ion-bound nitrilotriacetic acid (NTA-Ni) adapter at its pore constriction is suitable for the simultaneous sensing of different vitamin Bs, including vitamin B1 (thiamine), vitamin B3 (nicotinic acid and nicotinamide), vitamin B5 (pantothenic acid), and vitamin B6 (pyridoxine, pyridoxal, and pyridoxamine). Assisted by a custom machine learning algorithm, all seven vitamin Bs can be fully distinguished, reporting a general accuracy of 99.9%. This method was further validated in the rapid analysis of commercial cosmetics and natural food, suggesting its potential uses in food and drug administration.
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Affiliation(s)
- Yusheng Ouyang
- 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
| | - Kefan 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
| | - 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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10
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Soriano-Ursúa MA, Cordova-Chávez RI, Farfan-García ED, Kabalka G. Boron-containing compounds as labels, drugs, and theranostic agents for diabetes and its complications. World J Diabetes 2024; 15:1060-1069. [PMID: 38983826 PMCID: PMC11229952 DOI: 10.4239/wjd.v15.i6.1060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/25/2024] [Accepted: 03/28/2024] [Indexed: 06/11/2024] Open
Abstract
Diabetes is a disease with a high global burden. Current strategies have failed to limit the advancement and impact of the disease. Successful early diagnosis and treatment will require the development of new agents. In this sense, boron-containing compounds have been reported as agents with the ability to reduce glycemia and lipidemia. They have also been used for labeling and measuring carbohydrates and other molecules linked to the initial stages of diabetes and its progression. In addition, certain boron compounds bind to molecules related to diabetes development and their biological activity in the regulation of elevated glycemia. Finally, it should be noted that some boron compounds appear to exert beneficial effects on diabetes complications such as accelerating wound healing while ameliorating pain in diabetic patients.
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Affiliation(s)
- Marvin A Soriano-Ursúa
- Department of Physiology, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico
| | | | | | - George Kabalka
- Department of Chemistry, The University of Tennessee, Knoxville, TN 37996, United States
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11
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Cordova-Chávez RI, Trujillo-Ferrara JG, Padilla-Martínez II, González-Espinosa H, Abad-García A, Farfán-García ED, Ortega-Camarillo C, Contreras-Ramos A, Soriano-Ursúa MA. One-Step Synthesis, Crystallography, and Acute Toxicity of Two Boron-Carbohydrate Adducts That Induce Sedation in Mice. Pharmaceuticals (Basel) 2024; 17:781. [PMID: 38931447 PMCID: PMC11206247 DOI: 10.3390/ph17060781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/08/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Boronic acids form diester bonds with cis-hydroxyl groups in carbohydrates. The formation of these adducts could impair the physical and chemical properties of precursors, even their biological activity. Two carbohydrate derivatives from d-fructose and d-arabinose and phenylboronic acid were synthesized in a straightforward one-step procedure and chemically characterized via spectroscopy and X-ray diffraction crystallography. Additionally, an acute toxicity test was performed to determine their lethal dose 50 (LD50) values by using Lorke's method. Analytical chemistry assays confirmed the formation of adducts by the generation of diester bonds with the β-d-pyranose of carbohydrates, including signals corresponding to the formation of new bonds, such as the stretching of B-O bonds. NMR spectra yielded information about the stereoselectivity in the synthesis reaction: Just one signal was found in the range for the anomeric carbon in the 13C NMR spectra of both adducts. The acute toxicity tests showed that the LD50 value for both compounds was 1265 mg/kg, while the effective dose 50 (ED50) for sedation was 531 mg/kg. However, differences were found in the onset and lapse of sedation. For example, the arabinose derivative induced sedation for more than 48 h at 600 mg/kg, while the fructose derivative induced sedation for less than 6 h at the same dose without the death of the mice. Thus, we report for the first time two boron-containing carbohydrate derivatives inducing sedation after intraperitoneal administration. They are bioactive and highly safe agents. Further biological evaluation is desirable to explore their medical applications.
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Affiliation(s)
- Ricardo Ivan Cordova-Chávez
- Laboratorio de Neurofisiología, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Mexico City 11340, Mexico; (R.I.C.-C.); (H.G.-E.); (A.A.-G.)
- Laboratorio de Bioquímica, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Mexico City 11340, Mexico;
| | - José G. Trujillo-Ferrara
- Laboratorio de Bioquímica, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Mexico City 11340, Mexico;
| | - Itzia I. Padilla-Martínez
- Laboratorio de Química Supramolecular y Nanociencias, Unidad Profesional Interdisciplinaria de Biotecnología, Instituto Politécnico Nacional, Av. Acueducto s/n, Barrio la Laguna Ticomán, Mexico City 07340, Mexico;
| | - Héctor González-Espinosa
- Laboratorio de Neurofisiología, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Mexico City 11340, Mexico; (R.I.C.-C.); (H.G.-E.); (A.A.-G.)
| | - Antonio Abad-García
- Laboratorio de Neurofisiología, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Mexico City 11340, Mexico; (R.I.C.-C.); (H.G.-E.); (A.A.-G.)
| | - Eunice D. Farfán-García
- Laboratorio de Bioquímica, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Mexico City 11340, Mexico;
| | - Clara Ortega-Camarillo
- Medical Research Unit in Biochemistry, Specialties Hospital, National Medical Center SXXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. Doctores, Alc. Cuauhtémoc, Mexico City 06720, Mexico;
| | - Alejandra Contreras-Ramos
- Laboratory of Molecular Biology in the Congenital Malformations Unit, Children’s Hospital of Mexico Federico Gomez (HIMFG), Calle Dr. Marques 162, Col. Doctores, Alc. Cuahutémoc, Mexico City 06720, Mexico;
| | - Marvin A. Soriano-Ursúa
- Laboratorio de Neurofisiología, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Mexico City 11340, Mexico; (R.I.C.-C.); (H.G.-E.); (A.A.-G.)
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12
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Kizer ME, R. Dwyer J. Editors' Choice-Perspective-Deciphering the Glycan Kryptos by Solid-State Nanopore Single-Molecule Sensing: A Call for Integrated Advancements Across Glyco- and Nanopore Science. ECS SENSORS PLUS 2024; 3:020604. [PMID: 38799647 PMCID: PMC11125560 DOI: 10.1149/2754-2726/ad49b0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/07/2024] [Indexed: 05/29/2024]
Abstract
Glycans, or complex carbohydrates, are information-rich biopolymers critical to many biological processes and with considerable importance in pharmaceutical therapeutics. Our understanding, though, is limited compared to other biomolecules such as DNA and proteins. The greater complexity of glycan structure and the limitations of conventional chemical analysis methods hinder glycan studies. Auspiciously, nanopore single-molecule sensors-commercially available for DNA sequencing-hold great promise as a tool for enabling and advancing glycan analysis. We focus on two key areas to advance nanopore glycan characterization: molecular surface coatings to enhance nanopore performance including by molecular recognition, and high-quality glycan chemical standards for training.
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Affiliation(s)
- Megan E. Kizer
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States of America
| | - Jason R. Dwyer
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island, 02881, United States of America
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13
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Yao G, Tian Y, Ke W, Fang J, Ma S, Li T, Cheng X, Xia B, Wen L, Gao Z. Direct Identification of Complex Glycans via a Highly Sensitive Engineered Nanopore. J Am Chem Soc 2024; 146:13356-13366. [PMID: 38602480 DOI: 10.1021/jacs.4c02081] [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: 04/12/2024]
Abstract
The crucial roles that glycans play in biological systems are determined by their structures. However, the analysis of glycan structures still has numerous bottlenecks due to their inherent complexities. The nanopore technology has emerged as a powerful sensor for DNA sequencing and peptide detection. This has a significant impact on the development of a related research area. Currently, nanopores are beginning to be applied for the detection of simple glycans, but the analysis of complex glycans by this technology is still challenging. Here, we designed an engineered α-hemolysin nanopore M113R/T115A to achieve the sensing of complex glycans at micromolar concentrations and under label-free conditions. By extracting characteristic features to depict a three-dimensional (3D) scatter plot, glycans with different numbers of functional groups, various chain lengths ranging from disaccharide to decasaccharide, and distinct glycosidic linkages could be distinguished. Molecular dynamics (MD) simulations show different behaviors of glycans with β1,3- or β1,4-glycosidic bonds in nanopores. More importantly, the designed nanopore system permitted the discrimination of each glycan isomer with different lengths in a mixture with a separation ratio of over 0.9. This work represents a proof-of-concept demonstration that complex glycans can be analyzed using nanopore sequencing technology.
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Affiliation(s)
- Guangda Yao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
- Lingang Laboratory, Shanghai 200031, China
| | - Yinping Tian
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Wenjun Ke
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Fang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Shengzhou Ma
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Tiehai Li
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xi Cheng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou 330106, China
| | - Bingqing Xia
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liuqing Wen
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhaobing Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
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14
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Lu W, Zhao X, Li M, Li Y, Zhang C, Xiong Y, Li J, Zhou H, Ye X, Li X, Wang J, Liang X, Qing G. Precise Structural Analysis of Neutral Glycans Using Aerolysin Mutant T240R Nanopore. ACS NANO 2024; 18:12412-12426. [PMID: 38693619 DOI: 10.1021/acsnano.4c01571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Glycans play vital roles in nearly all life processes of multicellular organisms, and understanding these activities is inseparable from elucidating the biological significance of glycans. However, glycan research has lagged behind that of DNA and protein due to the challenges posed by structural heterogeneity and isomerism (i.e., structures with equal molecular weights) the lack of high-efficiency structural analysis techniques. Nanopore technology has emerged as a sensitive single-molecule biosensor, shining a light on glycan analysis. However, a significant number of glycans are small and uncharged, making it challenging to elicit identifiable nanopore signals. Here we introduce a R-binaphthyl tag into glycans, which enhances the cation-π interaction between the derivatized glycan molecules and the nanopore interface, enabling the detection of neutral glycans with an aerolysin nanopore. This approach allows for the distinction of di-, tri-, and tetrasaccharides with monosaccharide resolution and has the potential for group discrimination, the monitoring of enzymatic transglycosylation reactions. Notably, the aerolysin mutant T240R achieves unambiguous identification of six disaccharide isomers, trisaccharide and tetrasaccharide linkage isomers. Molecular docking simulations reveal that multiple noncovalent interactions occur between residues R282, K238, and R240 and the glycans and R-binaphthyl tag, significantly slowing down their translocation across the nanopore. Importantly, we provide a demonstration of the kinetic translocation process of neutral glycan isomers, establishing a solid theoretical foundation for glycan nanopore analysis. The development of our technology could promote the analysis of glycan structural isomers and has the potential for nanopore-based glycan structural determination and sequencing.
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Affiliation(s)
- Wenqi Lu
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xinjia Zhao
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Minmin Li
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Yuting Li
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, P. R. China
| | - Chen Zhang
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, P. R. China
| | - Yuting Xiong
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Jiaqi Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Han Zhou
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, P. R. China
| | - Xianlong Ye
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, P. R. China
| | - Xiaonong Li
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, P. R. China
| | - Jing Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Xinmiao Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, P. R. China
| | - Guangyan Qing
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
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15
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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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16
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Aktas Eken G, Huang Y, Prucker O, Rühe J, Ober C. Advancing Glucose Sensing Through Auto-Fluorescent Polymer Brushes: From Surface Design to Nano-Arrays. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2309040. [PMID: 38334235 DOI: 10.1002/smll.202309040] [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: 10/08/2023] [Revised: 12/23/2023] [Indexed: 02/10/2024]
Abstract
Designing smart (bio)interfaces with the capability to sense and react to changes in local environments offers intriguing possibilities for new surface-based sensing devices and technologies. Polymer brushes make ideal materials to design such adaptive and responsive interfaces given their large variety of functional and structural possibilities as well as their outstanding abilities to respond to physical, chemical, and biological stimuli. Herein, a practical sensory interface for glucose detection based on auto-fluorescent polymer brushes decorated with phenylboronic acid (PBA) receptors is presented. The glucose-responsive luminescent surfaces, which are capable of translating conformational transitions triggered by pH variations and binding events into fluorescent readouts without the need for fluorescent dyes, are grown from both nanopatterned and non-patterned substrates. Two-photon laser scanning confocal microscopy and atomic force microscopy (AFM) analyses reveal the relationship between the brush conformation and glucose concentration and confirm that the phenylboronic acid functionalized brushes can bind glucose over a range of physiologically relevant concentrations in a reversible manner. The combination of auto-fluorescent polymer brushes with synthetic receptors presents a promising avenue for designing innovative and robust sensing systems, which are essential for various biomedical applications, among other uses.
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Affiliation(s)
- Gozde Aktas Eken
- Materials Science and Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Yuming Huang
- Materials Science and Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Oswald Prucker
- Laboratory for Chemistry and Physics of Interfaces, Department of Microsystems Engineering (IMTEK), University of Freiburg, Georges-Köhler-Allee 103, 79110, Freiburg, Germany
| | - Jürgen Rühe
- Laboratory for Chemistry and Physics of Interfaces, Department of Microsystems Engineering (IMTEK), University of Freiburg, Georges-Köhler-Allee 103, 79110, Freiburg, Germany
- Cluster of Excellence livMatS @FIT, Freiburg Center of Interactive Materials and Bioinspired Technologies, University of Freiburg, Goerges-Köhler-Allee 105, 79110, Freiburg, Germany
| | - Christopher Ober
- Materials Science and Engineering, Cornell University, Ithaca, NY, 14853, USA
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17
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Zhao Y, Su Z, Zhang X, Wu D, Wu Y, Li G. Recent advances in nanopore-based analysis for carbohydrates and glycoconjugates. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:1454-1467. [PMID: 38415741 DOI: 10.1039/d3ay02040a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Saccharides are not only the basic constituents and nutrients of living organisms, but also participate in various life activities, and play important roles in cell recognition, immune regulation, development, cancer, etc. The analysis of carbohydrates and glycoconjugates is a necessary means to study their transformations and physiological roles in living organisms. Existing detection techniques can hardly meet the requirements for the analysis of carbohydrates and glycoconjugates in complex matrices as they are expensive, involve complex derivatization, and are time-consuming. Nanopore sensing technology, which is amplification-free and label-free, and is a high-throughput process, provides a new solution for the identification and sequencing of carbohydrates and glycoconjugates. This review highlights recent advances in novel nanopore-based single-molecule sensing technologies for the detection of carbohydrates and glycoconjugates and discusses the advantages and challenges of nanopore sensing technologies. Finally, current issues and future perspectives are discussed with the aim of improving the performance of nanopores in complex media diagnostic applications, as well as providing a new direction for the quantification of glycan chains and the study of glycan chain properties and functions.
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Affiliation(s)
- Yan Zhao
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Zhuoqun Su
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Xue Zhang
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Di Wu
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
| | - Yongning Wu
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing 100021, China
| | - Guoliang Li
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China.
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18
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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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19
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Zhang S, Cao Z, Fan P, Sun W, Xiao Y, Zhang P, Wang Y, Huang S. Discrimination of Disaccharide Isomers of Different Glycosidic Linkages Using a Modified MspA Nanopore. Angew Chem Int Ed Engl 2024; 63:e202316766. [PMID: 38116834 DOI: 10.1002/anie.202316766] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/17/2023] [Accepted: 12/19/2023] [Indexed: 12/21/2023]
Abstract
Disaccharides are composed of two monosaccharide subunits joined by a glycosidic linkage in an α or β configuration. Different combinations of isomeric monosaccharide subunits and different glycosidic linkages result in different isomeric disaccharide products. Thus, direct discrimination of these disaccharide isomers from a mixture is extremely difficult. In this paper, a hetero-octameric Mycobacterium smegmatis porin A (MspA) nanopore conjugated with a phenylboronic acid (PBA) adapter was applied for disaccharide sensing, with which three most widely known disaccharides in nature, including sucrose, lactose and maltose, were clearly discriminated. Besides, all six isomeric α-D-glucopyranosyl-D-fructoses, differing only in their glycosidic linkages, were also well resolved. Assisted by a custom machine learning algorithm, a 0.99 discrimination accuracy is achieved. Nanopore discrimination of disaccharide isomers with different glycosidic linkages, which has never been previously demonstrated, is inspiring for nanopore saccharide sequencing. This sensing capacity was also applied in direct identification of isomaltulose additives in a commercial sucrose-free yogurt, from which isomaltulose, lactose and L-lactic acid were simultaneously detected.
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Affiliation(s)
- Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Zhenyuan Cao
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Pingping Fan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Wen Sun
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Yunqi Xiao
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yuqin Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
- Institute for the Environment and Health, Nanjing University Suzhou Campus, Suzhou, 215163, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
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20
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Hong Y, Weng Y, Wu Q, Qi LY, Fan LJ. Conjugated Polyelectrolyte Containing a High Density of Pendant Phenylboronic Acid Groups for Dopamine Detection. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 37931325 DOI: 10.1021/acsami.3c10513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
A fluorescent sensing system based on a conjugated polyelectrolyte was constructed to detect dopamine (DA) in complex samples. The conjugated polymer PFPE-PBA with poly[fluorenyl-alt-p-phenyleneethynylene] (PFPE) as the backbone and carrying four pendant phenylboronic acid (PBA) groups in each repeat unit was synthesized. PFPE-PBA was found to have good solubility in polar solvents. After optimization, glycine-NaOH at pH 10 was selected as the buffer, and the solvent composition of the system was set to methanol/water (9/1 by volume). Titration experiments showed that DA could effectively quench the fluorescence of the polymer solution with a response time within 60 s and a limit of detection of 23 nM. Polyols, cations, and other possible interfering substances do not significantly affect the fluorescence of the polymer, thereby allowing for the highly selective detection of DA. Furthermore, quantitative determination of DA in spiked serum and artificial urine samples was successfully demonstrated, with recoveries ranging from 96.7 to 104%. Preliminary mechanism studies suggest that the pedant PBAs capture DA via reaction with the catechol group, and the fluorescence quenching is most likely due to the photoinduced electron transfer between the aromatic part of DA and the conjugated backbone. This study provides a general strategy for the future design of conjugated polyelectrolyte-based sensing systems.
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Affiliation(s)
- Ying Hong
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Department of Polymer Science and Engineering, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, P.R. China
| | - Yuchen Weng
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Department of Polymer Science and Engineering, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, P.R. China
| | - Qin Wu
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Department of Polymer Science and Engineering, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, P.R. China
| | - Lu-Yue Qi
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Soochow University, Suzhou 215004, P.R. China
| | - Li-Juan Fan
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Department of Polymer Science and Engineering, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, P.R. China
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21
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Chen Q, Han M, Yang Y, Zhou H, Chen J, Liu W. Real-time assay of invertase activity using isoquinolinylboronic acid as turn-on fluorescent sensor. Anal Bioanal Chem 2023; 415:5297-5309. [PMID: 37439855 DOI: 10.1007/s00216-023-04841-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/20/2023] [Accepted: 07/03/2023] [Indexed: 07/14/2023]
Abstract
Invertase is the key enzyme involved in several crucial biological processes by hydrolyzing sucrose for production of glucose and fructose. Invertase plays important roles in the fields of food, pharmacy, cosmetics, biofuels, and agriculture. Detection of invertase activity is urgently necessary for scientific research and industrial processes. Herein, a continuous fluorometric method was developed for real-time detection of invertase activity. 8-Isoquinolinylboronic acid responded to fructose by formation of a fluorescent complex in turn-on manner, and served as a fluorescent sensor to selectively recognize fructose in ternary enzymatic mixture containing sucrose and glucose. The limit of detection (LOD) for fructose was 0.07 mM. Progress curve for fructose production was established by directly and continuously monitoring the fluorescence for invertase reaction with sucrose as substrate. Initial velocity was obtained to characterize invertase activity. LOD for invertase assay was 0.10 U·mL-1. Km and υmax for invertase were determined as 7.70 mM and 0.86 mM·min-1, respectively. Copper ion was demonstrated to inhibit the invertase activity with IC50 of 33.61 mM. Applicability in high-throughput screening for inhibitor was demonstrated. The proposed method allows for real-time, simple, and rapidly monitoring the invertase activity. It has a broad range of potential applications for kinetics and screening inhibitor.
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Affiliation(s)
- Qinfei Chen
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Mengqi Han
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Yang Yang
- Emergency Department, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, 610065, China
| | - Hong Zhou
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Jiadong Chen
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Wenbin Liu
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China.
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22
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Xia B, Fang J, Ma S, Ma M, Yao G, Li T, Cheng X, Wen L, Gao Z. Mapping the Acetylamino and Carboxyl Groups on Glycans by Engineered α-Hemolysin Nanopores. J Am Chem Soc 2023; 145:18812-18824. [PMID: 37527445 DOI: 10.1021/jacs.3c03563] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Glycan is a crucial class of biological macromolecules with important biological functions. Functional groups determine the chemical properties of glycans, which further affect their biological activities. However, the structural complexity of glycans has set a technical hurdle for their direct identification. Nanopores have emerged as highly sensitive biosensors that are capable of detecting and characterizing various analytes. Here, we identified the functional groups on glycans with a designed α-hemolysin nanopore containing arginine mutations (M113R), which is specifically sensitive to glycans with acetamido and carboxyl groups. Molecular dynamics simulations indicated that the acetamido and carboxyl groups of the glycans produce unique electrical signatures by forming polar and electrostatic interactions with the M113R nanopores. Using these electrical features as the fingerprints, we mapped the length of the glycans containing acetamido and carboxyl groups at the monosaccharide, disaccharide, and trisaccharide levels. This proof-of-concept study provides a promising foundation for developing single-molecule glycan fingerprinting libraries and demonstrates the capability of biological nanopores in glycan sequencing.
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Affiliation(s)
- Bingqing Xia
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Jie Fang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210046, China
| | - Shengzhou Ma
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Mengyao Ma
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Guangda Yao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
- Lingang Laboratory, School of Life Science and Technology, Shanghai Tech University, Shanghai 200031, China
| | - Tiehai Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Xi Cheng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou, China
| | - Liuqing Wen
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zhaobing Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210046, China
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23
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Jin S, Li Y, Yang L, Li W, Zhou P. Analysis of tri-benzeneboronic esters of monosaccharides formed in aqueous solution by MALDI-TOF MS and DFT calculations. Anal Bioanal Chem 2023; 415:2775-2780. [PMID: 37071139 DOI: 10.1007/s00216-023-04685-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/22/2023] [Accepted: 04/03/2023] [Indexed: 04/19/2023]
Abstract
The affinity interactions between boronic acids and sugars have been successfully exploited in many fields, such as the sensing of saccharides, selective enrichment of glycoconjugates, and drug delivery. However, despite multiple techniques having been adopted to investigate the reaction of boronate affinity, the pathway of boronate esters formation under aqueous conditions remains controversial. We report a MALDI-MS approach to investigate the interactions between phenylboronic acid and monosaccharides in neutral aqueous solution by using polylevodopa as an innovative substrate instead of conventional matrix. A series of unusual tri-benzeneboronic esters were then revealed. The mass spectrometry data indicate that they bear a dibenzenepyroboronate cyclic ester moiety with seven-membered ring or eight-membered ring. With the aid of theoretical computations, their most likely geometrical structures are elucidated, and these tri-benzeneboronic esters are proposed to be formed via a boroxine binding monosaccharide pathway. This work provides more insight into the mechanism of boronate affinity interaction between boronic acid and sugars and proves the developed MALDI-MS approach is promising for studying interactions between small molecules.
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Affiliation(s)
- Shanxia Jin
- School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Yaqin Li
- School of Chemistry and Chemical Engineering, Wuhan Textile University, Wuhan, 430200, China
| | - Liuquan Yang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
| | - Wei Li
- School of Chemistry and Chemical Engineering, Wuhan Textile University, Wuhan, 430200, China
| | - Ping Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China.
- Center of Analysis and Testing, Wuhan University, Wuhan, 430072, China.
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24
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Li M, Xiong Y, Cao Y, Zhang C, Li Y, Ning H, Liu F, Zhou H, Li X, Ye X, Pang Y, Zhang J, Liang X, Qing G. Identification of tagged glycans with a protein nanopore. Nat Commun 2023; 14:1737. [PMID: 36977665 PMCID: PMC10050315 DOI: 10.1038/s41467-023-37348-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
Structural complexity of glycans derived from the diversities in composition, linage, configuration, and branching considerably complicates structural analysis. Nanopore-based single-molecule sensing offers the potential to elucidate glycan structure and even sequence glycan. However, the small molecular size and low charge density of glycans have restricted direct nanopore detection of glycan. Here we show that glycan sensing can be achieved using a wild-type aerolysin nanopore by introducing a facile glycan derivatization strategy. The glycan molecule can induce impressive current blockages when moving through the nanopore after being connected with an aromatic group-containing tag (plus a carrier group for the neutral glycan). The obtained nanopore data permit the identification of glycan regio- and stereoisomers, glycans with variable monosaccharide numbers, and distinct branched glycans, either independently or with the use of machine learning methods. The presented nanopore sensing strategy for glycans paves the way towards nanopore glycan profiling and potentially sequencing.
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Affiliation(s)
- Minmin Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Jiangxi Province Key Laboratory of Polymer Micro/Nano Manufacturing and Devices, School of Chemistry, Biology and Materials Science, East China University of Technology, Nanchang, 330013, China
| | - Yuting Xiong
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Jiangxi Province Key Laboratory of Polymer Micro/Nano Manufacturing and Devices, School of Chemistry, Biology and Materials Science, East China University of Technology, Nanchang, 330013, China
| | - Yuchen Cao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Chen Zhang
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang, 330000, China
| | - Yuting Li
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang, 330000, China
| | - Hanwen Ning
- Department of Statistics, Zhongnan University of Economics and Law, Wuhan, 430073, China
| | - Fan Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Han Zhou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang, 330000, China
| | - Xiaonong Li
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang, 330000, China
| | - Xianlong Ye
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang, 330000, China
| | - Yue Pang
- College of Life Science, Liaoning Normal University, Dalian, 116081, China
| | - Jiaming Zhang
- Department of Statistics, Zhongnan University of Economics and Law, Wuhan, 430073, China
| | - Xinmiao Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
- Jiangxi Provincial Key Laboratory for Pharmacodynamic Material Basis of Traditional Chinese Medicine, Ganjiang Chinese Medicine Innovation Center, Nanchang, 330000, China.
| | - Guangyan Qing
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
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25
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Liang L, Qin F, Wang S, Wu J, Li R, Wang Z, Ren M, Liu D, Wang D, Astruc D. Overview of the materials design and sensing strategies of nanopore devices. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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26
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Yang L, Sun Z, Zhang S, Sun Y, Li H. Chiral Transport in Nanochannel Based Artificial Drug Transporters. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2205274. [PMID: 36464638 DOI: 10.1002/smll.202205274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 10/23/2022] [Indexed: 06/17/2023]
Abstract
The precise regulation of chiral drug transmembrane transport can be achieved through drug transporters in living organisms. However, implementing this process in vitro is still a formidable challenge due to the complexity of the biological systems that control drug enantiomeric transport. Herein, a facile and feasible strategy is employed to construct chiral L-tyrosine-modified nanochannels (L-Tyr nanochannels) based on polyethylene terephthalate film, which could enhance the chiral recognition of propranolol isomers (R-/S-PPL) for transmembrane transport. Moreover, conventional fluorescence spectroscopy, patch-clamp technology, laser scanning confocal microscopy, and picoammeter technology are employed to evaluate the performance of nanochannels. The results show that the L-Tyr nanochannel have better chiral selectivity for R-/S-PPL compared with the L-tryptophan (L-Trp) channel, and the chiral selectivity coefficient is improved by about 4.21-fold. Finally, a detailed theoretical analysis of the chirality selectivity mechanism is carried out. The findings would not only enrich the basic theory research related to chiral drug transmembrane transport, but also provide a new idea for constructing artificial channels to separate chiral drugs.
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Affiliation(s)
- Lei Yang
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Zhongyue Sun
- College of Chemical Engineering, North China University of Science and Technology, Tangshan, 063210, P. R. China
| | - Siyun Zhang
- State Key Laboratory of Separation Membrane and Membrane Process, School of Chemistry, Tiangong University, Tianjin, 300387, P. R. China
| | - Yue Sun
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, 430065, P. R. China
- State Key Laboratory of Separation Membrane and Membrane Process, School of Chemistry, Tiangong University, Tianjin, 300387, P. R. China
| | - Haibing Li
- Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
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27
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Wang Y, Li Y, Zhou X, Zhang W, Zhang S, Xi D. Detection of Tobacco Bacterial Wilt Caused by Ralstonia solanacearum by Combining Polymerase Chain Reaction with an α-Hemolysin Nanopore. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:332. [PMID: 36678085 PMCID: PMC9863824 DOI: 10.3390/nano13020332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 06/17/2023]
Abstract
Tobacco bacterial wilt is a serious disease caused by the soil-borne bacterium Ralstonia solanacearum (R. solanacearum). Herein, a rapid and purification-free α-hemolysin (α-HL) nanopore-sensing strategy based on polymerase chain reaction (PCR) and lambda exonuclease digestion was established to detect R. solanacearum. A 198-nucleotide-long single-stranded DNA was obtained via asymmetric PCR or the lambda exonuclease-mediated digestion of the PCR product. The DNA fragment produced unique long-lived, current-blocking signals when it passed through the α-HL nanopore. This sensing approach can allow for the determination of R. solanacearum in tobacco samples and can be conveniently extended to other DNA monitoring because of the extremely wide range of PCR applications.
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Affiliation(s)
- Ying Wang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Life Science, Linyi University, Linyi 276005, China
| | - Yusen Li
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Life Science, Linyi University, Linyi 276005, China
| | - Xin Zhou
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Life Science, Linyi University, Linyi 276005, China
| | - Wenna Zhang
- Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Linyi 276000, China
| | - Shusheng Zhang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Life Science, Linyi University, Linyi 276005, China
| | - Dongmei Xi
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Life Science, Linyi University, Linyi 276005, China
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28
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Cao M, Zhang L, Tang H, Qiu X, Li Y. Single-Molecule Investigation of the Protein-Aptamer Interactions and Sensing Application Inside the Single Glass Nanopore. Anal Chem 2022; 94:17405-17412. [PMID: 36475604 DOI: 10.1021/acs.analchem.2c02660] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Solid-state nanopores offer a nanoconfined space for a single-molecule sensing strategy. Evaluating the behavior of proteins and protein-related interactions at the single-molecule level is becoming more and more important for a better understanding of biological processes and diseases. In this work, the aptamer-functionalized nanopore was prepared as the sensing platform for kinetic analysis of the carcinoembryonic antigen (CEA) with its aptamers, which is an important cancer biomarker. CEA molecules were captured by the aptamers immobilized on the inner surface of the nanopore, and there was a complicated interaction between the CEA molecules and the aptamer, which is the process of association and dissociation. This could be used to measure the dynamics of aptamer-protein interactions without labeling. The kinetic analysis could be evaluated at the single-molecule level to interpret the dissociation constants of the binding and dissociation processes. Results showed that the translocation of CEA molecules in a functionalized nanopore had a deep blockades degree and long duration compared with nanopore modified with bare gold, which could be used for CEA sensing. This protein and protein-related interaction we designed provides new insights for evaluating the binding affinity, which will be beneficial for protein sensing and immunoassays.
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Affiliation(s)
- Mengya Cao
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu241000, People's Republic of China
| | - Lijun Zhang
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu241000, People's Republic of China
| | - Haoran Tang
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu241000, People's Republic of China
| | - Xia Qiu
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu241000, People's Republic of China
| | - Yongxin Li
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu241000, People's Republic of China
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29
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Ying YL, Hu ZL, Zhang S, Qing Y, Fragasso A, Maglia G, Meller A, Bayley H, Dekker C, Long YT. Nanopore-based technologies beyond DNA sequencing. NATURE NANOTECHNOLOGY 2022; 17:1136-1146. [PMID: 36163504 DOI: 10.1038/s41565-022-01193-2] [Citation(s) in RCA: 220] [Impact Index Per Article: 73.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 06/02/2022] [Indexed: 06/16/2023]
Abstract
Inspired by the biological processes of molecular recognition and transportation across membranes, nanopore techniques have evolved in recent decades as ultrasensitive analytical tools for individual molecules. In particular, nanopore-based single-molecule DNA/RNA sequencing has advanced genomic and transcriptomic research due to the portability, lower costs and long reads of these methods. Nanopore applications, however, extend far beyond nucleic acid sequencing. In this Review, we present an overview of the broad applications of nanopores in molecular sensing and sequencing, chemical catalysis and biophysical characterization. We highlight the prospects of applying nanopores for single-protein analysis and sequencing, single-molecule covalent chemistry, clinical sensing applications for single-molecule liquid biopsy, and the use of synthetic biomimetic nanopores as experimental models for natural systems. We suggest that nanopore technologies will continue to be explored to address a number of scientific challenges as control over pore design improves.
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Affiliation(s)
- Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, People's Republic of China
| | - Zheng-Li Hu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, People's Republic of China
| | - Shengli Zhang
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Yujia Qing
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Alessio Fragasso
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
| | - Amit Meller
- Faculty of Biomedical Engineering, Technion-IIT, Haifa, Israel.
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, Oxford, UK.
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, People's Republic of China.
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30
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Synthesis and Photophysics Characterization of Boronic Styril and Distyryl BODIPYs for Water-Based Dye-Sensitized Solar Cells. Biomimetics (Basel) 2022; 7:biomimetics7030110. [PMID: 35997430 PMCID: PMC9397057 DOI: 10.3390/biomimetics7030110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/26/2022] [Accepted: 08/04/2022] [Indexed: 11/25/2022] Open
Abstract
In this study, two boronic acid BODIPYs are obtained through a microwave-assisted Knoevenagel reaction. The aim is to use them for the first time as dyes in a photosensitized solar cell (DSSC) to mimic chlorophyll photosynthesis, harvesting solar light and converting it into electricity. The microwave-assisted Knoevenagel reaction is a straightforward approach to extending the molecular conjugation of the dye and is applied for the first time to synthesize BODIPY’s boronic acid derivatives. These derivatives have proved to be very useful for covalent deposition on titania. This work studies the photo-physical and electrochemical properties. Moreover, the photovoltaic performances of these two new dyes as sensitizers for DSSC are discussed. Experimental data show that both dyes exhibit photosensitizing activities in acetonitrile and water. In particular, in all the experiments, distyryl BODIPY was more efficient than styryl BODIPY. In this study, demonstrating the use of a natural component as a water-based electrolyte for boronic BODIPY sensitizers, we open new possibilities for the development of water-based solar cells.
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31
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Hu C, Jia W, Liu Y, Wang Y, Zhang P, Chen H, Huang S. Single‐Molecule Sensing of Acidic Catecholamine Metabolites Using a Programmable Nanopore. Chemistry 2022; 28:e202201033. [DOI: 10.1002/chem.202201033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Indexed: 11/05/2022]
Affiliation(s)
- Chengzhen Hu
- 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
| | - Yao Liu
- 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
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
| | - Hong‐Yuan Chen
- 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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32
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Liu Y, Zhang S, Wang Y, Wang L, Cao Z, Sun W, Fan P, Zhang P, Chen HY, Huang S. Nanopore Identification of Alditol Epimers and Their Application in Rapid Analysis of Alditol-Containing Drinks and Healthcare Products. J Am Chem Soc 2022; 144:13717-13728. [PMID: 35867993 DOI: 10.1021/jacs.2c04595] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Alditols, which have a sweet taste but produce much lower calories than natural sugars, are widely used as artificial sweeteners. Alditols are the reduced forms of monosaccharide aldoses, and different alditols are diastereomers or epimers of each other and direct and rapid identification by conventional methods is difficult. Nanopores, which are emerging single-molecule sensors with exceptional resolution when engineered appropriately, are useful for the recognition of diastereomers and epimers. In this work, direct distinguishing of alditols corresponding to all 15 monosaccharide aldoses was achieved by a boronic acid-appended hetero-octameric Mycobacterium smegmatis porin A (MspA) nanopore (MspA-PBA). Thirteen alditols including glycerol, erythritol, threitol, adonitol, arabitol, xylitol, mannitol, sorbitol, allitol, dulcitol, iditol, talitol, and gulitol (l-sorbitol) could be fully distinguished, and their sensing features constitute a complete nanopore alditol database. To automate event classification, a custom machine-learning algorithm was developed and delivered a 99.9% validation accuracy. This strategy was also used to identify alditol components in commercially available "zero-sugar" drinks and healthcare products, suggesting their use in rapid and sensitive quality control for the food and medical industry.
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Affiliation(s)
- Yao Liu
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Liying Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Zhenyuan Cao
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Wen Sun
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Pingping Fan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
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33
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Mapping the conformational energy landscape of Abl kinase using ClyA nanopore tweezers. Nat Commun 2022; 13:3541. [PMID: 35725977 PMCID: PMC9209526 DOI: 10.1038/s41467-022-31215-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 06/07/2022] [Indexed: 02/06/2023] Open
Abstract
Protein kinases play central roles in cellular regulation by catalyzing the phosphorylation of target proteins. Kinases have inherent structural flexibility allowing them to switch between active and inactive states. Quantitative characterization of kinase conformational dynamics is challenging. Here, we use nanopore tweezers to assess the conformational dynamics of Abl kinase domain, which is shown to interconvert between two major conformational states where one conformation comprises three sub-states. Analysis of kinase-substrate and kinase-inhibitor interactions uncovers the functional roles of relevant states and enables the elucidation of the mechanism underlying the catalytic deficiency of an inactive Abl mutant G321V. Furthermore, we obtain the energy landscape of Abl kinase by quantifying the population and transition rates of the conformational states. These results extend the view on the dynamic nature of Abl kinase and suggest nanopore tweezers can be used as an efficient tool for other members of the human kinome. Quantitative characterization of kinase conformational dynamics remains challenging. Here, the authors show that protein nanopore tweezers allow analyzing the conformational energy landscape and ligand binding of the Abl kinase domain.
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34
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Zhang S, Cao Z, Fan P, Wang Y, Jia W, Wang L, Wang K, Liu Y, Du X, Hu C, Zhang P, Chen HY, Huang S. A Nanopore‐Based Saccharide Sensor. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | | | | | | | | | | | | | - Yao Liu
- Nanjing University Chemistry CHINA
| | | | | | | | | | - Shuo Huang
- Nanjing University Chemistry 163 Xianlin AveSchool of Chemistry and Chemical EngineeringXixia District 210023 Nanjing CHINA
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35
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Zhang S, Cao Z, Fan P, Wang Y, Jia W, Wang L, Wang K, Liu Y, Du X, Hu C, Zhang P, Chen HY, Huang S. A Nanopore-Based Saccharide Sensor. Angew Chem Int Ed Engl 2022; 61:e202203769. [PMID: 35718742 DOI: 10.1002/anie.202203769] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Indexed: 12/19/2022]
Abstract
Saccharides play critical roles in many forms of cellular activities. Saccharide structures are however complicated and similar, setting a technical hurdle for direct identification. Nanopores, which are emerging single molecule tools sensitive to minor structural differences between analytes, can be engineered to identity saccharides. A hetero-octameric Mycobacterium smegmatis porin A nanopore containing a phenylboronic acid was prepared, and was able to clearly identify nine monosaccharide types, including D-fructose, D-galactose, D-mannose, D-glucose, L-sorbose, D-ribose, D-xylose, L-rhamnose and N-acetyl-D-galactosamine. Minor structural differences between saccharide epimers can also be distinguished. To assist automatic event classification, a machine learning algorithm was developed, with which a general accuracy score of 0.96 was achieved. This sensing strategy is generally suitable for other saccharide types and may bring new insights to nanopore saccharide sequencing.
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Affiliation(s)
- 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
| | - 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
| | - 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
| | - 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
| | - 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
| | - Liying 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
| | - Kefan 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
| | - Yao Liu
- 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
| | - Xiaoyu Du
- 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
| | - Chengzhen Hu
- 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
| | - Hong-Yuan Chen
- 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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36
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Li T, Liu J, Sun XL, Wan WM, Xiao L, Qian Q. Boronic acid-containing polymeric nanomaterials via polymerization induced self-assembly as fructose sensor. POLYMER 2022. [DOI: 10.1016/j.polymer.2022.125005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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37
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Abstract
Nucleoside analogues are reagents that resemble the structure of natural nucleosides and are widely applied in antiviral and anticancer therapy. Molnupiravir, a recently reported nucleoside analogue drug, has shown its inhibitory effect against SARS-CoV-2. Rapid tracing of molnupiravir and its metabolites is important in the evaluation of its pharmacology effect, but direct sensing of molnupiravir as a single molecule has not been reported to date. Here, we demonstrate a nanopore-based sensor with which direct sensing of molnupiravir and its two major metabolites β-d-N4-hydroxycytidine and its triphosphate can be achieved simultaneously. In conjunction with a custom machine learning algorithm, an accuracy of 92% was achieved. This sensing strategy may be useful in the current pandemic and is in principle suitable for other nucleoside analogue drugs.
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Affiliation(s)
- 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
| | - Chengzhen Hu
- 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
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
| | - Hong-Yuan Chen
- 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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38
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Jiang X, Pan T, Lang C, Zeng C, Hou J, Xu J, Luo Q, Hou C, Liu J. Single-Molecule Observation of Selenoenzyme Intermediates in a Semisynthetic Seleno-α-Hemolysin Nanoreactor. Anal Chem 2022; 94:8433-8440. [PMID: 35621827 DOI: 10.1021/acs.analchem.2c01204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of monitoring methods to capture short-lived intermediates is crucial for kinetic mechanism validation of enzymatic reaction steps. In this work, a semisynthetic selenoenzyme nanoreactor was constructed by introducing the unnatural amino acid (Sec) into the lumen of the α-hemolysin (αHL) nanopore. This nanoreactor not only created a highly confined space to trap the enzyme-substrate complex for a highly efficient antioxidant activity but also provided a single channel to characterize a series of selenoenzyme intermediates in the whole catalytic cycle through electrochemical analysis. In particular, the unstable intermediate of SeOH can be clearly detected by the characteristic blocking current. The duration time corresponding to the lifetime of each intermediate that stayed within the nanopore was also determined. This label-free approach showed a high detection sensitivity and temporal-spatial resolution to scrutinize a continuous enzymatic process, which would facilitate uncovering the mysteries of selenoenzyme catalysis at the single-molecule level.
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Affiliation(s)
- Xiaojia Jiang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Tiezheng Pan
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Chao Lang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Chao Zeng
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Jinxing Hou
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Jiayun Xu
- College of Material Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, China
| | - Quan Luo
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China.,Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China.,Key Laboratory of Emergency and Trauma, Ministry of Education, College of Emergency and Trauma, Hainan Medical University, Haikou 571199, China
| | - Chunxi Hou
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Junqiu Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China.,College of Material Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, China
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39
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Jia W, Hu C, Wang Y, Liu Y, Wang L, Zhang S, Zhu Q, Gu Y, Zhang P, Ma J, Chen HY, Huang S. Identification of Single-Molecule Catecholamine Enantiomers Using a Programmable Nanopore. ACS NANO 2022; 16:6615-6624. [PMID: 35394745 DOI: 10.1021/acsnano.2c01017] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Enantiomers, chiral isomers with opposite chirality, typically demonstrate differences in their pharmacological activity, metabolism, and toxicity. However, direct discrimination between enantiomers is challenging due to their similar physiochemical properties. Following the strategy of programmable nanoreactors for stochastic sensing (PNRSS), introduction of phenylboronic acid (PBA) to a Mycobacterium smegmatis porin A (MspA) assists in the identification of the enantiomers of norepinephrine and epinephrine. Using a machine learning algorithm, identification of the enantiomers has been achieved with an accuracy of 98.2%. The enantiomeric excess (ee) of a mixture of enantiomeric catecholamines was measured to determine the enantiomeric purity. This sensing strategy is a faster method for the determination of ee values than liquid chromatography-mass spectrometry and is useful as a quality control in the industrial production of enantiomeric drugs.
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Affiliation(s)
- 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
| | - Chengzhen Hu
- 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
| | - Yao Liu
- 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
| | - Liying 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
| | - 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
| | - Qiang Zhu
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Yuming Gu
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, 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
| | - Jing Ma
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Hong-Yuan Chen
- 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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40
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Tang H, Wang H, Zhao D, Cao M, Zhu Y, Li Y. Nanopore-Based Single-Entity Electrochemistry for the Label-Free Monitoring of Single-Molecule Glycoprotein-Boronate Affinity Interaction and Its Sensing Application. Anal Chem 2022; 94:5715-5722. [PMID: 35362966 DOI: 10.1021/acs.analchem.2c00860] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Nanopipettes provide a promising confined space that enables advances in single-molecule analysis, and their unique conical tubular structure is also suitable for single-cell analysis. In this work, functionalized-nanopore-based single-entity electrochemistry (SEE) analysis tools were developed for the label-free monitoring of single-molecule glycoprotein-boronate affinity interaction for the first time, and immunoglobulin G (IgG, one of the important biomarkers for many diseases such as COVID-19 and cancers) was employed as the model glycoprotein. The principle of this method is based on a single glycoprotein molecule passing through 4-mercaptophenylboronic acid (4-MPBA)-modified nanopipettes under a bias voltage and in the meantime interacting with the boronate group from modified 4-MPBA. This translocation and affinity interaction process can generate distinguishable current blockade signals. Based on the statistical analysis of these signals, the equilibrium association constant (κa) of single-molecule glycoprotein-boronate affinity interaction was obtained. The results show that the κa of IgG in the confined nanopore at the single-molecule level is much larger than that measured in the open system at the ensemble level, which is possibly due to the enhanced multivalent synergistic binding in the restricted space. Moreover, the functionalized-nanopore-based SEE analysis tools were further applied for the label-free detection of IgG, and the results indicate that our method has potential application value for the detection of glycoproteins in real samples, which also paves way for the single-cell analysis of glycoproteins.
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Affiliation(s)
- Haoran Tang
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P. R. China
| | - Hao Wang
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P. R. China
| | - Dandan Zhao
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P. R. China
| | - Mengya Cao
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P. R. China
| | - Yanyan Zhu
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P. R. China
| | - Yongxin Li
- Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, P. R. China
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41
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Carrod AJ, Graglia F, Male L, Le Duff C, Simpson P, Elsherif M, Ahmed Z, Butt H, Xu G, Kam‐Wing Lo K, Bertoncello P, Pikramenou Z. Photo- and Electrochemical Dual-Responsive Iridium Probe for Saccharide Detection. Chemistry 2022; 28:e202103541. [PMID: 34811834 PMCID: PMC9299874 DOI: 10.1002/chem.202103541] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Indexed: 11/19/2022]
Abstract
Dual detection systems are of interest for rapid, accurate data collection in sensing systems and in vitro testing. We introduce an IrIII complex with a boronic acid receptor site attached to the 2-phenylpyridine ligand as an ideal probe with photo- and electrochemical signals that is sensitive to monosaccharide binding in aqueous solution. The complex displays orange luminescence at 618 nm, which is reduced by 70 and 40 % upon binding of fructose and glucose, respectively. The electro-chemiluminescent signal of the complex also shows a direct response to monosaccharide binding. The IrIII complex shows the same response upon incorporation into hydrogel matrices as in solution, thus demonstrating the potential of its integration into a device, as a nontoxic, simple-to-use tool to observe sugar binding over physiologically relevant pH ranges and saccharide concentrations. Moreover, the complex's luminescence is responsive to monosaccharide presence in cancer cells.
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Affiliation(s)
- Andrew J. Carrod
- School of ChemistryUniversity of Birmingham EdgbastonBirminghamB15 2TTUK
| | | | - Louise Male
- School of ChemistryUniversity of Birmingham EdgbastonBirminghamB15 2TTUK
| | - Cécile Le Duff
- School of ChemistryUniversity of Birmingham EdgbastonBirminghamB15 2TTUK
| | - Peter Simpson
- School of EngineeringUniversity of Birmingham EdgbastonBirminghamB15 2TTUK
| | - Mohamed Elsherif
- School of EngineeringUniversity of Birmingham EdgbastonBirminghamB15 2TTUK
| | - Zubair Ahmed
- College of Medical and Dental SciencesUniversity of Birmingham EdgbastonBirminghamB15 2TTUK
| | - Haider Butt
- School of EngineeringUniversity of Birmingham EdgbastonBirminghamB15 2TTUK
| | - Guang‐Xi Xu
- Department of ChemistryCity University of Hong KongTat Chee AvenueHong KongChina
| | - Kenneth Kam‐Wing Lo
- Department of ChemistryCity University of Hong KongTat Chee AvenueHong KongChina
| | | | - Zoe Pikramenou
- School of ChemistryUniversity of Birmingham EdgbastonBirminghamB15 2TTUK
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42
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Wei Z, Yao E, Cheng Y, Hu J, Liu Y. Insight into the dehydration of high-concentration fructose to 5-hydroxymethylfurfural in oxygen-containing polar aprotic solvents. NEW J CHEM 2022. [DOI: 10.1039/d2nj01339h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A high 5-HMF yield of 85.4% was achieved in polar aprotic oxygen-containing solvent with strong electrophilic maleic acid by quenching DHH.
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Affiliation(s)
- Zuojun Wei
- Key Laboratory of Biomass Chemical Engineering of the Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, 38 Zheda Road, Xihu District, Hangzhou 310027, P. R. China
- Institute of Zhejiang University–Quzhou, 78 Jinhua Boulevard North, Quzhou 324000, P. R. China
| | - En Yao
- Key Laboratory of Biomass Chemical Engineering of the Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, 38 Zheda Road, Xihu District, Hangzhou 310027, P. R. China
- Institute of Zhejiang University–Quzhou, 78 Jinhua Boulevard North, Quzhou 324000, P. R. China
| | - Yuran Cheng
- Key Laboratory of Biomass Chemical Engineering of the Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, 38 Zheda Road, Xihu District, Hangzhou 310027, P. R. China
- Institute of Zhejiang University–Quzhou, 78 Jinhua Boulevard North, Quzhou 324000, P. R. China
| | - Jinbo Hu
- College of Pharmaceutical Science, Zhejiang University of Technology, 1 GongDa Road, Wukang Street, Deqing County, HuZhou 313200, P. R. China
| | - Yingxin Liu
- College of Pharmaceutical Science, Zhejiang University of Technology, 1 GongDa Road, Wukang Street, Deqing County, HuZhou 313200, P. R. China
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43
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Kanyan D, Horacek-Glading M, Wildervanck MJ, Söhnel T, Ware DC, Brothers PJ. O-BODIPYs as fluorescent labels for sugars: glucose, xylose and ribose. Org Chem Front 2022. [DOI: 10.1039/d1qo01418h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Fluorescent 1 : 1, 1 : 2 and 1 : 3 sugar-O-BODIPY conjugates of glucose, xylose and ribose were characterised by 1H–11B HMBC and 11B NMR to discriminate between boron bound to 1,2-, 1,3- or 1,4-diol sites and furanose/pyranose sugar forms.
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Affiliation(s)
- Deepika Kanyan
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Miriana Horacek-Glading
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Martijn J. Wildervanck
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Tilo Söhnel
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - David C. Ware
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Penelope J. Brothers
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
- Research School of Chemistry, Australian National University, 137 Sullivan's Creek Road, Canberra ACT 2601, Australia
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44
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Zhang L, Burns N, Jordan M, Jayasinghe L, Guo P. Macromolecule sensing and tumor biomarker detection by harnessing terminal size and hydrophobicity of viral DNA packaging motor channels into membranes and flow cells. Biomater Sci 2021; 10:167-177. [PMID: 34812812 DOI: 10.1039/d1bm01264a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Biological nanopores for single-pore sensing have the advantage of size homogeneity, structural reproducibility, and channel amenability. In order to translate this to clinical applications, the functional biological nanopore must be inserted into a stable system for high-throughput analysis. Here we report factors that control the rate of pore insertion into polymer membrane and analyte translocation through the channel of viral DNA packaging motors of Phi29, T3 and T7. The hydrophobicity of aminol or carboxyl terminals and their relation to the analyte translocation were investigated. It was found that both the size and the hydrophobicity of the pore terminus are critical factors for direct membrane insertion. An N-terminus or C-terminus hydrophobic mutation is crucial for governing insertion orientation and subsequent macromolecule translocation due to the one-way traffic property. The N- or C-modification led to two different modes of application. The C-terminal insertion permits translocation of analytes such as peptides to enter the channel through the N terminus, while N-terminus insertion prevents translocation but offers the measurement of gating as a sensing parameter, thus generating a tool for detection of markers. A urokinase-type Plasminogen Activator Receptor (uPAR) binding peptide was fused into the C-terminal of Phi29 nanopore to serve as a probe for uPAR protein detection. The uPAR has proven to be a predictive biomarker in several types of cancer, including breast cancer. With an N-terminal insertion, the binding of the uPAR antigen to individual peptide probe induced discretive steps of current reduction due to the induction of channel gating. The distinctive current signatures enabled us to distinguish uPAR positive and negative tumor cell lines. This finding provides a theoretical basis for a robust biological nanopore sensing system for high-throughput macromolecular sensing and tumor biomarker detection.
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Affiliation(s)
- Long Zhang
- Center for RNA Nanobiotechnology and Nanomedicine; College of Pharmacy; Dorothy M. Davis Heart and Lung Research Institute; James Comprehensive Cancer Center; College of Medicine; The Ohio State University, Columbus, OH 43210, USA.
| | - Nicolas Burns
- Center for RNA Nanobiotechnology and Nanomedicine; College of Pharmacy; Dorothy M. Davis Heart and Lung Research Institute; James Comprehensive Cancer Center; College of Medicine; The Ohio State University, Columbus, OH 43210, USA.
| | - Michael Jordan
- Oxford Nanopore Technologies Ltd, Gosling Building, Edmund Halley Road, Oxford Science Park, Oxford, OX4 4DQ, UK
| | - Lakmal Jayasinghe
- Oxford Nanopore Technologies Ltd, Gosling Building, Edmund Halley Road, Oxford Science Park, Oxford, OX4 4DQ, UK
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine; College of Pharmacy; Dorothy M. Davis Heart and Lung Research Institute; James Comprehensive Cancer Center; College of Medicine; The Ohio State University, Columbus, OH 43210, USA.
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45
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Lin T, Huang X, Guo L, Zhou S, Li X, Liu Y, Hu J, Chen X, Xiong Y. Boronate affinity-assisted oriented antibody conjugation on quantum dot nanobeads for improved detection performance in lateral flow immunoassay. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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46
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Raabe M, Heck AJ, Führer S, Schauenburg D, Pieszka M, Wang T, Zegota MM, Nuhn L, Ng DYW, Kuan SL, Weil T. Assembly of pH-Responsive Antibody-Drug-Inspired Conjugates. Macromol Biosci 2021; 22:e2100299. [PMID: 34791790 DOI: 10.1002/mabi.202100299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/11/2021] [Indexed: 01/12/2023]
Abstract
With the advent of chemical strategies that allow the design of smart bioconjugates, peptide- and protein-drug conjugates are emerging as highly efficient therapeutics to overcome limitations of conventional treatment, as exemplified by antibody-drug conjugates (ADCs). While targeting peptides serve similar roles as antibodies to recognize overexpressed receptors on diseased cell surfaces, peptide-drug conjugates suffer from poor stability and bioavailability due to their low molecular weights. Through a combination of a supramolecular protein-based assembly platform and a pH-responsive linker, the authors devise herein the convenient assembly of a trivalent protein-drug conjugate. The conjugate should ideally possess distinct features of ADCs such as 1) recognition sites that recognize cell receptor and are arranged on 2) distinct locations on a high molecular weight protein scaffold, 3) a stimuli-responsive linker, as well as 4) an attached payload such as a drug molecule. These AD-like conjugates target cancer cells that overexpress somatostatin receptors, can enable controlled release in the microenvironment of cancer cells through a new pH-responsive biotin linker, and exhibit stability in biological media.
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Affiliation(s)
- Marco Raabe
- Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz, 55128, Germany.,Institute of Inorganic Chemistry I, Ulm University, Albert-Einstein-Allee 11, Ulm, 89081, Germany.,Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan
| | - Astrid Johanna Heck
- Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz, 55128, Germany
| | - Siska Führer
- Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz, 55128, Germany
| | - Dominik Schauenburg
- Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz, 55128, Germany
| | - Michaela Pieszka
- Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz, 55128, Germany.,Institute of Inorganic Chemistry I, Ulm University, Albert-Einstein-Allee 11, Ulm, 89081, Germany
| | - Tao Wang
- Institute of Inorganic Chemistry I, Ulm University, Albert-Einstein-Allee 11, Ulm, 89081, Germany.,Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 600213, P. R. China
| | - Maksymilian Marek Zegota
- Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz, 55128, Germany.,Institute of Inorganic Chemistry I, Ulm University, Albert-Einstein-Allee 11, Ulm, 89081, Germany
| | - Lutz Nuhn
- Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz, 55128, Germany
| | - David Y W Ng
- Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz, 55128, Germany
| | - Seah Ling Kuan
- Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz, 55128, Germany.,Institute of Inorganic Chemistry I, Ulm University, Albert-Einstein-Allee 11, Ulm, 89081, Germany
| | - Tanja Weil
- Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz, 55128, Germany.,Institute of Inorganic Chemistry I, Ulm University, Albert-Einstein-Allee 11, Ulm, 89081, Germany
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47
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Post-translational insertion of boron in proteins to probe and modulate function. Nat Chem Biol 2021; 17:1245-1261. [PMID: 34725511 PMCID: PMC8604732 DOI: 10.1038/s41589-021-00883-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 08/25/2021] [Indexed: 11/16/2022]
Abstract
Boron is absent in proteins, yet is a micronutrient. It possesses unique bonding that could expand biological function including modes of Lewis acidity not available to typical elements of life. Here we show that post-translational Cβ–Bγ bond formation provides mild, direct, site-selective access to the minimally sized residue boronoalanine (Bal) in proteins. Precise anchoring of boron within complex biomolecular systems allows dative bond-mediated, site-dependent protein Lewis acid–base-pairing (LABP) by Bal. Dynamic protein-LABP creates tunable inter- and intramolecular ligand–host interactions, while reactive protein-LABP reveals reactively accessible sites through migratory boron-to-oxygen Cβ–Oγ covalent bond formation. These modes of dative bonding can also generate de novo function, such as control of thermo- and proteolytic stability in a target protein, or observation of transient structural features via chemical exchange. These results indicate that controlled insertion of boron facilitates stability modulation, structure determination, de novo binding activities and redox-responsive ‘mutation’. ![]()
Post-translational site-selective formation of boronoalanine in proteins enables applications of boron for binding partner capture, footprinting of interactions with reactive oxygen species, proteolytic control and mapping of transient structures.
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48
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Qian T, Zhao C, Wang R, Chen X, Hou J, Wang H, Zhang H. Synthetic azobenzene-containing metal-organic framework ion channels toward efficient light-gated ion transport at the subnanoscale. NANOSCALE 2021; 13:17396-17403. [PMID: 34642709 DOI: 10.1039/d1nr04595d] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Artificial nanochannels with diverse responsive properties have been widely developed to replicate the smart gating functionalities of biological ion channels. However, in these traditional nanochannels, common responsive molecules are usually too small to efficiently block the large channels under the closed states, leading to weak gating performances. Herein, we report carboxylated azobenzene-coordinated metal-organic-framework (AZO-MOF) ion channels with impressive light-gating properties. The AZO-MOF ion channels were synthesized by the confined growth of AZO-MOFs, composed of light-responsive AZO-containing ligands, non-responsive ligands and metal clusters, into ion-track-etched polymer nanochannels. The AZO-MOF ion channels with an appropriate number of AZO ligands showed a well-maintained crystalline and three-dimensional porous structure, including nanoscale cavities and subnanoscale windows for LiCl conduction. Meanwhile, the AZO-containing ligands bend and stretch upon light irradiation to open and close the pathways, thus gating the ion flux through the AZO-MOF ion channels with high on-off ratios up to 40.2, which is ∼2.3-30 times those of AZO-encapsulated MOF ion channels and AZO-modified nanochannels. This work suggests ways to achieve subnanoscaled gating of ion transport by angstrom-porous MOFs coordinated by stimuli-responsive ligands.
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Affiliation(s)
- Tianyue Qian
- Department of Chemical Engineering, Monash University, Clayton, Victoria 3800, Australia.
| | - Chen Zhao
- Chemical and Environmental Engineering, School of Engineering, RMIT University, Melbourne, Victoria 3000, Australia.
| | - Ruoxin Wang
- Department of Chemical Engineering, Monash University, Clayton, Victoria 3800, Australia.
| | - Xiaofang Chen
- Department of Chemical Engineering, Monash University, Clayton, Victoria 3800, Australia.
| | - Jue Hou
- Manufacturing, CSIRO, Clayton, Victoria 3168, Australia
| | - Huanting Wang
- Department of Chemical Engineering, Monash University, Clayton, Victoria 3800, Australia.
| | - Huacheng Zhang
- Chemical and Environmental Engineering, School of Engineering, RMIT University, Melbourne, Victoria 3000, Australia.
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49
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Zegota M, Müller MA, Lantzberg B, Kizilsavas G, Coelho JAS, Moscariello P, Martínez-Negro M, Morsbach S, Gois PMP, Wagner M, Ng DYW, Kuan SL, Weil T. Dual Stimuli-Responsive Dynamic Covalent Peptide Tags: Toward Sequence-Controlled Release in Tumor-like Microenvironments. J Am Chem Soc 2021; 143:17047-17058. [PMID: 34632780 PMCID: PMC8532147 DOI: 10.1021/jacs.1c06559] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Indexed: 12/11/2022]
Abstract
Dynamic covalent chemistry (DCvC) has emerged as a versatile synthetic tool for devising stable, stimuli-responsive linkers or conjugates. The interplay of binding affinity, association and dissociation constants exhibits a strong influence on the selectivity of the reaction, the conversion rate, as well as the stability in aqueous solutions. Nevertheless, dynamic covalent interactions often exhibit fast binding and fast dissociation events or vice versa, affecting their conversion rates or stabilities. To overcome the limitation in linker design, we reported herein dual responsive dynamic covalent peptide tags combining a pH responsive boronate ester with fast association and dissociation rates, and a redox-active disulfide with slow formation and dissociation rate. Precoordination by boronic acid-catechol interaction improves self-sorting and selectivity in disulfide formation into heterodimers. The resulting bis-peptide conjugate exhibited improved complex stability in aqueous solution and acidic tumor-like extracellular microenvironment. Furthermore, the conjugate responds to pH changes within the physiological range as well as to redox conditions found inside cancer cells. Such tags hold great promise, through cooperative effects, for controlling the stability of bioconjugates under dilution in aqueous media, as well as designing intelligent pharmaceutics that react to distinct biological stimuli in cells.
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Affiliation(s)
- Maksymilian
Marek Zegota
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute
of Inorganic Chemistry I, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | | | - Bellinda Lantzberg
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Gönül Kizilsavas
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Jaime A. S. Coelho
- Centro
de Química Estrutural, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisbon, Portugal
| | | | - María Martínez-Negro
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Svenja Morsbach
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Pedro M. P. Gois
- Research
Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisbon, Portugal
| | - Manfred Wagner
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - David Y. W. Ng
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Seah Ling Kuan
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute
of Inorganic Chemistry I, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Tanja Weil
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute
of Inorganic Chemistry I, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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50
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Abstract
Chemical reactions of single molecules, caused by rapid formation or breaking of chemical bonds, are difficult to observe even with state-of-the-art instruments. A biological nanopore can be engineered into a single molecule reactor, capable of detecting the binding of a monatomic ion or the transient appearance of chemical intermediates. Pore engineering of this type is however technically challenging, which has significantly restricted further development of this technique. We propose a versatile strategy, "programmable nano-reactors for stochastic sensing" (PNRSS), by which a variety of single molecule reactions of hydrogen peroxide, metal ions, ethylene glycol, glycerol, lactic acid, vitamins, catecholamines or nucleoside analogues can be observed directly. PNRSS presents a refined sensing resolution which can be further enhanced by an artificial intelligence algorithm. Remdesivir, a nucleoside analogue and an investigational anti-viral drug used to treat COVID-19, can be distinguished from its active triphosphate form by PNRSS, suggesting applications in pharmacokinetics or drug screening.
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