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Jiang Y, Wang R, Ye C, Wang X, Wang D, Du Q, Liang H, Zhang S, Gao P. Stimuli-Responsive Ion Transport Regulation in Nanochannels by Adhesion-Induced Functionalization of Macroscopic Outer Surface. ACS APPLIED MATERIALS & INTERFACES 2024. [PMID: 38924711 DOI: 10.1021/acsami.4c02299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
Responsive regulation of ion transport through nanochannels is crucial in the design of smart nanofluidic devices for sequencing, sensing, and water-energy nexus. Functionalization of the inner wall of the nanochannel enhances interaction with ions and fluid but restricts versatile chemical approaches and accurate characterizations of fluidic interfaces. Herein, we reveal a responsive regulating mechanism of ion transport through nanochannels by polydopamine (PDA)-induced functionalization on the macroscopic outer surface of nanochannels. Responsive molecules were codeposited with PDA on the outer surface of nanochannels and formed a valve of nanometer thickness to manually manipulate ion transport by changing its gap spacing, surface charge, and wettability under external stimulus. The response ratio can be up to 100-fold by maximizing the proportion of responsive molecules on the outer surface. Laminating the codepositions of different responsive molecules with PDA on the channel's outer surface produces multiple responses. A nearly universal adhesion of PDA with responsive molecules on the open outer surface induces nanochannels responsive to different external stimuli with variable response ratios and arbitrary combinations. The results challenge the primary role of functionalization on the nanoconfined interface of nanofluidics and open opportunities for developing new-style nanofluidic devices through the functionalization of macroscopic interface.
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Affiliation(s)
- You Jiang
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P. R. China
| | - Rongsheng Wang
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P. R. China
| | - Chunxi Ye
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P. R. China
| | - Xinmeng Wang
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P. R. China
| | - Dagui Wang
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P. R. China
| | - Qiujiao Du
- School of Mathematics and Physics, China University of Geosciences, Wuhan 430074, P. R. China
| | - Huageng Liang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, P. R. China
| | - Shouwei Zhang
- National Local Joint Laboratory for Advanced Textile Processing and Clean Production, Wuhan Textile University, Wuhan 430200, P. R. China
| | - Pengcheng Gao
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P. R. China
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2
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Yang J, Pan T, Xie Z, Yuan W, Ho HP. In-tube micro-pyramidal silicon nanopore for inertial-kinetic sensing of single molecules. Nat Commun 2024; 15:5132. [PMID: 38879544 PMCID: PMC11180207 DOI: 10.1038/s41467-024-48630-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 05/06/2024] [Indexed: 06/19/2024] Open
Abstract
Electrokinetic force has been the major choice for driving the translocation of molecules through a nanopore. However, the use of this approach is limited by an uncontrollable translocation speed, resulting in non-uniform conductance signals with low conformational sensitivity, which hinders the accurate discrimination of the molecules. Here, we show the use of inertial-kinetic translocation induced by spinning an in-tube micro-pyramidal silicon nanopore fabricated using photovoltaic electrochemical etch-stop technique for biomolecular sensing. By adjusting the kinetic properties of a funnel-shaped centrifugal force field while maintaining a counter-balanced state of electrophoretic and electroosmotic effect in the nanopore, we achieved regulated translocation of proteins and obtained stable signals of long and adjustable dwell times and high conformational sensitivity. Moreover, we demonstrated instantaneous sensing and discrimination of molecular conformations and longitudinal monitoring of molecular reactions and conformation changes by wirelessly measuring characteristic features in current blockade readouts using the in-tube nanopore device.
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Affiliation(s)
- Jianxin Yang
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Tianle Pan
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zhenming Xie
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wu Yuan
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Ho-Pui Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China.
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3
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Baldelli M, Di Muccio G, Sauciuc A, Morozzo Della Rocca B, Viola F, Balme S, Bonini A, Maglia G, Chinappi M. Controlling Electroosmosis in Nanopores Without Altering the Nanopore Sensing Region. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2401761. [PMID: 38860821 DOI: 10.1002/adma.202401761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/24/2024] [Indexed: 06/12/2024]
Abstract
Nanopores are powerful tools for single-molecule sensing of biomolecules and nanoparticles. The signal coming from the molecule to be analyzed strongly depends on its interaction with the narrower section of the nanopore (constriction) that may be tailored to increase sensing accuracy. Modifications of nanopore constriction have also been commonly used to induce electroosmosis, that favors the capture of molecules in the nanopore under a voltage bias and independently of their charge. However, engineering nanopores for increasing both electroosmosis and sensing accuracy is challenging. Here it is shown that large electroosmotic flows can be achieved without altering the nanopore constriction. Using continuum electrohydrodynamic simulations, it is found that an external charged ring generates strong electroosmosis in cylindrical nanopores. Similarly, for conical nanopores it is shown that moving charges away from the cone tip still results in an electroosmotic flow (EOF), whose intensity reduces increasing the diameter of the nanopore section where charges are placed. This paradigm is applied to engineered biological nanopores showing, via atomistic simulations and experiments, that mutations outside the constriction induce a relatively intense electroosmosis. This strategy provides much more flexibility in nanopore design since electroosmosis can be controlled independently from the constriction, which can be optimized to improve sensing accuracy.
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Affiliation(s)
- Matteo Baldelli
- Department of Industrial Engeenering, University of Rome Tor Vergata, Roma, 00133, Italy
| | - Giovanni Di Muccio
- Department of Mechanical and Aerospace Engineering, University of Rome Sapienza, Roma, 00184, Italy
| | - Adina Sauciuc
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Groningen, 9747 AG, The Netherlands
| | | | | | - Sébastien Balme
- Institut Europeen des Membranes, UMR5635, University of Montpellier ENCSM CNRS, Montpellier, 34095, France
| | - Andrea Bonini
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Groningen, 9747 AG, The Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Groningen, 9747 AG, The Netherlands
| | - Mauro Chinappi
- Department of Industrial Engeenering, University of Rome Tor Vergata, Roma, 00133, Italy
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4
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Ma H, Pan SQ, Wang WL, Yue X, Xi XH, Yan S, Wu DY, Wang X, Liu G, Ren B. Surface-Enhanced Raman Spectroscopy: Current Understanding, Challenges, and Opportunities. ACS NANO 2024; 18:14000-14019. [PMID: 38764194 DOI: 10.1021/acsnano.4c02670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Abstract
While surface-enhanced Raman spectroscopy (SERS) has experienced substantial advancements since its discovery in the 1970s, it is an opportunity to celebrate achievements, consider ongoing endeavors, and anticipate the future trajectory of SERS. In this perspective, we encapsulate the latest breakthroughs in comprehending the electromagnetic enhancement mechanisms of SERS, and revisit CT mechanisms of semiconductors. We then summarize the strategies to improve sensitivity, selectivity, and reliability. After addressing experimental advancements, we comprehensively survey the progress on spectrum-structure correlation of SERS showcasing their important role in promoting SERS development. Finally, we anticipate forthcoming directions and opportunities, especially in deepening our insights into chemical or biological processes and establishing a clear spectrum-structure correlation.
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Affiliation(s)
- Hao Ma
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Si-Qi Pan
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Center for Marine Environmental Chemistry & Toxicology, Xiamen University, Xiamen 361102, China
| | - Wei-Li Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Center for Marine Environmental Chemistry & Toxicology, Xiamen University, Xiamen 361102, China
| | - Xiaxia Yue
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xiao-Han Xi
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Sen Yan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - De-Yin Wu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xiang Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Guokun Liu
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Center for Marine Environmental Chemistry & Toxicology, Xiamen University, Xiamen 361102, China
| | - Bin Ren
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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5
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Tian R, Ma W, Wang L, Xie W, Wang Y, Yin Y, Weng T, He S, Fang S, Liang L, Wang L, Wang D, Bai J. The combination of DNA nanostructures and materials for highly sensitive electrochemical detection. Bioelectrochemistry 2024; 157:108651. [PMID: 38281367 DOI: 10.1016/j.bioelechem.2024.108651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/30/2024]
Abstract
Due to the wide range of electrochemical devices available, DNA nanostructures and material-based technologies have been greatly broadened. They have been actively used to create a variety of beautiful nanostructures owing to their unmatched programmability. Currently, a variety of electrochemical devices have been used for rapid sensing of biomolecules and other diagnostic applications. Here, we provide a brief overview of recent advances in DNA-based biomolecular assays. Biosensing platform such as electrochemical biosensor, nanopore biosensor, and field-effect transistor biosensors (FET), which are equipped with aptamer, DNA walker, DNAzyme, DNA origami, and nanomaterials, has been developed for amplification detection. Under the optimal conditions, the proposed biosensor has good amplification detection performance. Further, we discussed the challenges of detection strategies in clinical applications and offered the prospect of this field.
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Affiliation(s)
- Rong Tian
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China.
| | - Wenhao Ma
- Bioengineering College of Chongqing University, Chongqing 400044, PR China
| | - Lue Wang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, PR China
| | - Wanyi Xie
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China
| | - Yunjiao Wang
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China
| | - Yajie Yin
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China
| | - Ting Weng
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China
| | - Shixuan He
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China
| | - Shaoxi Fang
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China
| | - Liyuan Liang
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China
| | - Liang Wang
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China.
| | - Deqiang Wang
- Chongqing School, University of Chinese Academy of Sciences & Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 400714, PR China.
| | - Jingwei Bai
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, PR China
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6
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Jiang Q, Shang Y, Xie Y, Ding B. DNA Origami: From Molecular Folding Art to Drug Delivery Technology. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2301035. [PMID: 37715333 DOI: 10.1002/adma.202301035] [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: 02/02/2023] [Revised: 05/08/2023] [Indexed: 09/17/2023]
Abstract
DNA molecules that store genetic information in living creatures can be repurposed as building blocks to construct artificial architectures, ranging from the nanoscale to the microscale. The precise fabrication of self-assembled DNA nanomaterials and their various applications have greatly impacted nanoscience and nanotechnology. More specifically, the DNA origami technique has realized the assembly of various nanostructures featuring rationally predesigned geometries, precise addressability, and versatile programmability, as well as remarkable biocompatibility. These features have elevated DNA origami from academic interest to an emerging class of drug delivery platform for a wide range of diseases. In this minireview, the latest advances in the burgeoning field of DNA-origami-based innovative platforms for regulating biological functions and delivering versatile drugs are presented. Challenges regarding the novel drug vehicle's safety, stability, targeting strategy, and future clinical translation are also discussed.
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Affiliation(s)
- Qiao Jiang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yingxu Shang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, P. R. China
| | - Yiming Xie
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, P. R. China
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, P. R. China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, P. R. China
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7
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Ju H, Cheng L, Li M, Mei K, He S, Jia C, Guo X. Single-Molecule Electrical Profiling of Peptides and Proteins. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401877. [PMID: 38639403 DOI: 10.1002/advs.202401877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/03/2024] [Indexed: 04/20/2024]
Abstract
In recent decades, there has been a significant increase in the application of single-molecule electrical analysis platforms in studying proteins and peptides. These advanced analysis methods have the potential for deep investigation of enzymatic working mechanisms and accurate monitoring of dynamic changes in protein configurations, which are often challenging to achieve in ensemble measurements. In this work, the prominent research progress in peptide and protein-related studies are surveyed using electronic devices with single-molecule/single-event sensitivity, including single-molecule junctions, single-molecule field-effect transistors, and nanopores. In particular, the successful commercial application of nanopores in DNA sequencing has made it one of the most promising techniques in protein sequencing at the single-molecule level. From single peptides to protein complexes, the correlation between their electrical characteristics, structures, and biological functions is gradually being established. This enables to distinguish different molecular configurations of these biomacromolecules through real-time electrical monitoring of their life activities, significantly improving the understanding of the mechanisms underlying various life processes.
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Affiliation(s)
- Hongyu Ju
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, P. R. China
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Li Cheng
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Mengmeng Li
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Kunrong Mei
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Suhang He
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Chuancheng Jia
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
| | - Xuefeng Guo
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Microscale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, 300350, P. R. China
- Beijing National Laboratory for Molecular Sciences, National Biomedical Imaging Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
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8
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Li X, Wang Y, Zhang S, Zhang P, Huang S. Nanopore Identification of N-Acetylation by Hydroxylamine Deacetylation (NINAHD). ACS Sens 2024; 9:1359-1371. [PMID: 38449100 DOI: 10.1021/acssensors.3c02350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
N-Acetyl modification, a chemical modification commonly found on biomacromolecules, plays a crucial role in the regulation of cell activities and is related to a variety of diseases. However, due to the instability of N-acetyl modification, accurate and rapid identification of N-acetyl modification with a low measurement cost is still technically challenging. Here, based on hydroxylamine deacetylation and nanopore single molecule chemistry, a universal sensing strategy for N-acetyl modification has been developed. Acetohydroxamic acid (AHA), which is produced by the hydroxylamine deacetylation reaction and serves as a reporter for N-acetylation identification, is specifically sensed by a phenylboronic acid (PBA)-modified Mycobacterium smegmatis porin A (MspA). With this strategy, N-acetyl modifications on RNA, DNA, proteins, and glycans were identified, demonstrating its generality. Specifically, histones can be treated with hydroxylamine deacetylation, from which the generated AHA can represent the amount of N-acetyl modification detected by a nanopore sensor. The unique event features of AHA also demonstrate the robustness of sensing against other interfering analytes in the environment.
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Affiliation(s)
- Xinyue Li
- 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
| | - 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
| | - 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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9
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Ma C, Xu W, Liu W, Xu C, Qin G, Chen D, Sha J. Confined Transport Behavior of Biomolecules within Tilted Nanopores. J Phys Chem B 2024; 128:2792-2798. [PMID: 38471969 DOI: 10.1021/acs.jpcb.3c07417] [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: 03/14/2024]
Abstract
The transport behavior of biomolecules at the confined nanoscale is very different from that of the bulk state. Numerous disease diagnostics and targeted drug treatments are performed based on nanochannels in cells. The specific structure and shape of nanochannels play an important role in the behavior and efficiency of substance transport. In this paper, we fabricated nanopores with different tilt angles and the same diameters using focused ion beam. The capture frequency and the blocking current amplitude of λ-DNA within large-angle nanopores decrease obviously, suggesting an increase in the energy barrier of large-angle nanopores and the fact that they stretch biomolecules to thinness. Most importantly, large-angle nanopores slow down λ-DNA transport by 2-4 times. MD simulations find that the sloped electroosmotic flow inside the tilted nanopores is the main factor contributing to the transport phenomena. The increase in the capture time of biomolecules by nanopores assists in obtaining more biological information from the current trajectories. Our study provides a new understanding of substance transport in specially shaped nanopores, which can be instrumental in providing fresh inspiration and approaches to the biomedical field.
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Affiliation(s)
- Chaofan Ma
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Wei Xu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Wei Liu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Changhui Xu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Guangle Qin
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
- Jiangsu Automation Research Institute, Lianyungang, Jiangsu 222000, China
| | - Dapeng Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
- Jiangsu Automation Research Institute, Lianyungang, Jiangsu 222000, China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
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10
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Fan P, Zhang S, Wang Y, Li T, Zhang H, Zhang P, Huang S. Nanopore analysis of salvianolic acids in herbal medicines. Nat Commun 2024; 15:1970. [PMID: 38443335 PMCID: PMC10915175 DOI: 10.1038/s41467-024-45543-1] [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: 05/10/2023] [Accepted: 01/24/2024] [Indexed: 03/07/2024] Open
Abstract
Natural herbs, which contain pharmacologically active compounds, have been used historically as medicines. Conventionally, the analysis of chemical components in herbal medicines requires time-consuming sample separation and state-of-the-art analytical instruments. Nanopore, a versatile single molecule sensor, might be suitable to identify bioactive compounds in natural herbs. Here, a phenylboronic acid appended Mycobacterium smegmatis porin A (MspA) nanopore is used as a sensor for herbal medicines. A variety of bioactive compounds based on salvianolic acids, including caffeic acid, protocatechuic acid, protocatechualdehyde, salvianic acid A, rosmarinic acid, lithospermic acid, salvianolic acid A and salvianolic acid B are identified. Using a custom machine learning algorithm, analyte identification is performed with an accuracy of 99.0%. This sensing principle is further used with natural herbs such as Salvia miltiorrhiza, Rosemary and Prunella vulgaris. No complex sample separation or purification is required and the sensing device is highly portable.
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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
| | - 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
| | - Tian Li
- 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
| | - Hanhan 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
| | - 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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11
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Dorey A, Howorka S. Nanopore DNA sequencing technologies and their applications towards single-molecule proteomics. Nat Chem 2024; 16:314-334. [PMID: 38448507 DOI: 10.1038/s41557-023-01322-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 07/14/2023] [Indexed: 03/08/2024]
Abstract
Sequencing of nucleic acids with nanopores has emerged as a powerful tool offering rapid readout, high accuracy, low cost and portability. This label-free method for sequencing at the single-molecule level is an achievement on its own. However, nanopores also show promise for the technologically even more challenging sequencing of polypeptides, something that could considerably benefit biological discovery, clinical diagnostics and homeland security, as current techniques lack portability and speed. Here we survey the biochemical innovations underpinning commercial and academic nanopore DNA/RNA sequencing techniques, and explore how these advances can fuel developments in future protein sequencing with nanopores.
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Affiliation(s)
- Adam Dorey
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK.
| | - Stefan Howorka
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK.
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12
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Li M, Muthukumar M. Electro-osmotic flow in nanoconfinement: Solid-state and protein nanopores. J Chem Phys 2024; 160:084905. [PMID: 38411234 DOI: 10.1063/5.0185574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/05/2024] [Indexed: 02/28/2024] Open
Abstract
Electro-osmotic flow (EOF) is a phenomenon where fluid motion occurs in porous materials or micro/nano-channels when an external electric field is applied. In the particular example of single-molecule electrophoresis using single nanopores, the role of EOF on the translocation velocity of the analyte molecule through the nanopore is not fully understood. The complexity arises from a combination of effects from hydrodynamics in restricted environments, electrostatics emanating from charge decorations and geometry of the pores. We address this fundamental issue using the Poisson-Nernst-Planck and Navier-Stokes (PNP-NS) equations for cylindrical solid-state nanopores and three representative protein nanopores (α-hemolysin, MspA, and CsgG). We present the velocity profiles inside the nanopores as a function of charge decoration and geometry of the pore and applied electric field. We report several unexpected results: (a) The apparent charges of the protein nanopores are different from their net charge and the surface charge of the whole protein geometry, and the net charge of inner surface is consistent with the apparent charge. (b) The fluid velocity depends non-monotonically on voltage. The three protein nanopores exhibit unique EOF and velocity-voltage relations, which cannot be simply deduced from their net charge. Furthermore, effective point mutations can significantly change both the direction and the magnitude of EOF. The present computational analysis offers an opportunity to further understand the origins of the speed of transport of charged macromolecules in restricted space and to design desirable nanopores for tuning the speed of macromolecules through nanopores.
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Affiliation(s)
- Minglun Li
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Murugappan Muthukumar
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, USA
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13
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Stuber A, Schlotter T, Hengsteler J, Nakatsuka N. Solid-State Nanopores for Biomolecular Analysis and Detection. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2024; 187:283-316. [PMID: 38273209 DOI: 10.1007/10_2023_240] [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: 01/27/2024]
Abstract
Advances in nanopore technology and data processing have rendered DNA sequencing highly accessible, unlocking a new realm of biotechnological opportunities. Commercially available nanopores for DNA sequencing are of biological origin and have certain disadvantages such as having specific environmental requirements to retain functionality. Solid-state nanopores have received increased attention as modular systems with controllable characteristics that enable deployment in non-physiological milieu. Thus, we focus our review on summarizing recent innovations in the field of solid-state nanopores to envision the future of this technology for biomolecular analysis and detection. We begin by introducing the physical aspects of nanopore measurements ranging from interfacial interactions at pore and electrode surfaces to mass transport of analytes and data analysis of recorded signals. Then, developments in nanopore fabrication and post-processing techniques with the pros and cons of different methodologies are examined. Subsequently, progress to facilitate DNA sequencing using solid-state nanopores is described to assess how this platform is evolving to tackle the more complex challenge of protein sequencing. Beyond sequencing, we highlight the recent developments in biosensing of nucleic acids, proteins, and sugars and conclude with an outlook on the frontiers of nanopore technologies.
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Affiliation(s)
- Annina Stuber
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Tilman Schlotter
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Julian Hengsteler
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland
| | - Nako Nakatsuka
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich, Switzerland.
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14
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Yamazaki H, Peng Z, Kawano R, Shoji K. The potential of nanopore technologies toward empowering biophysical research: Brief history, basic principle and applications. Biophys Physicobiol 2023; 21:e210003. [PMID: 38803335 PMCID: PMC11128298 DOI: 10.2142/biophysico.bppb-v21.0003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 12/22/2023] [Indexed: 05/29/2024] Open
Affiliation(s)
- Hirohito Yamazaki
- Top Runner Incubation Center for Academia-Industry Fusion, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
- Department of Mechanical Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Zugui Peng
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 185-8588, Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 185-8588, Japan
| | - Kan Shoji
- Department of Mechanical Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
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15
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Zheng F, Alawami M, Zhu J, Platnich CM, Sha J, Keyser UF, Chen K. DNA Carrier-Assisted Molecular Ping-Pong in an Asymmetric Nanopore. NANO LETTERS 2023; 23:11145-11151. [PMID: 38033205 PMCID: PMC10722531 DOI: 10.1021/acs.nanolett.3c03605] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/28/2023] [Accepted: 11/28/2023] [Indexed: 12/02/2023]
Abstract
Nanopore analysis relies on ensemble averaging of translocation signals obtained from numerous molecules, requiring a relatively high sample concentration and a long turnaround time from the sample to results. The recapture and subsequent re-reading of the same molecule is a promising alternative that enriches the signal information from a single molecule. Here, we describe how an asymmetric nanopore improves molecular ping-pong by promoting the recapture of the molecule in the trans reservoir. We also demonstrate that the molecular recapture could be improved by linking the target molecule to a long DNA carrier to reduce the diffusion, thereby achieving over 100 recapture events. Using this ping-pong methodology, we demonstrate its use in accurately resolving nanostructure motifs along a DNA scaffold through repeated detection. Our method offers novel insights into the control of DNA polymer dynamics within nanopore confinement and opens avenues for the development of a high-fidelity DNA detection platform.
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Affiliation(s)
- Fei Zheng
- Cavendish Laboratory, University of Cambridge, CB3 0HE Cambridge, United Kingdom
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Mohammed Alawami
- Cavendish Laboratory, University of Cambridge, CB3 0HE Cambridge, United Kingdom
| | - Jinbo Zhu
- Cavendish Laboratory, University of Cambridge, CB3 0HE Cambridge, United Kingdom
- School of Biomedical Engineering, Faculty of Medicine, Dalian University of Technology, Dalian 116024, China
| | - Casey M Platnich
- Cavendish Laboratory, University of Cambridge, CB3 0HE Cambridge, United Kingdom
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, CB3 0HE Cambridge, United Kingdom
| | - Kaikai Chen
- Cavendish Laboratory, University of Cambridge, CB3 0HE Cambridge, United Kingdom
- School of Nanoscience and Nanotechnology, University of Chinese Academy of Sciences, Beijing 101408, China
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16
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Zheng YW, Yu SY, Li Z, Xu YT, Zhao WW, Jiang D, Chen HY, Xu JJ. High-Precision Single-Cell microRNA Therapy by a Functional Nanopipette with Sensitive Photoelectrochemical Feedback. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023:e2307067. [PMID: 37972263 DOI: 10.1002/smll.202307067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/15/2023] [Indexed: 11/19/2023]
Abstract
This work proposes the concept of single-cell microRNA (miR) therapy and proof-of-concept by engineering a nanopipette for high-precision miR-21-targeted therapy in a single HeLa cell with sensitive photoelectrochemical (PEC) feedback. Targeting the representative oncogenic miR-21, the as-functionalized nanopipette permits direct intracellular drug administration with precisely controllable dosages, and the corresponding therapeutic effects can be sensitively transduced by a PEC sensing interface that selectively responds to the indicator level of cytosolic caspase-3. The experimental results reveal that injection of ca. 4.4 × 10-20 mol miR-21 inhibitor, i.e., 26488 copies, can cause the obvious therapeutic action in the targeted cell. This work features a solution to obtain the accurate knowledge of how a certain miR-drug with specific dosages treats the cells and thus provides an insight into futuristic high-precision clinical miR therapy using personalized medicine, provided that the prerequisite single-cell experiments are courses of personalized customization.
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Affiliation(s)
- You-Wei Zheng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Si-Yuan Yu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Zheng Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yi-Tong Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Wei-Wei Zhao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Dechen Jiang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
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17
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Yin YD, Chen FF, Hu J, Yang L, Song XT, Wu GR, Xu M, Gu ZY. Solid-State Nanopore Distinguishes Ferritin and Apo-Ferritin with Identical Exteriors through Amplified Flexibility at Single-Molecule Level. Anal Chem 2023; 95:16496-16504. [PMID: 37916987 DOI: 10.1021/acs.analchem.3c02041] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Protein identification and discrimination at the single-molecule level are big challenges. Solid-state nanopores as a sensitive biosensor have been used for protein analysis, although it is difficult to discriminate proteins with similar structures in the traditional discrimination method based on the current blockage fraction. Here, we select ferritin and apo-ferritin as the model proteins that exhibit identical exterior and different interior structures and verify the practicability of their discrimination with flexibility features by the strategy of gradually decreasing the nanopore size. We show that the larger nanopore (relative to the protein size) has no obvious effect on discriminating two proteins. Then, the comparable-sized nanopore plays a key role in discriminating two proteins based on the dwell time and fraction distribution, and the conformational changes of both proteins are also studied with this nanopore. Finally, in the smaller nanopore, the protein molecules are trapped rather than translocated, where two proteins are obviously discriminated through the current fluctuation caused by the vibration of proteins. This strategy has potential in the discrimination of other important similar proteins.
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Affiliation(s)
- Yun-Dong Yin
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Fang-Fang Chen
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Jun Hu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Lei Yang
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Xi-Tong Song
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Guo-Rong Wu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Ming Xu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Zhi-Yuan Gu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
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18
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Schmid S. An external speed control for nanopore reads. NATURE NANOTECHNOLOGY 2023; 18:1261-1262. [PMID: 37550576 DOI: 10.1038/s41565-023-01477-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Affiliation(s)
- Sonja Schmid
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands.
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19
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Huang Y, Liu L, Luo C, Liu W, Lou X, Jiang L, Xia F. Solid-state nanochannels for bio-marker analysis. Chem Soc Rev 2023; 52:6270-6293. [PMID: 37581902 DOI: 10.1039/d2cs00865c] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
Bio-markers, such as ions, small molecules, nucleic acids, peptides, proteins and cells, participate in the construction of living organisms and play important roles in biological processes. It is of great significance to accurately detect these bio-markers for studying their basic functions, the development of molecular diagnosis and to better understand life processes. Solid-state nanochannel-based sensing systems have been demonstrated for the detection of bio-markers, due to their rapid, label-free and high-throughput screening, with high sensitivity and specificity. Generally, studies on solid-state nanochannels have focused on probes on the inner-wall (PIW), ignoring probes on the outer-surface (POS). As a result, the direct detection of cells is difficult to realize by these inner-wall focused nanochannels. Moreover, the sensitivity for detecting ions, small molecules, nucleic acids, peptides and proteins requires further improvement. Recent research has focused on artificial solid-state nanochannels with POS, which have demonstrated the ability to independently regulate ion transport. This design not only contributes to the in situ detection of large analytes, such as cells, but also provides promising opportunities for ultra-high sensitivity detection with a clear mechanism. In this tutorial review, we present an overview of the detection principle used for solid-state nanochannels, inner-wall focused nanochannels and outer-surface focused nanochannels. Furthermore, we discuss the remaining challenges faced by current nanochannel technologies and provide insights into their prospects.
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Affiliation(s)
- Yu Huang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
- Zhejiang Institute, China University of Geosciences, Hangzhou, 311305, China
| | - Lingxiao Liu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Cihui Luo
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Wei Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210046, China
| | - Xiaoding Lou
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Lei Jiang
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of the Ministry of Education, School of Chemistry and Environment, Beihang University, Beijing 100191, China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
- Zhejiang Institute, China University of Geosciences, Hangzhou, 311305, China
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20
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He L, Charron M, Mensing P, Briggs K, Adams J, de Haan H, Tabard-Cossa V. DNA origami characterized via a solid-state nanopore: insights into nanostructure dimensions, rigidity and yield. NANOSCALE 2023; 15:14043-14054. [PMID: 37580994 DOI: 10.1039/d3nr01873c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
Due to their programmability via specific base pairing, self-assembled DNA origami structures have proven to be useful for a wide variety of applications, including diagnostics, molecular computation, drug delivery, and therapeutics. Measuring and characterizing these structures is therefore of great interest and an important part of quality control. Here, we show the extent to which DNA nanostructures can be characterized by a solid-state nanopore; a non-destructive, label-free, single-molecule sensor capable of electrically detecting and characterizing charged biomolecules. We demonstrate that in addition to geometrical dimensions, nanopore sensing can provide information on the mechanical properties, assembly yield, and stability of DNA nanostructures. For this work, we use a model structure consisting of a 3 helix-bundle (3HB), i.e. three interconnected DNA double helices using a M13 scaffold folded twice on itself by short DNA staple strands, and translocate it through solid-state nanopores fabricated by controlled breakdown. We present detailed analysis of the passage characteristics of 3HB structures through nanopores under different experimental conditions which suggest that segments of locally higher flexibility are present along the nanostructure contour that allow for the otherwise rigid 3HB to fold inside nanopores. By characterizing partially melted 3HB structures, we find that locally flexible segments are likely due to short staple oligomers missing from the fully assembled structure. The 3HB used herein is a prototypical example to establish nanopores as a sensitive, non-destructive, and label-free alternative to conventional techniques such as gel electrophoresis with which to characterize DNA nanostructures.
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Affiliation(s)
- Liqun He
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada.
| | - Martin Charron
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada.
| | - Philipp Mensing
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada.
| | - Kyle Briggs
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada.
| | - Jonathan Adams
- Faculty of Science, Ontario Tech University, Oshawa, Ontario, Canada
| | - Hendrick de Haan
- Faculty of Science, Ontario Tech University, Oshawa, Ontario, Canada
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21
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Svirelis J, Adali Z, Emilsson G, Medin J, Andersson J, Vattikunta R, Hulander M, Järlebark J, Kolman K, Olsson O, Sakiyama Y, Lim RYH, Dahlin A. Stable trapping of multiple proteins at physiological conditions using nanoscale chambers with macromolecular gates. Nat Commun 2023; 14:5131. [PMID: 37612271 PMCID: PMC10447545 DOI: 10.1038/s41467-023-40889-4] [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: 02/07/2023] [Accepted: 08/11/2023] [Indexed: 08/25/2023] Open
Abstract
The possibility to detect and analyze single or few biological molecules is very important for understanding interactions and reaction mechanisms. Ideally, the molecules should be confined to a nanoscale volume so that the observation time by optical methods can be extended. However, it has proven difficult to develop reliable, non-invasive trapping techniques for biomolecules under physiological conditions. Here we present a platform for long-term tether-free (solution phase) trapping of proteins without exposing them to any field gradient forces. We show that a responsive polymer brush can make solid state nanopores switch between a fully open and a fully closed state with respect to proteins, while always allowing the passage of solvent, ions and small molecules. This makes it possible to trap a very high number of proteins (500-1000) inside nanoscale chambers as small as one attoliter, reaching concentrations up to 60 gL-1. Our method is fully compatible with parallelization by imaging arrays of nanochambers. Additionally, we show that enzymatic cascade reactions can be performed with multiple native enzymes under full nanoscale confinement and steady supply of reactants. This platform will greatly extend the possibilities to optically analyze interactions involving multiple proteins, such as the dynamics of oligomerization events.
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Affiliation(s)
- Justas Svirelis
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Zeynep Adali
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Gustav Emilsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Jesper Medin
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - John Andersson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Radhika Vattikunta
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Mats Hulander
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Julia Järlebark
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Krzysztof Kolman
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Oliver Olsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Yusuke Sakiyama
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, 4056, Basel, Switzerland
| | - Roderick Y H Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, 4056, Basel, Switzerland
| | - Andreas Dahlin
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden.
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22
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Xing Y, Rottensteiner A, Ciccone J, Howorka S. Functional Nanopores Enabled with DNA. Angew Chem Int Ed Engl 2023; 62:e202303103. [PMID: 37186432 DOI: 10.1002/anie.202303103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/17/2023]
Abstract
Membrane-spanning nanopores are used in label-free single-molecule sensing and next-generation portable nucleic acid sequencing, and as powerful research tools in biology, biophysics, and synthetic biology. Naturally occurring protein and peptide pores, as well as synthetic inorganic nanopores, are used in these applications, with their limitations. The structural and functional repertoire of nanopores can be considerably expanded by functionalising existing pores with DNA strands and by creating an entirely new class of nanopores with DNA nanotechnology. This review outlines progress in this area of functional DNA nanopores and outlines developments to open up new applications.
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Affiliation(s)
- Yongzheng Xing
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
| | - Alexia Rottensteiner
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
| | - Jonah Ciccone
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
| | - Stefan Howorka
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H 0AJ, UK
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23
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Jiang T, Yi L, Liu X, Ivanov AP, Edel JB, Tang L. Fabrication of electron tunneling probes for measuring single-protein conductance. Nat Protoc 2023; 18:2579-2599. [PMID: 37420088 DOI: 10.1038/s41596-023-00846-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 04/21/2023] [Indexed: 07/09/2023]
Abstract
Studying the electrical properties of individual proteins is a prominent research area in the field of bioelectronics. Electron tunnelling or quantum mechanical tunnelling (QMT) probes can act as powerful tools for investigating the electrical properties of proteins. However, current fabrication methods for these probes often have limited reproducibility, unreliable contact or inadequate binding of proteins onto the electrodes, so better solutions are required. Here, we detail a generalizable and straightforward set of instructions for fabricating simple, nanopipette-based, tunnelling probes, suitable for measuring conductance in single proteins. Our QMT probe is based on a high-aspect-ratio dual-channel nanopipette that integrates a pair of gold tunneling electrodes with a gap of less than 5 nm, fabricated via the pyrolytic deposition of carbon followed by the electrochemical deposition of gold. The gold tunneling electrodes can be functionalized using an extensive library of available surface modifications to achieve single-protein-electrode contact. We use a biotinylated thiol modification, in which a biotin-streptavidin-biotin bridge is used to form the single-protein junction. The resulting protein-coupled QMT probes enable the stable electrical measurement of the same single protein in solution for up to several hours. We also describe the analysis method used to interpret time-dependent single-protein conductance measurements, which can provide essential information for understanding electron transport and exploring protein dynamics. The total time required to complete the protocol is ~33 h and it can be carried out by users trained in less than 24 h.
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Affiliation(s)
- Tao Jiang
- State Key Laboratory of Modern Optical Instrumentation, Institute of Quantum Sensing, Interdisciplinary Centre for Quantum Information, College of Optical Science and Engineering, International Research Center for Advanced Photonics, Zhejiang University, Hangzhou, China
| | - Long Yi
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK
| | - Xu Liu
- State Key Laboratory of Modern Optical Instrumentation, Institute of Quantum Sensing, Interdisciplinary Centre for Quantum Information, College of Optical Science and Engineering, International Research Center for Advanced Photonics, Zhejiang University, Hangzhou, China
| | - Aleksandar P Ivanov
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK
| | - Joshua B Edel
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, London, UK
| | - Longhua Tang
- State Key Laboratory of Modern Optical Instrumentation, Institute of Quantum Sensing, Interdisciplinary Centre for Quantum Information, College of Optical Science and Engineering, International Research Center for Advanced Photonics, Zhejiang University, Hangzhou, China.
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24
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Straathof S, Di Muccio G, Yelleswarapu M, Alzate Banguero M, Wloka C, van der Heide NJ, Chinappi M, Maglia G. Protein Sizing with 15 nm Conical Biological Nanopore YaxAB. ACS NANO 2023; 17:13685-13699. [PMID: 37458334 PMCID: PMC10373527 DOI: 10.1021/acsnano.3c02847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Nanopores are promising single-molecule tools for the electrical identification and sequencing of biomolecules. However, the characterization of proteins, especially in real-time and in complex biological samples, is complicated by the sheer variety of sizes and shapes in the proteome. Here, we introduce a large biological nanopore, YaxAB for folded protein analysis. The 15 nm cis-opening and a 3.5 nm trans-constriction describe a conical shape that allows the characterization of a wide range of proteins. Molecular dynamics showed proteins are captured by the electroosmotic flow, and the overall resistance is largely dominated by the narrow trans constriction region of the nanopore. Conveniently, proteins in the 35-125 kDa range remain trapped within the conical lumen of the nanopore for a time that can be tuned by the external bias. Contrary to cylindrical nanopores, in YaxAB, the current blockade decreases with the size of the trapped protein, as smaller proteins penetrate deeper into the constriction region than larger proteins do. These characteristics are especially useful for characterizing large proteins, as shown for pentameric C-reactive protein (125 kDa), a widely used health indicator, which showed a signal that could be identified in the background of other serum proteins.
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Affiliation(s)
- Sabine Straathof
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Giovanni Di Muccio
- Department of Industrial Engineering, University of Rome Tor Vergata, Via del Politecnico 1, 00133 Rome, Italy
| | - Maaruthy Yelleswarapu
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Melissa Alzate Banguero
- Department of Industrial Engineering, University of Rome Tor Vergata, Via del Politecnico 1, 00133 Rome, Italy
| | - Carsten Wloka
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
- Experimental Ophthalmology, Department of Ophthalmology, Charité - Universitätsmedizin Berlin, A Corporate Member of Freie Universität, Humboldt-University, The Berlin Institute of Health, Berlin 10178, Germany
| | - Nieck Jordy van der Heide
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Mauro Chinappi
- Department of Industrial Engineering, University of Rome Tor Vergata, Via del Politecnico 1, 00133 Rome, Italy
| | - Giovanni Maglia
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
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25
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Soni N, Chandra Verma N, Talor N, Meller A. Over 30-Fold Enhancement in DNA Translocation Dynamics through Nanoscale Pores Coated with an Anionic Surfactant. NANO LETTERS 2023; 23:4609-4616. [PMID: 37149783 DOI: 10.1021/acs.nanolett.3c01096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Solid-state nanopores (ssNPs) are single-molecule sensors capable of label-free quantification of different biomolecules, which have become highly versatile with the introduction of different surface treatments. By modulating the surface charges of the ssNP, the electro-osmotic flow (EOF) can be controlled in turn affecting the in-pore hydrodynamic forces. Herein, we demonstrate that negative charge surfactant coating to ssNPs generates EOF that slows-down DNA translocation speed by >30-fold, without deterioration of the NP noise, hence significantly improving its performances. Consequently, surfactant-coated ssNPs can be used to reliably sense short DNA fragments at high voltage bias. To shed light on the EOF phenomena inside planar ssNPs, we introduce visualization of the electrically neutral fluorescent molecule's flow, hence decoupling the electrophoretic from EOF forces. Finite elements simulations are then used to show that EOF is likely responsible for in-pore drag and size-selective capture rate. This study broadens ssNPs use for multianalyte sensing in a single device.
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Affiliation(s)
- Neeraj Soni
- Russell Berrie Nanotechnology Institute, Technion IIT, Haifa 3200003, Israel
- Department of Biomedical Engineering, Technion IIT, Haifa 3200003, Israel
| | | | - Noam Talor
- Department of Biomedical Engineering, Technion IIT, Haifa 3200003, Israel
| | - Amit Meller
- Russell Berrie Nanotechnology Institute, Technion IIT, Haifa 3200003, Israel
- Department of Biomedical Engineering, Technion IIT, Haifa 3200003, Israel
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26
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Chen X, Zhou S, Wang Y, Zheng L, Guan S, Wang D, Wang L, Guan X. Nanopore Single-molecule Analysis of Biomarkers: Providing Possible Clues to Disease Diagnosis. Trends Analyt Chem 2023; 162:117060. [PMID: 38106545 PMCID: PMC10722900 DOI: 10.1016/j.trac.2023.117060] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Biomarker detection has attracted increasing interest in recent years due to the minimally or non-invasive sampling process. Single entity analysis of biomarkers is expected to provide real-time and accurate biological information for early disease diagnosis and prognosis, which is critical to the effective disease treatment and is also important in personalized medicine. As an innovative single entity analysis method, nanopore sensing is a pioneering single-molecule detection technique that is widely used in analytical bioanalytical fields. In this review, we overview the recent progress of nanopore biomarker detection as new approaches to disease diagnosis. In highlighted studies, nanopore was focusing on detecting biomarkers of different categories of communicable and noncommunicable diseases, such as pandemic Covid-19, AIDS, cancers, neurologic diseases, etc. Various sensitive and selective nanopore detecting strategies for different types of biomarkers are summarized. In addition, the challenges, opportunities, and direction for future development of nanopore-based biomarker sensors are also discussed.
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Affiliation(s)
- Xiaohan Chen
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing School, University of Chinese Academy of Science, Chongqing, 400714, China
| | - Shuo Zhou
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing School, University of Chinese Academy of Science, Chongqing, 400714, China
| | - Yunjiao Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing School, University of Chinese Academy of Science, Chongqing, 400714, China
| | - Ling Zheng
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing School, University of Chinese Academy of Science, Chongqing, 400714, China
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Sarah Guan
- Hinsdale Central High School, Hinsdale, IL 60521, USA
| | - Deqiang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing School, University of Chinese Academy of Science, Chongqing, 400714, China
| | - Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing School, University of Chinese Academy of Science, Chongqing, 400714, China
- Chongqing Key Laboratory of Intelligent Medicine Engineering for Hepatopancreatobiliary Diseases, University of Chinese Academy of Sciences, Chongqing 401147, China
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, 60616, USA
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27
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Edkins AL, Zweckstetter M, Sawarkar R. Tenth International Symposium on the Hsp90 chaperone machine : Switzerland, October 19-23, 2022. Cell Stress Chaperones 2023; 28:231-237. [PMID: 37071341 PMCID: PMC10111302 DOI: 10.1007/s12192-023-01342-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] [Accepted: 03/21/2023] [Indexed: 04/19/2023] Open
Abstract
Hsp90 is a molecular chaperone responsible for regulating proteostasis under physiological and pathological conditions. Its central role in a range of diseases and potential as a drug target has focused efforts to understand its mechanisms and biological functions and to identify modulators that may form the basis for therapies. The 10th international conference on the Hsp90 chaperone machine was held in Switzerland in October 2022. The meeting was organized by Didier Picard (Geneva, Switzerland) and Johannes Buchner (Garching, Germany) with an advisory committee of Olivier Genest, Mehdi Mollapour, Ritwick Sawarkar, and Patricija van Oosten-Hawle. This was a much anticipated first in-person meeting of the Hsp90 community since 2018 after the COVID-19 pandemic led to the postponement of the 2020 meeting. The conference remained true to the tradition of sharing novel data ahead of publication, providing unparalleled depth of insight for both experts and newcomers to the field.
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Affiliation(s)
- Adrienne L. Edkins
- Biomedical Biotechnology Research Unit (BioBRU), Department of Microbiology and Biochemistry, Rhodes University, Makhanda, South Africa
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
- Department for NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Ritwick Sawarkar
- Medical Research Council (MRC) and Department of Genetics, University of Cambridge, Cambridge, UK
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28
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Yousefi A, Ying C, Parmenter CD, Assadipapari M, Sanderson G, Zheng Z, Xu L, Zargarbashi S, Hickman GJ, Cousins RB, Mellor CJ, Mayer M, Rahmani M. Optical Monitoring of In Situ Iron Loading into Single, Native Ferritin Proteins. NANO LETTERS 2023; 23:3251-3258. [PMID: 37053043 PMCID: PMC10141409 DOI: 10.1021/acs.nanolett.3c00042] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Ferritin is a protein that stores and releases iron to prevent diseases associated with iron dysregulation in plants, animals, and bacteria. The conversion between iron-loaded holo-ferritin and empty apo-ferritin is an important process for iron regulation. To date, studies of ferritin have used either ensemble measurements to quantify the characteristics of a large number of proteins or single-molecule approaches to interrogate labeled or modified proteins. Here we demonstrate the first real-time study of the dynamics of iron ion loading and biomineralization within a single, unlabeled ferritin protein. Using optical nanotweezers, we trapped single apo- and holo-ferritins indefinitely, distinguished one from the other, and monitored their structural dynamics in real time. The study presented here deepens the understanding of the iron uptake mechanism of ferritin proteins, which may lead to new therapeutics for iron-related diseases.
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Affiliation(s)
- Arman Yousefi
- Advanced
Optics and Photonics Laboratory, Department of Engineering, School
of Science and Technology, Nottingham Trent
University, Nottingham NG118 NS, United
Kingdom
| | - Cuifeng Ying
- Advanced
Optics and Photonics Laboratory, Department of Engineering, School
of Science and Technology, Nottingham Trent
University, Nottingham NG118 NS, United
Kingdom
- Email
for C.Y.:
| | | | - Mahya Assadipapari
- Advanced
Optics and Photonics Laboratory, Department of Engineering, School
of Science and Technology, Nottingham Trent
University, Nottingham NG118 NS, United
Kingdom
| | - Gabriel Sanderson
- Advanced
Optics and Photonics Laboratory, Department of Engineering, School
of Science and Technology, Nottingham Trent
University, Nottingham NG118 NS, United
Kingdom
| | - Ze Zheng
- Advanced
Optics and Photonics Laboratory, Department of Engineering, School
of Science and Technology, Nottingham Trent
University, Nottingham NG118 NS, United
Kingdom
| | - Lei Xu
- Advanced
Optics and Photonics Laboratory, Department of Engineering, School
of Science and Technology, Nottingham Trent
University, Nottingham NG118 NS, United
Kingdom
| | - Saaman Zargarbashi
- Advanced
Optics and Photonics Laboratory, Department of Engineering, School
of Science and Technology, Nottingham Trent
University, Nottingham NG118 NS, United
Kingdom
| | - Graham J. Hickman
- School
of Science and Technology, Nottingham Trent
University, Nottingham NG11 8NS, United
Kingdom
| | - Richard B. Cousins
- Nanoscale
and Microscale Research Centre, University
of Nottingham, Nottingham NG7 2RD, United
Kingdom
| | - Christopher J. Mellor
- School
of Physics and Astronomy, University of
Nottingham, Nottingham NG7 2RD, United
Kingdom
| | - Michael Mayer
- Adolphe
Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700 Fribourg, Switzerland
| | - Mohsen Rahmani
- Advanced
Optics and Photonics Laboratory, Department of Engineering, School
of Science and Technology, Nottingham Trent
University, Nottingham NG118 NS, United
Kingdom
- Email for M.R.:
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29
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Zhan P, Peil A, Jiang Q, Wang D, Mousavi S, Xiong Q, Shen Q, Shang Y, Ding B, Lin C, Ke Y, Liu N. Recent Advances in DNA Origami-Engineered Nanomaterials and Applications. Chem Rev 2023; 123:3976-4050. [PMID: 36990451 PMCID: PMC10103138 DOI: 10.1021/acs.chemrev.3c00028] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Indexed: 03/31/2023]
Abstract
DNA nanotechnology is a unique field, where physics, chemistry, biology, mathematics, engineering, and materials science can elegantly converge. Since the original proposal of Nadrian Seeman, significant advances have been achieved in the past four decades. During this glory time, the DNA origami technique developed by Paul Rothemund further pushed the field forward with a vigorous momentum, fostering a plethora of concepts, models, methodologies, and applications that were not thought of before. This review focuses on the recent progress in DNA origami-engineered nanomaterials in the past five years, outlining the exciting achievements as well as the unexplored research avenues. We believe that the spirit and assets that Seeman left for scientists will continue to bring interdisciplinary innovations and useful applications to this field in the next decade.
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Affiliation(s)
- Pengfei Zhan
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Andreas Peil
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Qiao Jiang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Dongfang Wang
- School
of Biomedical Engineering and Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou 215123, China
| | - Shikufa Mousavi
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Qiancheng Xiong
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
| | - Qi Shen
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Molecular Biophysics and Biochemistry, Yale University, 266
Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Yingxu Shang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Baoquan Ding
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Chenxiang Lin
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Biomedical Engineering, Yale University, 17 Hillhouse Avenue, New Haven, Connecticut 06511, United States
| | - Yonggang Ke
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Na Liu
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Max Planck
Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, Germany
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30
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Babaei E, Wright D, Gordon R. Fringe Dielectrophoresis Nanoaperture Optical Trapping with Order of Magnitude Speed-Up for Unmodified Proteins. NANO LETTERS 2023; 23:2877-2882. [PMID: 36999922 DOI: 10.1021/acs.nanolett.3c00208] [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: 06/19/2023]
Abstract
Single molecule analysis of proteins in an aqueous environment without modification (e.g., labels or tethers) elucidates their biophysics and interactions relevant to drug discovery. By combining fringe-field dielectrophoresis with nanoaperture optical tweezers we demonstrate an order of magnitude faster time-to-trap for proteins when the counter electrode is outside of the solution. When the counter electrode is inside the solution (the more common configuration found in the literature), electrophoresis speeds up the trapping of polystyrene nanospheres, but this was not effective for proteins in general. Since time-to-trap is critical for high-thoughput analysis, these findings are a major advancement to the nanoaperture optical trapping technique for protein analysis.
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Affiliation(s)
- Elham Babaei
- Department of Electrical and Computer Engineering, University of Victoria, 3800 Finnerty Road, Victoria, BC, Canada V8P5C2
| | - Demelza Wright
- Department of Electrical and Computer Engineering, University of Victoria, 3800 Finnerty Road, Victoria, BC, Canada V8P5C2
| | - Reuven Gordon
- Department of Electrical and Computer Engineering, University of Victoria, 3800 Finnerty Road, Victoria, BC, Canada V8P5C2
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31
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Jeong KB, Ryu M, Kim JS, Kim M, Yoo J, Chung M, Oh S, Jo G, Lee SG, Kim HM, Lee MK, Chi SW. Single-molecule fingerprinting of protein-drug interaction using a funneled biological nanopore. Nat Commun 2023; 14:1461. [PMID: 37015934 PMCID: PMC10073129 DOI: 10.1038/s41467-023-37098-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/01/2023] [Indexed: 04/06/2023] Open
Abstract
In drug discovery, efficient screening of protein-drug interactions (PDIs) is hampered by the limitations of current biophysical approaches. Here, we develop a biological nanopore sensor for single-molecule detection of proteins and PDIs using the pore-forming toxin YaxAB. Using this YaxAB nanopore, we demonstrate label-free, single-molecule detection of interactions between the anticancer Bcl-xL protein and small-molecule drugs as well as the Bak-BH3 peptide. The long funnel-shaped structure and nanofluidic characteristics of the YaxAB nanopore enable the electro-osmotic trapping of diverse folded proteins and high-resolution monitoring of PDIs. Distinctive nanopore event distributions observed in the two-dimensional (ΔI/Io-versus-IN) plot illustrate the ability of the YaxAB nanopore to discriminate individual small-molecule drugs bound to Bcl-xL from non-binders. Taken together, our results present the YaxAB nanopore as a robust platform for label-free, ultrasensitive, single-molecule detection of PDIs, opening up a possibility for low-cost, highly efficient drug discovery against diverse drug targets.
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Affiliation(s)
- Ki-Baek Jeong
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Critical Diseases Diagnostics Convergence Research Center, KRIBB, Daejeon, 34141, Republic of Korea
| | - Minju Ryu
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Jin-Sik Kim
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Critical Diseases Diagnostics Convergence Research Center, KRIBB, Daejeon, 34141, Republic of Korea
| | - Minsoo Kim
- Department of Physics, Sungkyunkwan University, Suwon, Gyeonggi, 16419, Republic of Korea
| | - Jejoong Yoo
- Department of Physics, Sungkyunkwan University, Suwon, Gyeonggi, 16419, Republic of Korea
| | - Minji Chung
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Sohee Oh
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Gyunghee Jo
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea
| | - Seong-Gyu Lee
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea
| | - Ho Min Kim
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Mi-Kyung Lee
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Critical Diseases Diagnostics Convergence Research Center, KRIBB, Daejeon, 34141, Republic of Korea.
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon, 34113, Republic of Korea.
| | - Seung-Wook Chi
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon, 34113, Republic of Korea.
- School of Pharmacy, Sungkyunkwan University, Suwon, Gyeonggi, 16419, Republic of Korea.
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32
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Li J, Huang B, Wang Y, Li A, Wang Y, Pan Y, Chai J, Liu Z, Zhai Y. Light-Driven Conversion of Silicon Nitride Nanopore to Nanonet for Single-Protein Trapping Analysis. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2210342. [PMID: 36823450 DOI: 10.1002/adma.202210342] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/12/2023] [Indexed: 06/18/2023]
Abstract
The single-molecule technique for investigation of an unlabeled protein in solution is very attractive but with great challenges. Nanopore sensing as a label-free tool can be used for collecting the structural information of individual proteins, but currently offers only limited capabilities due to the fast translocation of the target. Here, a reliable and facile method is developed to convert the silicon nitride nanopore to a stable nanonet platform for single-entity sensing by electrophoretic or electroosmotic trapping. A nanonet is fabricated based on a material reorganization process caused by electron-beam and light-irradiation treatment. Using protein molecules as a model, it is revealed that the solid-state nanonet can produce collision and trapping flipping signals of the protein, which provides more structural information than traditional nanopore sensing. More importantly, thanks to the excellent stability of the solid-state silicon nitride nanonet, it is demonstrated that the ultraviolet-light-irradiation-induced structural-change process of an individual protein can be captured. The developed nanonet supplies a robust platform for single-entity studies but is not limited to proteins.
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Affiliation(s)
- Jing Li
- The Institute for Advanced Studies (IAS), Wuhan University, Wuhan, 430072, P. R. China
| | - Bintong Huang
- The Institute for Advanced Studies (IAS), Wuhan University, Wuhan, 430072, P. R. China
| | - Yuanhao Wang
- The Institute for Advanced Studies (IAS), Wuhan University, Wuhan, 430072, P. R. China
| | - Aijia Li
- The Institute for Advanced Studies (IAS), Wuhan University, Wuhan, 430072, P. R. China
| | - Yong Wang
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, 314400, P. R. China
- College of Life Sciences, Shanghai Institute for Advanced Study, Institute of Quantitative Biology, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Yangyang Pan
- Department of Engineering Mechanics, School of Civil Engineering, Wuhan University, Wuhan, Hubei, 430072, P. R. China
| | - Jia Chai
- The Institute for Advanced Studies (IAS), Wuhan University, Wuhan, 430072, P. R. China
| | - Ze Liu
- Department of Engineering Mechanics, School of Civil Engineering, Wuhan University, Wuhan, Hubei, 430072, P. R. China
| | - Yueming Zhai
- The Institute for Advanced Studies (IAS), Wuhan University, Wuhan, 430072, P. R. China
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33
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Wang X, Thomas TM, Ren R, Zhou Y, Zhang P, Li J, Cai S, Liu K, Ivanov AP, Herrmann A, Edel JB. Nanopore Detection Using Supercharged Polypeptide Molecular Carriers. J Am Chem Soc 2023; 145:6371-6382. [PMID: 36897933 PMCID: PMC10037339 DOI: 10.1021/jacs.2c13465] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
The analysis at the single-molecule level of proteins and their interactions can provide critical information for understanding biological processes and diseases, particularly for proteins present in biological samples with low copy numbers. Nanopore sensing is an analytical technique that allows label-free detection of single proteins in solution and is ideally suited to applications, such as studying protein-protein interactions, biomarker screening, drug discovery, and even protein sequencing. However, given the current spatiotemporal limitations in protein nanopore sensing, challenges remain in controlling protein translocation through a nanopore and relating protein structures and functions with nanopore readouts. Here, we demonstrate that supercharged unstructured polypeptides (SUPs) can be genetically fused with proteins of interest and used as molecular carriers to facilitate nanopore detection of proteins. We show that cationic SUPs can substantially slow down the translocation of target proteins due to their electrostatic interactions with the nanopore surface. This approach enables the differentiation of individual proteins with different sizes and shapes via characteristic subpeaks in the nanopore current, thus facilitating a viable route to use polypeptide molecular carriers to control molecular transport and as a potential system to study protein-protein interactions at the single-molecule level.
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Affiliation(s)
- Xiaoyi Wang
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London W12 0BZ, U.K
| | - Tina-Marie Thomas
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056 Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Ren Ren
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London W12 0BZ, U.K
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0NN, U.K
| | - Yu Zhou
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056 Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Peng Zhang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Jingjing Li
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Shenglin Cai
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London W12 0BZ, U.K
| | - Kai Liu
- Engineering Research Center of Advanced Rare Earth Materials, (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Aleksandar P Ivanov
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London W12 0BZ, U.K
| | - Andreas Herrmann
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056 Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Joshua B Edel
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, London W12 0BZ, U.K
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34
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Wen C, Bertosin E, Shi X, Dekker C, Schmid S. Orientation-Locked DNA Origami for Stable Trapping of Small Proteins in the Nanopore Electro-Osmotic Trap. NANO LETTERS 2023; 23:788-794. [PMID: 36507712 PMCID: PMC9912335 DOI: 10.1021/acs.nanolett.2c03569] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/05/2022] [Indexed: 06/18/2023]
Abstract
Nanopores are versatile single-molecule sensors offering a simple label-free readout with great sensitivity. We recently introduced the nanopore electro-osmotic trap (NEOtrap) which can trap and sense single unmodified proteins for long times. The trapping is achieved by the electro-osmotic flow (EOF) generated from a DNA-origami sphere docked onto the pore, but thermal fluctuations of the origami limited the trapping of small proteins. Here, we use site-specific cholesterol functionalization of the origami sphere to firmly link it to the lipid-coated nanopore. We can lock the origami in either a vertical or horizontal orientation which strongly modulates the EOF. The optimized EOF greatly enhances the trapping capacity, yielding reduced noise, reduced measurement heterogeneity, an increased capture rate, and 100-fold extended observation times. We demonstrate the trapping of a variety of single proteins, including small ones down to 14 kDa. The cholesterol functionalization significantly expands the application range of the NEOtrap technology.
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Affiliation(s)
- Chenyu Wen
- NanoDynamicsLab,
Laboratory of Biophysics, Wageningen University, Stippeneng 4, Wageningen, 6708 WE, The Netherlands
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, Delft, 2629 HZ, The Netherlands
| | - Eva Bertosin
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, Delft, 2629 HZ, The Netherlands
| | - Xin Shi
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, Delft, 2629 HZ, The Netherlands
| | - Cees Dekker
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, Delft, 2629 HZ, The Netherlands
| | - Sonja Schmid
- NanoDynamicsLab,
Laboratory of Biophysics, Wageningen University, Stippeneng 4, Wageningen, 6708 WE, The Netherlands
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35
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Feng N, Peng X, Wang Z, Yu X, Shentu X, Chen Y. Label-Free Microchannel Immunosensor Based on Antibody–Antigen Biorecognition-Induced Charge Quenching. Anal Chem 2022; 94:16778-16786. [DOI: 10.1021/acs.analchem.2c03675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Niu Feng
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan430070, Hubei, China
| | - Xuewen Peng
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan430070, Hubei, China
| | - Zhipan Wang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan430070, Hubei, China
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Science, China Jiliang University, Hangzhou310000, Zhejiang, China
| | - Xuping Shentu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Science, China Jiliang University, Hangzhou310000, Zhejiang, China
| | - Yiping Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan430070, Hubei, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Pengfei Road, Dapeng District, Shenzhen518120, Guangdong, China
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36
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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: 106] [Impact Index Per Article: 53.0] [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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37
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Ghimire ML, Cox BD, Winn CA, Rockett TW, Schifano NP, Slagle HM, Gonzalez F, Bertino MF, Caputo GA, Reiner JE. Selective Detection and Characterization of Small Cysteine-Containing Peptides with Cluster-Modified Nanopore Sensing. ACS NANO 2022; 16:17229-17241. [PMID: 36214366 DOI: 10.1021/acsnano.2c07842] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
It was recently demonstrated that one can monitor ligand-induced structure fluctuations of individual thiolate-capped gold nanoclusters using resistive-pulse nanopore sensing. The magnitude of the fluctuations scales with the size of the capping ligand, and it was later shown one can observe ligand exchange in this nanopore setup. We expand on these results by exploring the different types of current fluctuations associated with peptide ligands attaching to tiopronin-capped gold nanoclusters. We show here that the fluctuations can be used to identify the attaching peptide through either the magnitude of the peptide-induced current jumps or the onset of high-frequency current fluctuations. Importantly, the peptide attachment process requires that the peptide contains a cysteine residue. This suggests that nanopore-based monitoring of peptide attachments with thiolate-capped clusters could provide a means for selective detection of cysteine-containing peptides. Finally, we demonstrate the cluster-based protocol with various peptide mixtures to show that one can identify more than one cysteine-containing peptide in a mixture.
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Affiliation(s)
- Madhav L Ghimire
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Bobby D Cox
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Cole A Winn
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Thomas W Rockett
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Nicholas P Schifano
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Hannah M Slagle
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Frank Gonzalez
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Massimo F Bertino
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Gregory A Caputo
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Joseph E Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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38
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Dematties D, Wen C, Zhang SL. A Generalized Transformer-Based Pulse Detection Algorithm. ACS Sens 2022; 7:2710-2720. [PMID: 36039873 PMCID: PMC9513795 DOI: 10.1021/acssensors.2c01218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Pulse-like signals are ubiquitous in the field of single molecule analysis, e.g., electrical or optical pulses caused by analyte translocations in nanopores. The primary challenge in processing pulse-like signals is to capture the pulses in noisy backgrounds, but current methods are subjectively based on a user-defined threshold for pulse recognition. Here, we propose a generalized machine-learning based method, named pulse detection transformer (PETR), for pulse detection. PETR determines the start and end time points of individual pulses, thereby singling out pulse segments in a time-sequential trace. It is objective without needing to specify any threshold. It provides a generalized interface for downstream algorithms for specific application scenarios. PETR is validated using both simulated and experimental nanopore translocation data. It returns a competitive performance in detecting pulses through assessing them with several standard metrics. Finally, the generalization nature of the PETR output is demonstrated using two representative algorithms for feature extraction.
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Affiliation(s)
- Dario Dematties
- Northwestern
Argonne Institute of Science and Engineering, Northwestern University, 2205 Tech Drive Suite 1-160, Evanston, 60208 Illinois, United States,Mathematics
and Computer Science Division, Argonne National
Laboratory, 9700 S. Cass
Avenue, Lemont, 60439 Illinois, United States
| | - Chenyu Wen
- NanoDynamicsLab,
Laboratory of Biophysics, Wageningen University, Stippeneng 4, Wageningen 6708 WE, The
Netherlands,Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands
| | - Shi-Li Zhang
- Department
of Electrical Engineering, Uppsala University, Lägerhyddsvägen 1,
752 37, SE-751 03 Uppsala, Sweden,
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39
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Yang L, Hu J, Li MC, Xu M, Gu ZY. Solid-state nanopore: chemical modifications, interactions, and functionalities. Chem Asian J 2022; 17:e202200775. [PMID: 36071031 DOI: 10.1002/asia.202200775] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/06/2022] [Indexed: 11/08/2022]
Abstract
Nanopore technology is a burgeoning detection technology for single-molecular sensing and ion rectification. Solid-state nanopores have attracted more and more attention because of their higher stability and tunability than biological nanopores. However, solid-state nanopores still suffer the drawbacks of low signal-to-noise ratio and low resolution, which hinders their practical applications. Thus, developing operatical and useful methods to overcome the shortages of solid-state nanopores is urgently needed. Here, we summarize the recent research on nanopore modification to achieve this goal. Modifying solid-state nanopores with different coating molecules can improve the selectivity, sensitivity, and stability of nanopores. The modified molecules can introduce different functions into the nanopores, greatly expanding the applications of this novel detection technology. We hope that this review of nanopore modification will provide new ideas for this field.
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Affiliation(s)
- Lei Yang
- Nanjing Normal University, College of Chemistry and Materials Science, CHINA
| | - Jun Hu
- Nanjing Normal University, College of Chemistry and Materials Science, CHINA
| | - Min-Chao Li
- Nanjing Normal University, College of Chemistry and Materials Science, CHINA
| | - Ming Xu
- Nanjing Normal University, College of Chemistry and Materials Science, CHINA
| | - Zhi-Yuan Gu
- Nanjing Normal University, College of Chemistry and Materials Science, 1 Wenyuan Rd, 210023, Nanjing, CHINA
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40
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Jeong KB, Kim JS, Dhanasekar NN, Lee MK, Chi SW. Application of nanopore sensors for biomolecular interactions and drug discovery. Chem Asian J 2022; 17:e202200679. [PMID: 35929410 DOI: 10.1002/asia.202200679] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/04/2022] [Indexed: 11/07/2022]
Abstract
Biomolecular interactions, including protein-protein, protein-nucleic acid, and protein/nucleic acid-ligand interactions, play crucial roles in various cellular signaling and biological processes, and offer attractive therapeutic targets in numerous human diseases. Currently, drug discovery is limited by the low efficiency and high cost of conventional ensemble-averaging-based techniques for biomolecular interaction analysis and high-throughput drug screening. Nanopores are an emerging technology for single-molecule sensing of biomolecules. Owing to the robust advantages of single-molecule sensing, nanopore sensors have contributed tremendously to nucleic acid sequencing and disease diagnostics. In this minireview, we summarize the recent developments and outlooks in single-molecule sensing of various biomolecular interactions for drug discovery applications using biological and solid-state nanopore sensors.
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Affiliation(s)
- Ki-Baek Jeong
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, 34141, Daejeon, Republic of Korea
- Critical Diseases Diagnostics Convergence Research Center, KRIBB, 34141, Daejeon, Republic of Korea
| | - Jin-Sik Kim
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, 34141, Daejeon, Republic of Korea
- Critical Diseases Diagnostics Convergence Research Center, KRIBB, 34141, Daejeon, Republic of Korea
| | - Naresh Niranjan Dhanasekar
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, 34141, Daejeon, Republic of Korea
| | - Mi-Kyung Lee
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, 34141, Daejeon, Republic of Korea
- Critical Diseases Diagnostics Convergence Research Center, KRIBB, 34141, Daejeon, Republic of Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, 34113, Daejeon, Republic of Korea
| | - Seung-Wook Chi
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, 34141, Daejeon, Republic of Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, 34113, Daejeon, Republic of Korea
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41
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Soni N, Freundlich N, Ohayon S, Huttner D, Meller A. Single-File Translocation Dynamics of SDS-Denatured, Whole Proteins through Sub-5 nm Solid-State Nanopores. ACS NANO 2022; 16:11405-11414. [PMID: 35785960 PMCID: PMC7613183 DOI: 10.1021/acsnano.2c05391] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The ability to routinely identify and quantify the complete proteome from single cells will greatly advance medicine and basic biology research. To meet this challenge of single-cell proteomics, single-molecule technologies are being developed and improved. Most approaches, to date, rely on the analysis of polypeptides, resulting from digested proteins, either in solution or immobilized on a surface. Nanopore biosensing is an emerging single-molecule technique that circumvents surface immobilization and is optimally suited for the analysis of long biopolymers, as has already been shown for DNA sequencing. However, proteins, unlike DNA molecules, are not uniformly charged and harbor complex tertiary structures. Consequently, the ability of nanopores to analyze unfolded full-length proteins has remained elusive. Here, we evaluate the use of heat denaturation and the anionic surfactant sodium dodecyl sulfate (SDS) to facilitate electrokinetic nanopore sensing of unfolded proteins. Specifically, we characterize the voltage dependence translocation dynamics of a wide molecular weight range of proteins (from 14 to 130 kDa) through sub-5 nm solid-state nanopores, using a SDS concentration below the critical micelle concentration. Our results suggest that proteins' translocation dynamics are significantly slower than expected, presumably due to the smaller nanopore diameters used in our study and the role of the electroosmotic force opposing the translocation direction. This allows us to distinguish among the proteins of different molecular weights based on their dwell time and electrical charge deficit. Given the simplicity of the protein denaturation assay and circumvention of the tailor-made necessities for sensing protein of different folded sizes, shapes, and charges, this approach can facilitate the development of a whole proteome identification technique.
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Affiliation(s)
- Neeraj Soni
- Department
of Biomedical Engineering, Technion−IIT, Haifa, 3200003 Israel
- Russell
Berrie Nanotechnology Institute Technion−IIT, Haifa, 3200003 Israel
| | - Noam Freundlich
- Department
of Biomedical Engineering, Technion−IIT, Haifa, 3200003 Israel
| | - Shilo Ohayon
- Department
of Biomedical Engineering, Technion−IIT, Haifa, 3200003 Israel
| | - Diana Huttner
- Department
of Biomedical Engineering, Technion−IIT, Haifa, 3200003 Israel
| | - Amit Meller
- Department
of Biomedical Engineering, Technion−IIT, Haifa, 3200003 Israel
- Russell
Berrie Nanotechnology Institute Technion−IIT, Haifa, 3200003 Israel
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42
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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: 24] [Impact Index Per Article: 12.0] [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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43
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Ying C, Ma T, Xu L, Rahmani M. Localized Nanopore Fabrication via Controlled Breakdown. NANOMATERIALS 2022; 12:nano12142384. [PMID: 35889608 PMCID: PMC9323289 DOI: 10.3390/nano12142384] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/01/2022] [Accepted: 07/07/2022] [Indexed: 12/03/2022]
Abstract
Nanopore sensors provide a unique platform to detect individual nucleic acids, proteins, and other biomolecules without the need for fluorescent labeling or chemical modifications. Solid-state nanopores offer the potential to integrate nanopore sensing with other technologies such as field-effect transistors (FETs), optics, plasmonics, and microfluidics, thereby attracting attention to the development of commercial instruments for diagnostics and healthcare applications. Stable nanopores with ideal dimensions are particularly critical for nanopore sensors to be integrated into other sensing devices and provide a high signal-to-noise ratio. Nanopore fabrication, although having benefited largely from the development of sophisticated nanofabrication techniques, remains a challenge in terms of cost, time consumption and accessibility. One of the latest developed methods—controlled breakdown (CBD)—has made the nanopore technique broadly accessible, boosting the use of nanopore sensing in both fundamental research and biomedical applications. Many works have been developed to improve the efficiency and robustness of pore formation by CBD. However, nanopores formed by traditional CBD are randomly positioned in the membrane. To expand nanopore sensing to a wider biomedical application, controlling the localization of nanopores formed by CBD is essential. This article reviews the recent strategies to control the location of nanopores formed by CBD. We discuss the fundamental mechanism and the efforts of different approaches to confine the region of nanopore formation.
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Affiliation(s)
- Cuifeng Ying
- Advanced Optics and Photonics Laboratory, Department of Engineering, School of Science &Technology, Nottingham Trent University, Nottingham NG1 4FQ, UK; (L.X.); (M.R.)
- Correspondence:
| | - Tianji Ma
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation & Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, China;
| | - Lei Xu
- Advanced Optics and Photonics Laboratory, Department of Engineering, School of Science &Technology, Nottingham Trent University, Nottingham NG1 4FQ, UK; (L.X.); (M.R.)
| | - Mohsen Rahmani
- Advanced Optics and Photonics Laboratory, Department of Engineering, School of Science &Technology, Nottingham Trent University, Nottingham NG1 4FQ, UK; (L.X.); (M.R.)
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44
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Xing Y, Dorey A, Jayasinghe L, Howorka S. Highly shape- and size-tunable membrane nanopores made with DNA. NATURE NANOTECHNOLOGY 2022; 17:708-713. [PMID: 35484212 DOI: 10.1038/s41565-022-01116-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
Membrane nanopores are key for molecular transport in biology, portable DNA sequencing1-4, label-free single-molecule analysis5-14 and nanomedicine5. Transport traditionally relies on barrel-like channels of a few nanometres width, but there is considerable scientific and technological interest for much wider structures of tunable shape. Yet, these nanopores do not exist in nature and are challenging to build using existing de novo routes for proteins10,15-17. Here, we show that rational design with DNA can drastically expand the structural and functional range of membrane nanopores. Our design strategy bundles DNA duplexes into pore subunits that modularly arrange to form tunable pore shapes and lumen widths of up to tens of nanometres. Functional units for recognition or signalling can be optionally attached. By dialling in essential parameters, we demonstrate the utility and potential of the custom-engineered nanopores by electrical direct single-molecule sensing of 10-nm-sized proteins using widely used research and hand-held analysis devices. The designer nanopores illustrate how DNA nanotechnology can deliver functional biomolecular structures to be used in synthetic biology, single-molecule enzymology and biophysical analysis, as well as portable diagnostics and environmental screening.
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Affiliation(s)
- Yongzheng Xing
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK
| | - Adam Dorey
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK
| | | | - Stefan Howorka
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK.
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45
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Mereuta L, Asandei A, Dragomir I, Park J, Park Y, Luchian T. A Nanopore Sensor for Multiplexed Detection of Short Polynucleotides Based on Length-Variable, Poly-Arginine-Conjugated Peptide Nucleic Acids. Anal Chem 2022; 94:8774-8782. [PMID: 35666169 DOI: 10.1021/acs.analchem.2c01587] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Real-time and easy-to-use detection of nucleic acids is crucial for many applications, including medical diagnostics, genetic screening, forensic science, or monitoring the onset and progression of various diseases. Herein, an exploratory single-molecule approach for multiplexed discrimination among similar-sized single-stranded DNAs (ssDNA) is presented. The underlying strategy combined (i) a method based on length-variable, short arginine (poly-Arg) tags appended to peptide nucleic acid (PNA) probes, designed to hybridize with selected regions from complementary ssDNA targets (cDNA) in solution and (ii) formation and subsequent detection with the α-hemolysin nanopore of (poly-Arg)-PNA-cDNA duplexes containing two overhangs associated with the poly-Arg tail and the non-hybridized segment from ssDNA. We discovered that the length-variable poly-Arg tail marked distinctly the molecular processes associated with the nanopore-mediated duplexes capture, trapping and unzipping. This enabled the detection of ssDNA targets via the signatures of (poly-Arg)-PNA-cDNA blockade events, rendered most efficient from the β-barrel entrance of the nanopore, and scaled proportional in efficacy with a larger poly-Arg moiety. We illustrate the approach by sensing synthetic ssDNAs designed to emulate fragments from two regions of SARS-CoV-2 nucleocapsid phosphoprotein N-gene.
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Affiliation(s)
- Loredana Mereuta
- Department of Physics, Alexandru I. Cuza University, 700506 Iasi, Romania
| | - Alina Asandei
- Interdisciplinary Research Institute, Sciences Department, Alexandru I. Cuza University, 700506 Iasi, Romania
| | - Isabela Dragomir
- Interdisciplinary Research Institute, Sciences Department, Alexandru I. Cuza University, 700506 Iasi, Romania
| | - Jonggwan Park
- Department of Bioinformatics, Kongju National University, 38065 Kongju, Republic of Korea
| | - Yoonkyung Park
- Department of Biomedical Science and Research Center for Proteinaceous Materials (RCPM), Chosun University, 61452 Gwangju, Republic of Korea
| | - Tudor Luchian
- Department of Physics, Alexandru I. Cuza University, 700506 Iasi, Romania
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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: 8] [Impact Index Per Article: 4.0] [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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Tan X, Lv C, Chen H. Advances of nanopore-based sensing techniques for contaminants evaluation of food and agricultural products. Crit Rev Food Sci Nutr 2022; 63:10866-10879. [PMID: 35687354 DOI: 10.1080/10408398.2022.2085238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Food safety assurance systems are becoming more stringent in response to the growing food safety problems. Rapid, sensitive, and reliable detection technology is a prerequisite for the establishment of food safety assurance systems. Nanopore technology has been taken as one of the emerging technology capable of dealing with the detection of harmful contaminants as efficiently as possible due to the advantage of label-free, high-throughput, amplification-free, and rapid detection features. Start with the history of nanopore techniques, this review introduced the underlying knowledge of detection mechanism of nanopore-based sensing techniques. Meanwhile, sensing interfaces for the construction of nanopore sensors are comprehensively summarized. Moreover, this review covers the current advances of nanopore techniques in the application of food safety screening. Currently, the establishment of nanopore sensing devices is mainly based on the blocking current phenomenon. Sensing interfaces including biological nanopores, solid-state nanopores, DNA origami, and de novo designed nanopores can be used in the manufacture of sensing devices. Food harmful substances, including heavy metals, veterinary drugs, pesticide residues, food toxins, and other harmful substances can be quickly determined by nanopore-based sensors. Moreover, the combination of nanopore techniques with advanced materials has become one of the most effective methods to improve sensing properties.
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Affiliation(s)
- Xiaoyi Tan
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Chenyan Lv
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Hai Chen
- College of Food Science, Southwest University, Chongqing, China
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48
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Zhao Y, Iarossi M, De Fazio AF, Huang JA, De Angelis F. Label-Free Optical Analysis of Biomolecules in Solid-State Nanopores: Toward Single-Molecule Protein Sequencing. ACS PHOTONICS 2022; 9:730-742. [PMID: 35308409 PMCID: PMC8931763 DOI: 10.1021/acsphotonics.1c01825] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
Sequence identification of peptides and proteins is central to proteomics. Protein sequencing is mainly conducted by insensitive mass spectroscopy because proteins cannot be amplified, which hampers applications such as single-cell proteomics and precision medicine. The commercial success of portable nanopore sequencers for single DNA molecules has inspired extensive research and development of single-molecule techniques for protein sequencing. Among them, three challenges remain: (1) discrimination of the 20 amino acids as building blocks of proteins; (2) unfolding proteins; and (3) controlling the motion of proteins with nonuniformly charged sequences. In this context, the emergence of label-free optical analysis techniques for single amino acids and peptides by solid-state nanopores shows promise for addressing the first challenge. In this Perspective, we first discuss the current challenges of single-molecule fluorescence detection and nanopore resistive pulse sensing in a protein sequencing. Then, label-free optical methods are described to show how they address the single-amino-acid identification within single peptides. They include localized surface plasmon resonance detection and surface-enhanced Raman spectroscopy on plasmonic nanopores. Notably, we report new data to show the ability of plasmon-enhanced Raman scattering to record and discriminate the 20 amino acids at a single-molecule level. In addition, we discuss briefly the manipulation of molecule translocation and liquid flow in plasmonic nanopores for controlling molecule movement to allow high-resolution reading of protein sequences. We envision that a combination of Raman spectroscopy with plasmonic nanopores can succeed in single-molecule protein sequencing in a label-free way.
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Affiliation(s)
- Yingqi Zhao
- Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Marzia Iarossi
- Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | | | - Jian-An Huang
- Faculty
of Medicine, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 5 A, 90220 Oulu, Finland
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Wu J, Liang L, Zhang M, Zhu R, Wang Z, Yin Y, Yin B, Weng T, Fang S, Xie W, Wang L, Wang D. Single-Molecule Identification of the Conformations of Human C-Reactive Protein and Its Aptamer Complex with Solid-State Nanopores. ACS APPLIED MATERIALS & INTERFACES 2022; 14:12077-12088. [PMID: 35234028 DOI: 10.1021/acsami.2c00453] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Human C-reactive protein (CRP) is an established inflammatory biomarker and was proved to be potentially relevant to disease pathology and cancer progression. A large body of methodologies have been reported for CRP analysis, including electrochemical/optical biosensors, aptamer, or antibody-based detection. Although the detection limit is rather low until pg/uL, most of which are time-consuming and relatively expensive, and few of them provided CRP single-molecule information. This work demonstrated the nanopore-based approach for the characterization of CRP conformation under versatile conditions. With an optimized pore of 14 nm in diameter, we achieved the detection limit as low as 0.3 ng/μL, voltage polarity significantly influences the electro-osmotic force and CRP translocation behavior, and the pentameric conformation of CRP may dissociate into pro-inflammatory CRP isoforms and monomeric CRP at bias potential above 300 mV. CRP tends to translocate through nanopores faster along with the increase in pH values, due to more surface charge on both CRP and pore inner wall and stronger electro-osmotic force. The CRP could specifically bind with its aptamer of different concentrations to form complexes, and the complexes exhibited distinguishable nanopore translocation behavior compared with CRP alone. The variation of the molar ratio of aptamer significantly influences the orientation of CRP translocation. The plasma test under physiological conditions displayed the ability of the nanopore system on the CRP identification with a concentration of 3 ng/μL.
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Affiliation(s)
- Ji Wu
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Liyuan Liang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Mingkun Zhang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Rui Zhu
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Zhong Wang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Yajie Yin
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Bohua Yin
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Ting Weng
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Shaoxi Fang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Wanyi Xie
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Liang Wang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
| | - Deqiang Wang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
- Chongqing School, University of Chinese Academy of Science, Chongqing 400714, P. R. China
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Brady MM, Meyer AS. Cataloguing the proteome: Current developments in single-molecule protein sequencing. BIOPHYSICS REVIEWS 2022; 3:011304. [PMID: 38505228 PMCID: PMC10903494 DOI: 10.1063/5.0065509] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 01/13/2022] [Indexed: 03/21/2024]
Abstract
The cellular proteome is complex and dynamic, with proteins playing a critical role in cell-level biological processes that contribute to homeostasis, stimuli response, and disease pathology, among others. As such, protein analysis and characterization are of extreme importance in both research and clinical settings. In the last few decades, most proteomics analysis has relied on mass spectrometry, affinity reagents, or some combination thereof. However, these techniques are limited by their requirements for large sample amounts, low resolution, and insufficient dynamic range, making them largely insufficient for the characterization of proteins in low-abundance or single-cell proteomic analysis. Despite unique technical challenges, several single-molecule protein sequencing (SMPS) technologies have been proposed in recent years to address these issues. In this review, we outline several approaches to SMPS technologies and discuss their advantages, limitations, and potential contributions toward an accurate, sensitive, and high-throughput platform.
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Affiliation(s)
- Morgan M. Brady
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
| | - Anne S. Meyer
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
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