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Hu W, Zhang Z, Xiong W, Li M, Yan Y, Yang C, Zou Q, Lü JT, Tian H, Guo X. Direct flipping dynamics and quantized enrichment of chirality at single-molecule resolution. SCIENCE ADVANCES 2024; 10:eado1125. [PMID: 38996014 PMCID: PMC11244442 DOI: 10.1126/sciadv.ado1125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 06/06/2024] [Indexed: 07/14/2024]
Abstract
Chirality is an important aspect of nature, and numerous macroscopic methods have been developed to understand and control chirality. For the chiral tertiary amines, their flexible flipping process makes it possible to achieve high chiral controllability without bond formation and breaking. Here, we present a type of stable chiral single-molecule devices formed by tertiary amines, using graphene-molecule-graphene single-molecule junctions. These single-molecule devices allow real-time, in situ, and long-time measurements of the flipping process of an individual chiral nitrogen center with high temporal resolution. Temperature- and bias voltage-dependent experiments, along with theoretical investigations, revealed diverse chiral intermediates, indicating the regulation of the flipping dynamics by energy-related factors. Angle-dependent measurements further demonstrated efficient enrichment of chiral states using linearly polarized light by a symmetry-related factor. This approach offers a reliable means for understanding the chirality's origin, elucidating microscopic chirality regulation mechanisms, and aiding in the design of effective drugs.
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Affiliation(s)
- Weilin Hu
- Beijing National Laboratory for Molecular Sciences, National Biomedical Imaging Center, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, Beijing 100871, P. R. China
| | - Zhiyun Zhang
- Key Laboratory for Advanced Materials and Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Wan Xiong
- School of Physics, Institute for Quantum Science and Engineering and Wuhan National High Magnetic Field Center, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, P. R. China
| | - Mingyao Li
- Beijing National Laboratory for Molecular Sciences, National Biomedical Imaging Center, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, Beijing 100871, P. R. China
| | - Yong Yan
- Beijing National Laboratory for Molecular Sciences, National Biomedical Imaging Center, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, Beijing 100871, P. R. China
- Center for Molecular Systems and Organic Devices, Key Laboratory for Organic Electronics and Information Displays and Institute of Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing 210023, P. R. China
| | - Caiyao Yang
- Beijing National Laboratory for Molecular Sciences, National Biomedical Imaging Center, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, Beijing 100871, P. R. China
| | - Qi Zou
- Key Laboratory for Advanced Materials and Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Jing-Tao Lü
- School of Physics, Institute for Quantum Science and Engineering and Wuhan National High Magnetic Field Center, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, P. R. China
| | - He Tian
- Key Laboratory for Advanced Materials and Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Xuefeng Guo
- Beijing National Laboratory for Molecular Sciences, National Biomedical Imaging Center, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, Beijing 100871, P. R. China
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, College of Electronic Information and Optical Engineering, Nankai University, 38 Tongyan Road, Jinnan District, Tianjin 300350, P. R. China
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2
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Zhou X, Tang R, Li Y, Zhang S, Xi D. Label-free Sensing of Main Protease Activity of SARS-CoV-2 with an Aerolysin Nanopore. Chem Asian J 2022; 17:e202200747. [PMID: 36029274 PMCID: PMC9539354 DOI: 10.1002/asia.202200747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/24/2022] [Indexed: 11/07/2022]
Abstract
The main protease (Mpro ), which is highly conserved and plays a critical role in the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a natural biomarker for SARS-CoV-2. Accurate assessment of the Mpro activity is crucial for the detection of SARS-CoV-2. Herein, we report a nanopore-based sensing strategy that uses an enzyme-catalyzed cleavage reaction of a peptide substrate to measure the Mpro activity. The peptide was specifically cleaved by the Mpro , thereby releasing the output products that, when translocated through aerolysin, quantitatively produced the signature current events. The proposed method exhibited high sensitivity, allowing the detection of Mpro concentrations as low as 1 nM without the use of any signal amplification techniques. This simple, convenient, and label-free nanopore assay may expand the diagnostic tools for viruses.
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Affiliation(s)
- Xin Zhou
- Department Shandong Provincial Key Laboratory of Detection Technology for Tumor MarkersInstitution College of Life SciencesLinyi UniversityLinyi276005P. R. China
| | - Ruping Tang
- Department Shandong Provincial Key Laboratory of Detection Technology for Tumor MarkersInstitution College of Life SciencesLinyi UniversityLinyi276005P. R. China
| | - Yusen Li
- Department Shandong Provincial Key Laboratory of Detection Technology for Tumor MarkersInstitution College of Life SciencesLinyi UniversityLinyi276005P. R. China
| | - Shusheng Zhang
- Department Shandong Provincial Key Laboratory of Detection Technology for Tumor MarkersInstitution College of Life SciencesLinyi UniversityLinyi276005P. R. China
| | - Dongmei Xi
- Department Shandong Provincial Key Laboratory of Detection Technology for Tumor MarkersInstitution College of Life SciencesLinyi UniversityLinyi276005P. R. China
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3
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Hagan JT, Gonzalez A, Shi Y, Han GGD, Dwyer JR. Photoswitchable Binary Nanopore Conductance and Selective Electronic Detection of Single Biomolecules under Wavelength and Voltage Polarity Control. ACS NANO 2022; 16:5537-5544. [PMID: 35286058 DOI: 10.1021/acsnano.1c10039] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We fabricated photoregulated thin-film nanopores by covalently linking azobenzene photoswitches to silicon nitride pores with ∼10 nm diameters. The photoresponsive coatings could be repeatedly optically switched with deterministic ∼6 nm changes to the effective nanopore diameter and of ∼3× to the nanopore ionic conductance. The sensitivity to anionic DNA and a neutral complex carbohydrate biopolymer (maltodextrin) could be photoswitched "on" and "off" with an analyte selectivity set by applied voltage polarity. Photocontrol of nanopore state and mass transport characteristics is important for their use as ionic circuit elements (e.g., resistors and binary bits) and as chemically tuned filters. It expands single-molecule sensing capabilities in personalized medicine, genomics, glycomics, and, augmented by voltage polarity selectivity, especially in multiplexed biopolymer information storage schemes. We demonstrate repeatedly photocontrolled stable nanopore size, polarity, conductance, and sensing selectivity, by illumination wavelength and voltage polarity, with broad utility including single-molecule sensing of biologically and technologically important polymers.
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Affiliation(s)
- James T Hagan
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Alejandra Gonzalez
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02453, United States
| | - Yuran Shi
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02453, United States
| | - Grace G D Han
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02453, United States
| | - Jason R Dwyer
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island 02881, United States
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4
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Xie ZP, Liu SM, Zhai YM. Study on the Self-assembly and Signal Amplification Ability of Nucleic Acid Nanostructure with the Nanopipette. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2022.116307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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5
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Lu J, Jiang Y, Yu P, Jiang W, Mao L. Light-Controlled Ionic/Molecular Transport through Solid-State Nanopores and Nanochannels. Chem Asian J 2022; 17:e202200158. [PMID: 35324076 DOI: 10.1002/asia.202200158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/24/2022] [Indexed: 11/10/2022]
Abstract
Biological nanochannels perfectly operate in organisms and exquisitely control mass transmembrane transport for complex life process. Inspired by biological nanochannels, plenty of intelligent artificial solid-state nanopores and nanochannels are constructed based on various materials and methods with the development of nanotechnology. Specially, the light-controlled nanopores/nanochannels have attracted much attention due to the unique advantages in terms of that ion and molecular transport can be regulated remotely, spatially and temporally. According to the structure and function of biological ion channels, light-controlled solid-state nanopores/nanochannels can be divided into light-regulated ion channels with ion gating and ion rectification functions, and light-driven ion pumps with active ion transport property. In this review, we present a systematic overview of light-controlled ion channels and ion pumps according to the photo-responsive components in the system. Then, the related applications of solid-state nanopores/nanochannels for molecular sensing, water purification and energy conversion are discussed. Finally, a brief conclusion and short outlook are offered for future development of the nanopore/nanochannel field.
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Affiliation(s)
- Jiahao Lu
- Shandong University, School of Chemistry and Chemical Engineering, CHINA
| | - Yanan Jiang
- Beijing Normal University, College of Chemistry, CHINA
| | - Ping Yu
- Chinese Academy of Sciences, Institute of Chemistry, CHINA
| | - Wei Jiang
- Shandong University, School of Chemistry and Chemical Engineering, CHINA
| | - Lanqun Mao
- Beijing Normal University, College of Chemistry, No.19, Xinjiekouwai St, Haidian District, 100875, Beijing, CHINA
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6
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Lv P, Yang Y, Li S, Tan CS, Ming D. Biological nanopore approach for single‐molecule analysis of nucleobase modifications. ELECTROCHEMICAL SCIENCE ADVANCES 2021. [DOI: 10.1002/elsa.202100119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Pengrui Lv
- Academy of Medical Engineering and Translational Medicine Tianjin University Tianjin China
| | - Yongyi Yang
- Academy of Medical Engineering and Translational Medicine Tianjin University Tianjin China
| | - Shuang Li
- Academy of Medical Engineering and Translational Medicine Tianjin University Tianjin China
| | - Cherie S. Tan
- Academy of Medical Engineering and Translational Medicine Tianjin University Tianjin China
| | - Dong Ming
- Academy of Medical Engineering and Translational Medicine Tianjin University Tianjin China
- Department of Biomedical Engineering College of Precision Instruments and Optoelectronics Engineering Tianjin University Tianjin China
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7
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Bhatti H, Jawed R, Ali I, Iqbal K, Han Y, Lu Z, Liu Q. Recent advances in biological nanopores for nanopore sequencing, sensing and comparison of functional variations in MspA mutants. RSC Adv 2021; 11:28996-29014. [PMID: 35478559 PMCID: PMC9038099 DOI: 10.1039/d1ra02364k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 08/09/2021] [Indexed: 12/14/2022] Open
Abstract
Biological nanopores are revolutionizing human health by the great myriad of detection and diagnostic skills. Their nano-confined area and ingenious shape are suitable to investigate a diverse range of molecules that were difficult to identify with the previous techniques. Additionally, high throughput and label-free detection of target analytes instigated the exploration of new bacterial channel proteins such as Fragaceatoxin C (FraC), Cytolysin A (ClyA), Ferric hydroxamate uptake component A (FhuA) and Curli specific gene G (CsgG) along with the former ones, like α-hemolysin (αHL), Mycobacterium smegmatis porin A (MspA), aerolysin, bacteriophage phi 29 and Outer membrane porin G (OmpG). Herein, we discuss some well-known biological nanopores but emphasize on MspA and compare the effects of site-directed mutagenesis on the detection ability of its mutants in view of the surface charge distribution, voltage threshold and pore-analyte interaction. We also discuss illustrious and latest advances in biological nanopores for past 2-3 years due to limited space. Last but not the least, we elucidate our perspective for selecting a biological nanopore and propose some future directions to design a customized nanopore that would be suitable for DNA sequencing and sensing of other nontrivial molecules in question.
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Affiliation(s)
- Huma Bhatti
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
| | - Rohil Jawed
- School of Life Science and Technology, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China
| | - Irshad Ali
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
| | - Khurshid Iqbal
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
| | - Yan Han
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
| | - Quanjun Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University No. 2 Sipailou Nanjing 210096 People's Republic of China +86-25-83793283 +86-25-83793283
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8
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Tang Y, Zhuang Y, Zhang S, Smith ZJ, Li Y, Mu X, Li M, He C, Zheng X, Pan F, Gao T, Zhang L. Azo-Enhanced Raman Scattering for Enhancing the Sensitivity and Tuning the Frequency of Molecular Vibrations. ACS CENTRAL SCIENCE 2021; 7:768-780. [PMID: 34079895 PMCID: PMC8161494 DOI: 10.1021/acscentsci.1c00117] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Indexed: 05/14/2023]
Abstract
Raman scattering provides stable narrow-banded signals that potentially allow for multicolor microscopic imaging. The major obstacle for the applications of Raman spectroscopy and microscopy is the small cross section of Raman scattering that results in low sensitivity. Here, we report a new concept of azo-enhanced Raman scattering (AERS) by designing the intrinsic molecular structures using resonance Raman and concomitant fluorescence quenching strategies. Based on the selection of vibrational modes and the enhancing unit of azobenzenes, we obtained a library of AERS molecules with specific Raman signals in the fingerprint and silent frequency regions. The spectral characterization and molecular simulation revealed that the azobenzene unit conjugated to the vibrational modes significantly enhanced Raman signals due to the mechanism of extending the conjugation system, coupling the electronic-vibrational transitions, and improving the symmetry of vibrational modes. The nonradiative decay of azobenzene from the excited state quenched the commitment fluorescence, thus providing a clean background for identifying Raman scattering. The most sensitive AERS molecules produced Raman signals of more than 4 orders of magnitude compared to 5-ethynyl-2'-deoxyuridine (EdU). In addition, a frequency tunability of 10 distinct Raman bands was achieved by selecting different types of vibrational modes. This methodology of AERS allows for designing small-molecule Raman probes to visualize various entities in complex systems by multicolor spontaneous Raman imaging. It will open new prospects to explore innovative applications of AERS in interdisciplinary research fields.
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Affiliation(s)
- Yuchen Tang
- China
Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, Wuhan 430079, China
- College
of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Yongpeng Zhuang
- China
Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, Wuhan 430079, China
- College
of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Shaohua Zhang
- China
Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, Wuhan 430079, China
- College
of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Zachary J. Smith
- Department
of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei 230027, China
| | - Yuee Li
- School
of Information Science and Engineering, Lanzhou University, Lanzhou 730000, China
| | - Xijiao Mu
- School
of Information Science and Engineering, Lanzhou University, Lanzhou 730000, China
| | - Mengna Li
- China
Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, Wuhan 430079, China
- College
of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Caili He
- China
Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, Wuhan 430079, China
- College
of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Xingxing Zheng
- China
Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, Wuhan 430079, China
- College
of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Fangfang Pan
- China
Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, Wuhan 430079, China
- College
of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Tingjuan Gao
- China
Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, Wuhan 430079, China
- College
of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Lizhi Zhang
- China
Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, Wuhan 430079, China
- College
of Chemistry, Central China Normal University, Wuhan 430079, China
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9
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Tang J, Wu J, Zhu R, Wang Z, Zhao C, Tang P, Xie W, Wang D, Liang L. Reversible photo-regulation on the folding/unfolding of telomere G-quadruplexes with solid-state nanopores. Analyst 2021; 146:655-663. [PMID: 33206065 DOI: 10.1039/d0an01930e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The formation of G-quadruplexes (G4) in human telomere and other important biological regions inhibits the replication and transcription of DNA, thereby influencing further cell proliferation. The investigation of G4 formation and unfolding is vital for understanding their modulation in biological processes and life science. Photo regulation is a facile and sensitive approach for monitoring the structures of biomacromolecules and material surface properties. The nanopore-based technique is also prevalent for label-free single-molecule characterization with high accuracy. This study provides a combination of solid-state nanopore technology with light-switch as a platform for the modulation of human telomere G4 formation and splitting under switchable light exposure. The introduction of molecular switch, namely azobenzene moiety at different positions of the DNA sequence influences the formation and stability of G4. Three azobenzenes immobilized on each of the G-quartet plane (hTelo-3azo-p) or four azobenzenes on the same plane (hTelo-4azo-4p) of the human telomere G4 sequence realized the reversible control of G4 folding/unfolding at the temporal scale upon photo regulation, and the formation and splitting of G4 with hTelo-4azo-4p is slower and not thorough compared to that with hTelo-3azo-p due to the coplanar steric hindrance. Moreover, the G4 formation recorded with the combined nanopore and photo-responsive approach was also characterized with fluorescence, and the variation in the fluorescence intensity of the NMM and G4 complex exhibited a different tendency under reverse light irradiation due to the distinct interactions of NMM with the azobenzene-modified G4. Our study demonstrated a controllable and sensitive way for the manipulation of G4 structures, which will be inspiring for the intervention of G4-related cell senescence, cancer diagnosis and drug exploration.
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Affiliation(s)
- Jing Tang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China.
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10
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TANG J, WANG S, WU J, LIANG LY, WANG L, WANG DQ. Applications of Photo-Responsive Molecules in Nanopore-based Devices. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(20)60058-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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11
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Ariga K. The evolution of molecular machines through interfacial nanoarchitectonics: from toys to tools. Chem Sci 2020; 11:10594-10604. [PMID: 34094314 PMCID: PMC8162416 DOI: 10.1039/d0sc03164j] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 07/07/2020] [Indexed: 12/19/2022] Open
Abstract
Molecular machines are often regarded as molecular artworks and sometimes as fancy molecular toys. However, many researchers strive to operate molecular machines as useful tools for realistic practical applications. In this perspective article, shifting the working environment of molecular machines from solution to interfacial media is discussed from the viewpoint of their evolution from scientific toys to useful tools. Following a short description of traditional research into molecular machines in solution and their nanotechnological manipulation on clean solid surfaces, pioneering research into molecular machine operation at dynamic interfaces, such as liquid surfaces, is discussed, along with cutting-edge research into molecular machine functions in living cells and their models. Biomolecular machines within organisms are the products of evolution over billions of years. We may nanoarchitect such sophisticated functional systems with artificial molecular machines within much shorter periods.
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Affiliation(s)
- Katsuhiko Ariga
- WPI Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS) 1-1 Namiki Tsukuba Ibaraki 305-0044 Japan
- Graduate School of Frontier Sciences, The University of Tokyo 5-1-5 Kashiwanoha Kashiwa Chiba 277-8561 Japan
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12
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Huang G, Willems K, Bartelds M, van Dorpe P, Soskine M, Maglia G. Electro-Osmotic Vortices Promote the Capture of Folded Proteins by PlyAB Nanopores. NANO LETTERS 2020; 20:3819-3827. [PMID: 32271587 PMCID: PMC7227020 DOI: 10.1021/acs.nanolett.0c00877] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/06/2020] [Indexed: 05/19/2023]
Abstract
Biological nanopores are emerging as powerful tools for single-molecule analysis and sequencing. Here, we engineered the two-component pleurotolysin (PlyAB) toxin to assemble into 7.2 × 10.5 nm cylindrical nanopores with a low level of electrical noise in lipid bilayers, and we addressed the nanofluidic properties of the nanopore by continuum simulations. Surprisingly, proteins such as human albumin (66.5 kDa) and human transferrin (76-81 kDa) did not enter the nanopore. We found that the precise engineering of the inner surface charge of the PlyAB induced electro-osmotic vortices that allowed the electrophoretic capture of the proteins. Once inside the nanopore, two human plasma proteins could be distinguished by the characteristics of their current blockades. This fundamental understanding of the nanofluidic properties of nanopores provides a practical method to promote the capture and analysis of folded proteins by nanopores.
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Affiliation(s)
- Gang Huang
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Kherim Willems
- Department
of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium
- imec, Kapeldreef 75, 3001 Leuven, Belgium
| | - Mart Bartelds
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Pol van Dorpe
- imec, Kapeldreef 75, 3001 Leuven, Belgium
- Department
of Physics and Astronomy, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Misha Soskine
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Giovanni Maglia
- Groningen
Biomolecular Sciences & Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
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13
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Wei T, Lu S, Sun J, Xu Z, Yang X, Wang F, Ma Y, Shi YS, Chen X. Sanger's Reagent Sensitized Photocleavage of Amide Bond for Constructing Photocages and Regulation of Biological Functions. J Am Chem Soc 2020; 142:3806-3813. [PMID: 32023409 DOI: 10.1021/jacs.9b11357] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Photolabile groups offer promising tools to study biological processes with high spatial and temporal control. In the investigation, we designed and prepared several new glycine amide derivatives of Sanger's reagent and demonstrated that they serve as a new class of photocages for Zn2+ and an acetylcholinesterase (AChE) inhibitor. We showed that the mechanism for photocleavage of these substances involves initial light-driven cyclization between the 2,4-dinitrophenyl and glycine methylene groups to form acyl benzimidazole N-oxides, which undergo secondary photoinduced decarboxylation in association with rupture of an amide bond. The cleavage reactions proceed with modest to high quantum yields. We demonstrated that these derivatives can be used in targeted intracellular delivery of Zn2+, fluorescent imaging by light-triggered Zn2+ release, and regulation of biological processes including the enzymatic activity of carbonic anhydrase (CA), negative regulation of N-methyl-d-aspartate receptors (NMDARs), and pulse rate of cardiomyocytes. The successful proof-of-concept examples described above open a new avenue for using Sanger's reagent-based glycine amides as photocages for the exploration of complex cellular functions and signaling pathways.
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Affiliation(s)
- Tingwen Wei
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemistry and Chemical Engineering , Nanjing Tech University , Nanjing 210009 , China
| | - Sheng Lu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemistry and Chemical Engineering , Nanjing Tech University , Nanjing 210009 , China
| | - Jiahui Sun
- State Key Laboratory of Pharmaceutical Biotechnology , Nanjing University , Nanjing 210032 , China.,Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center , Nanjing University , Nanjing 210032 , China
| | - Zhijun Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemistry and Chemical Engineering , Nanjing Tech University , Nanjing 210009 , China
| | - Xiao Yang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemistry and Chemical Engineering , Nanjing Tech University , Nanjing 210009 , China
| | - Fang Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemistry and Chemical Engineering , Nanjing Tech University , Nanjing 210009 , China
| | - Yang Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemistry and Chemical Engineering , Nanjing Tech University , Nanjing 210009 , China
| | - Yun Stone Shi
- State Key Laboratory of Pharmaceutical Biotechnology , Nanjing University , Nanjing 210032 , China.,Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center , Nanjing University , Nanjing 210032 , China.,Chemistry and Biomedicine Innovation Center , Nanjing University , Nanjing 210032 , China
| | - Xiaoqiang Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemistry and Chemical Engineering , Nanjing Tech University , Nanjing 210009 , China
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14
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Zhang Z, Huang X, Qian Y, Chen W, Wen L, Jiang L. Engineering Smart Nanofluidic Systems for Artificial Ion Channels and Ion Pumps: From Single-Pore to Multichannel Membranes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1904351. [PMID: 31793736 DOI: 10.1002/adma.201904351] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/26/2019] [Indexed: 06/10/2023]
Abstract
Biological ion channels and ion pumps with intricate ion transport functions widely exist in living organisms and play irreplaceable roles in almost all physiological functions. Nanofluidics provides exciting opportunities to mimic these working processes, which not only helps understand ion transport in biological systems but also paves the way for the applications of artificial devices in many valuable areas. Recent progress in the engineering of smart nanofluidic systems for artificial ion channels and ion pumps is summarized. The artificial systems range from chemically and structurally diverse lipid-membrane-based nanopores to robust and scalable solid-state nanopores. A generic strategy of gate location design is proposed. The single-pore-based platform concept can be rationally extended into multichannel membrane systems and shows unprecedented potential in many application areas, such as single-molecule analysis, smart mass delivery, and energy conversion. Finally, some present underpinning issues that need to be addressed are discussed.
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Affiliation(s)
- Zhen Zhang
- Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Xiaodong Huang
- Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yongchao Qian
- Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Weipeng Chen
- Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Liping Wen
- Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Lei Jiang
- Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
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15
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Wu Z, Zhang L. Photoregulation between small DNAs and reversible photochromic molecules. Biomater Sci 2019; 7:4944-4962. [PMID: 31650136 DOI: 10.1039/c9bm01305a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Oligonucleotides are widely used biological materials in the fields of biomedicine, nanotechnology, and materials science. Due to the demands for the photoregulation of DNA activities, scientists are placing more and more research interest in the interactions between reversible photochromic molecules and DNAs. Photochromic molecules can work as switches for regulating the DNAs' behavior under light irradiation; meanwhile, DNAs also exert influence over the photochromic molecules. The photochromic molecules can be attached to DNAs either by covalent bonds or by noncovalent forces, which results in different regulative functions. Azobenzenes, spiropyrans, diarylethenes, and stilbene-like compounds are important photochromic molecules working as photoswitches. By summarizing their interactions with oligonucleotides, this review intends to facilitate the relevant research on oligonucleotides/photochromic molecules in the biological and medicinal fields and in materials science.
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Affiliation(s)
- Zhongtao Wu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53 Zhengzhou Rd, Qingdao, 266042, PR China.
| | - Lei Zhang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53 Zhengzhou Rd, Qingdao, 266042, PR China.
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16
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Xu Y, Lu B, Fu L, Zhai J. Asymmetric heterostructured SiO2/Al2O3 nanofluidic diodes modulating ionic transport for highly efficient light-gating device. Electrochim Acta 2019. [DOI: 10.1016/j.electacta.2019.05.084] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Gao R, Lin Y, Ying YL, Long YT. Nanopore-based sensing interface for single molecule electrochemistry. Sci China Chem 2019. [DOI: 10.1007/s11426-019-9509-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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18
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Wu R, Zhu Z, Xu X, Yu C, Li B. An investigation of solid-state nanopores on label-free metal-ion signalling via the transition of RNA-cleavage DNAzyme and the hybridization chain reaction. NANOSCALE 2019; 11:10339-10347. [PMID: 31107481 DOI: 10.1039/c9nr01666j] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Recent advances have proven solid-state nanopores as a powerful analysis platform that enables label-free and separation-free single-molecule analysis. However, the relatively low resolution still limits its application because many chemicals or targets with small sizes could not be recognized in a label-free condition. In this paper, we provide a possible solution that uses solid-state nanopores for small species signaling via the transition of huge DNA assembly products. DNAzyme responding to metal ions and the hybridization chain reaction (HCR) generating nanopore-detectable dsDNA concatamers are used as the transition model set. By the two-step DNAzyme-HCR transition, Pb2+ that was too tiny to be sensed was successfully recognized by the nanopore. The whole process happened in a completely homogeneous solution without any chemical modification. During condition optimization, we also discussed one possible application challenge that may affect the HCR signal-background distinction. Solid-state nanopores provide a potential solution to this challenge due to its ability to profile product length or even 3D structure information.
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Affiliation(s)
- Ruiping Wu
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, PR China.
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19
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Borsley S, Haugland MM, Oldknow S, Cooper JA, Burke MJ, Scott A, Grantham W, Vallejo J, Brechin EK, Lusby PJ, Cockroft SL. Electrostatic Forces in Field-Perturbed Equilibria: Nanopore Analysis of Cage Complexes. Chem 2019. [DOI: 10.1016/j.chempr.2019.03.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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20
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Cressiot B, Ouldali H, Pastoriza-Gallego M, Bacri L, Van der Goot FG, Pelta J. Aerolysin, a Powerful Protein Sensor for Fundamental Studies and Development of Upcoming Applications. ACS Sens 2019; 4:530-548. [PMID: 30747518 DOI: 10.1021/acssensors.8b01636] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The nanopore electrical approach is a breakthrough in single molecular level detection of particles as small as ions, and complex as biomolecules. This technique can be used for molecule analysis and characterization as well as for the understanding of confined medium dynamics in chemical or biological reactions. Altogether, the information obtained from these kinds of experiments will allow us to address challenges in a variety of biological fields. The sensing, design, and manufacture of nanopores is crucial to realize these objectives. For some time now, aerolysin, a pore forming toxin, and its mutants have shown high potential in real time analytical chemistry, size discrimination of neutral polymers, oligosaccharides, oligonucleotides and peptides at monomeric resolution, sequence identification, chemical modification on DNA, potential biomarkers detection, and protein folding analysis. This review focuses on the results obtained with aerolysin nanopores on the fields of chemistry, biology, physics, and biotechnology. We discuss and compare as well the results obtained with other protein channel sensors.
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Affiliation(s)
- Benjamin Cressiot
- LAMBE, Université
Evry, Université de Cergy-Pontoise, CNRS, CEA, Université
Paris-Saclay, 91025, Evry, France
| | - Hadjer Ouldali
- LAMBE, Université
Cergy-Pontoise, Université d’Evry, CNRS, CEA, Université
Paris-Seine, 95000, Cergy, France
| | - Manuela Pastoriza-Gallego
- LAMBE, Université
Cergy-Pontoise, Université d’Evry, CNRS, CEA, Université
Paris-Seine, 95000, Cergy, France
| | - Laurent Bacri
- LAMBE, Université
Evry, Université de Cergy-Pontoise, CNRS, CEA, Université
Paris-Saclay, 91025, Evry, France
| | | | - Juan Pelta
- LAMBE, Université
Evry, Université de Cergy-Pontoise, CNRS, CEA, Université
Paris-Saclay, 91025, Evry, France
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21
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Wang L, Zhu Z, Li B, Shao F. One-Dimensional Assemblies of a DNA Tetrahedron: Manipulations on the Structural Conformation and Single-Molecule Behaviors. ACS APPLIED BIO MATERIALS 2019; 2:1278-1285. [PMID: 35021375 DOI: 10.1021/acsabm.8b00834] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
DNA nanotechnology can construct various nanostructures with diverse functionalities. However, conformation fluctuations due to the structural flexibility of duplex DNA compromise the efficiency to realize the functionality and reactivity of DNA nanostructures. To understand and control the structural deviation from the design represents a major challenge as well as an opportunity for DNA nanotechnology. In the present work, two series of one-dimensional assemblies of DNA tetrahedrons (DTHs) were fabricated and applied to demonstrate the manipulations of conformation dynamics of a one-dimensional DTH assembly by simple variation on linkage styles at single-molecule resolution. A stepwise strategy allows both nanoassembly with a high fidelity in the number and sequence of DTH units to be assembled with a minimum number of linkage sequences. The characterization for these nanostructures with atomic force microscope (AFM) and a solid-state nanopore technique indicates the difference in conformation dynamics and bending stiffness between two analogous nanoassemblies both in the immobilized state on the surface and free state in solution. This work showed the power of fine-tuning the dynamic conformation of the nanostructures and could see the applications in single-molecule biosensing and functionalization of DNA nanostructures.
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Affiliation(s)
- Liying Wang
- Zhejiang University-University of Illinois at Urbana-Champaign Institute, Zhejiang University, Haining 314400, People's Republic of China.,Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
| | - Zhentong Zhu
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Science, Changchun, Jilin 130022, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bingling Li
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Science, Changchun, Jilin 130022, People's Republic of China
| | - Fangwei Shao
- Zhejiang University-University of Illinois at Urbana-Champaign Institute, Zhejiang University, Haining 314400, People's Republic of China.,Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
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22
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Si W, Yang H, Sha J, Zhang Y, Chen Y. Discrimination of single-stranded DNA homopolymers by sieving out G-quadruplex using tiny solid-state nanopores. Electrophoresis 2019; 40:2117-2124. [PMID: 30779188 DOI: 10.1002/elps.201800537] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 01/28/2019] [Accepted: 02/13/2019] [Indexed: 12/19/2022]
Abstract
Nanopore sensor has been developed as a promising technology for DNA sequencing at the single-base resolution. However, the discrimination of homopolymers composed of guanines from other nucleotides has not been clearly revealed due to the easily formed G-quadruplex in aqueous buffers. In this work, we report that a tiny silicon nitride nanopore was used to sieve out G tetramers to make sure only homopolymers composed of guanines could translocate through the nanopore, then the 20-nucleotide long ssDNA homopolymers could be identified and differentiated. It is found that the size of the nucleotide plays a major role in affecting the current blockade as well as the dwell time while DNA is translocating through the nanopore. By the comparison of translocation behavior of ssDNA homopolymers composed of nucleotides with different volumes, it is found that smaller nucleotides can lead to higher translocation speed and lower current blockage, which is also found and validated for the 105-nucleotide long homopolymers. The studies performed in this work will improve our understanding of nanopore-based DNA sequencing at single-base level.
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Affiliation(s)
- Wei Si
- School of Mechanical Engineering, Southeast University, Nanjing, P. R. China.,Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, P. R. China
| | - Haojie Yang
- School of Mechanical Engineering, Southeast University, Nanjing, P. R. China.,Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, P. R. China
| | - Jingjie Sha
- School of Mechanical Engineering, Southeast University, Nanjing, P. R. China.,Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, P. R. China
| | - Yin Zhang
- School of Mechanical Engineering, Southeast University, Nanjing, P. R. China.,Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, P. R. China
| | - Yunfei Chen
- School of Mechanical Engineering, Southeast University, Nanjing, P. R. China.,Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, P. R. China
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23
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Zhu Z, Wu R, Li B. Exploration of solid-state nanopores in characterizing reaction mixtures generated from a catalytic DNA assembly circuit. Chem Sci 2019; 10:1953-1961. [PMID: 30881624 PMCID: PMC6385554 DOI: 10.1039/c8sc04875d] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/12/2018] [Indexed: 12/18/2022] Open
Abstract
Recent advances have proven that using solid-state nanopores is a promising single molecular technique to enrich the DNA assembly signaling library. Other than using them for distinguishing structures, here we innovatively adapt solid-state nanopores for use in analyzing assembly mixtures, which is usually a tougher task for either traditional characterization techniques or nanopores themselves. A trigger induced DNA step polymerization (SP-CHA), producing three-way-DNA concatemers, is designed as a model. Through counting and integrating the translocation-induced current block when each concatemer passes through a glass conical glass nanopore, we propose an electrophoresis-gel like, but homogeneous, quantitative method that can comprehensively profile the "base-pair distribution" of SP-CHA concatemer mixtures. Due to the higher sensitivity, a number of super long concatemers that were previously difficult to detect via gel electrophoresis are also revealed. These ultra-concatemers, longer than 2 kbp, could provide a much enhanced signal-to-noise ratio for nanopores and are thus believed to be more accurate indicators for the existence of a trigger, which may be of benefit for further applications, such as molecular machines or biosensors.
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Affiliation(s)
- Zhentong Zhu
- State Key Lab of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Science , Changchun , Jilin 130022 , P. R. China .
- University of Chinese Academy of Sciences , Beijing , 100049 , China
| | - Ruiping Wu
- State Key Lab of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Science , Changchun , Jilin 130022 , P. R. China .
- University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Bingling Li
- State Key Lab of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Science , Changchun , Jilin 130022 , P. R. China .
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24
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Hu ZL, Li MY, Liu SC, Ying YL, Long YT. A lithium-ion-active aerolysin nanopore for effectively trapping long single-stranded DNA. Chem Sci 2019; 10:354-358. [PMID: 30746084 PMCID: PMC6334748 DOI: 10.1039/c8sc03927e] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/12/2018] [Indexed: 12/15/2022] Open
Abstract
Wild-type aerolysin (AeL) nanopores allow direct single nucleotide discrimination of very short oligonucleotides (≤10 nt) without labelling, which shows great potential for DNA sensing. To achieve real applications, one major obstacle of AeL is its poor capture ability of long single-stranded DNA (ssDNA, >10 nt). Here, we have proposed a novel and robust strategy for the electrostatic focusing of long ssDNA into a lithium-chloride (LiCl)-active AeL. By using this method, for the first time we have demonstrated AeL detection of ssDNA longer than 100 nt. Due to screening more negative charges, LiCl improves AeL capture ability of long ssDNA (i.e. 60 nt) by 2.63- to 10.23-fold compared to KCl. Further calculations and molecular dynamics simulations revealed that strong binding between Li+ and the negatively charged residue neutralized the AeL, leading to a reduction in the energy barrier for ssDNA capture. These findings facilitate the future high-throughput applications of AeL in genetic and epigenetic diagnostics.
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Affiliation(s)
- Zheng-Li Hu
- Key Laboratory for Advanced Materials , School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China . ; Tel: +86-21-64252339
| | - Meng-Yin Li
- Key Laboratory for Advanced Materials , School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China . ; Tel: +86-21-64252339
| | - Shao-Chuang Liu
- Key Laboratory for Advanced Materials , School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China . ; Tel: +86-21-64252339
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials , School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China . ; Tel: +86-21-64252339
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials , School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China . ; Tel: +86-21-64252339
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25
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Xie G, Li P, Zhao Z, Kong X, Zhang Z, Xiao K, Wang H, Wen L, Jiang L. Bacteriorhodopsin‐Inspired Light‐Driven Artificial Molecule Motors for Transmembrane Mass Transportation. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201809627] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Ganhua Xie
- CAS Key Laboratory of Bio-inspired Materials and Interfacial ScienceTechnical Institute of Physics and ChemistryChinese Academy of Sciences Beijing 100190 P. R. China
- Key Laboratory of Green PrintingInstitute of ChemistryChinese Academy of Sciences Beijing 100190 P. R. China
| | - Pei Li
- CAS Key Laboratory of Bio-inspired Materials and Interfacial ScienceTechnical Institute of Physics and ChemistryChinese Academy of Sciences Beijing 100190 P. R. China
| | - Zhiju Zhao
- College of Chemical Engineering and BiotechnologyXingtai University Xingtai 054001 P. R. China
| | - Xiang‐Yu Kong
- CAS Key Laboratory of Bio-inspired Materials and Interfacial ScienceTechnical Institute of Physics and ChemistryChinese Academy of Sciences Beijing 100190 P. R. China
| | - Zhen Zhang
- CAS Key Laboratory of Bio-inspired Materials and Interfacial ScienceTechnical Institute of Physics and ChemistryChinese Academy of Sciences Beijing 100190 P. R. China
| | - Kai Xiao
- CAS Key Laboratory of Bio-inspired Materials and Interfacial ScienceTechnical Institute of Physics and ChemistryChinese Academy of Sciences Beijing 100190 P. R. China
| | - Huanting Wang
- Department of Chemical EngineeringMonash University Clayton Victoria 3800 Australia
| | - Liping Wen
- CAS Key Laboratory of Bio-inspired Materials and Interfacial ScienceTechnical Institute of Physics and ChemistryChinese Academy of Sciences Beijing 100190 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Lei Jiang
- CAS Key Laboratory of Bio-inspired Materials and Interfacial ScienceTechnical Institute of Physics and ChemistryChinese Academy of Sciences Beijing 100190 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
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26
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Xie G, Li P, Zhao Z, Kong XY, Zhang Z, Xiao K, Wang H, Wen L, Jiang L. Bacteriorhodopsin-Inspired Light-Driven Artificial Molecule Motors for Transmembrane Mass Transportation. Angew Chem Int Ed Engl 2018; 57:16708-16712. [PMID: 30358031 DOI: 10.1002/anie.201809627] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 10/11/2018] [Indexed: 11/11/2022]
Abstract
In nature, biological machines and motors can selectively transport cargoes across the lipid membranes to efficiently perform various physiological functions via ion channels or ion pumps. It is interesting and challengeable to develop artificial motors and machines of nanodimensions to controllably regulate mass transport in compartmentalized systems. In this work, we show a system of artificial molecular motors that uses light energy to perform transmembrane molecule transport through synthetical nanochannels. After functionalizing the polymer nanochannels with azobenzene derivatives, these nanomachines exhibit autonomous selective transport behavior over a long distance upon simultaneous irradiation with UV (365 nm) and visible (430 nm) light. With new strategies or suitable materials for directed molecular movement, such device can be regarded as a precursor of artificial light-driven molecular pumps.
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Affiliation(s)
- Ganhua Xie
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Pei Li
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Zhiju Zhao
- College of Chemical Engineering and Biotechnology, Xingtai University, Xingtai, 054001, P. R. China
| | - Xiang-Yu Kong
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Zhen Zhang
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Kai Xiao
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Huanting Wang
- Department of Chemical Engineering, Monash University, Clayton, Victoria, 3800, Australia
| | - Liping Wen
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Lei Jiang
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
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27
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Zhu L, Xu Y, Ali I, Liu L, Wu H, Lu Z, Liu Q. Solid-State Nanopore Single-Molecule Sensing of DNAzyme Cleavage Reaction Assisted with Nucleic Acid Nanostructure. ACS APPLIED MATERIALS & INTERFACES 2018; 10:26555-26565. [PMID: 30016075 DOI: 10.1021/acsami.8b09505] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The detection and investigation of biomolecules at a single-molecule level is important for improving diagnosis in biomedicine. Solid-state nanopores are a unique tool that have the potential to accomplish this task because they are label-free and require only low sample consumption. However, the event-readouts of current small polymer molecules are still limited because of its relatively large size and low signal-to-noise ratios. Here, we present a rapid sensing approach for the detection of GR-5 DNAzyme cleaving specific substrate reactions using relatively larger size silicon nitride nanopores by introducing a type of nucleic acid nanostructure (DNA tetrahedron) as a carrier. The proposed method is convenient and sensitive enough to detect the cleavage reactions by identifying translocation events before and after reactions with nanomolar concentrations of the target sample. Furthermore, this assay was also carried out by using larger size nanopores (60 nm diameter) to achieve the DNAzyme cleavage sensing with the same sample concentration. This approach can improve event detectability of other smaller molecules' translocation, which opens up a wide range of applications for analytes detection by incorporating solid-state nanopores. Nucleic acid nanostructure-assisted nanopore sensing can promote the development of single-molecule studies.
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Affiliation(s)
- Libo Zhu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , No. 2, Sipailou , Nanjing 210096 , People's Republic of China
| | - Ying Xu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , No. 2, Sipailou , Nanjing 210096 , People's Republic of China
| | - Irshad Ali
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , No. 2, Sipailou , Nanjing 210096 , People's Republic of China
| | - Liping Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , No. 2, Sipailou , Nanjing 210096 , People's Republic of China
- Guizhou Institute of Technology , Guiyang , Guizhou 550003 , People's Republic of China
| | - Hongwen Wu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , No. 2, Sipailou , Nanjing 210096 , People's Republic of China
- Department of Medical Devices , First Affiliated Hospital of Nanchang University , Nanchang 330006 , China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , No. 2, Sipailou , Nanjing 210096 , People's Republic of China
| | - Quanjun Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , No. 2, Sipailou , Nanjing 210096 , People's Republic of China
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