51
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Ying YL, Long YT. Nanopore-Based Single-Biomolecule Interfaces: From Information to Knowledge. J Am Chem Soc 2019; 141:15720-15729. [DOI: 10.1021/jacs.8b11970] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
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52
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Luo MB, Wu F, Zhang S, Sun LZ. Effect of temperature on the escape of charged polymer chain from a repulsive nanopore. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1629435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Meng-Bo Luo
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Department of Physics, Zhejiang University, Hangzhou, People’s Republic of China
| | - Fan Wu
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Department of Physics, Zhejiang University, Hangzhou, People’s Republic of China
| | - Shuang Zhang
- College of Science, Beibu Gulf University, Qinzhou, People’s Republic of China
| | - Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou, People’s Republic of China
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53
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Guo X, Wetzel KS, Solleder SC, Spann S, Meier MAR, Wilhelm M, Luy B, Guthausen G. 1
H PFG‐NMR Diffusion Study on a Sequence‐Defined Macromolecule: Confirming Monodispersity. MACROMOL CHEM PHYS 2019. [DOI: 10.1002/macp.201900155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xiaoai Guo
- Institute for Chemical Technology and Polymer Chemistry Karlsruhe Institute of Technology (KIT) Engesserstrasse 18 76128 Karlsruhe Germany
| | - Katharina S. Wetzel
- Institute of Organic Chemistry (IOC) Materialwissenschaftliches Zentrum (MZE) Karlsruhe Institute of Technology (KIT) Strasse am Forum 7 76131 Karlsruhe Germany
| | - Susanne C. Solleder
- Institute of Organic Chemistry (IOC) Materialwissenschaftliches Zentrum (MZE) Karlsruhe Institute of Technology (KIT) Strasse am Forum 7 76131 Karlsruhe Germany
| | - Sebastian Spann
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 Karlsruhe Institute of Technology (KIT) Fritz‐Haber‐Weg 6 76131 Karlsruhe Germany
| | - Michael A. R. Meier
- Institute of Organic Chemistry (IOC) Materialwissenschaftliches Zentrum (MZE) Karlsruhe Institute of Technology (KIT) Strasse am Forum 7 76131 Karlsruhe Germany
| | - Manfred Wilhelm
- Institute for Chemical Technology and Polymer Chemistry Karlsruhe Institute of Technology (KIT) Engesserstrasse 18 76128 Karlsruhe Germany
| | - Burkhard Luy
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 Karlsruhe Institute of Technology (KIT) Fritz‐Haber‐Weg 6 76131 Karlsruhe Germany
| | - Gisela Guthausen
- Institute for Mechanical Process Engineering and Mechanics and Engler‐Bunte‐Institut Chair of Water Chemistry and Water Technology Karlsruhe Institute of Technology (KIT) Adenauerring 20b 76131 Karlsruhe Germany
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54
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Li MY, Wang YQ, Lu Y, Ying YL, Long YT. Single Molecule Study of Hydrogen Bond Interactions Between Single Oligonucleotide and Aerolysin Sensing Interface. Front Chem 2019; 7:528. [PMID: 31417894 PMCID: PMC6684785 DOI: 10.3389/fchem.2019.00528] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 07/11/2019] [Indexed: 01/06/2023] Open
Abstract
The aerolysin nanopore displays a charming sensing capability for single oligonucleotide discrimination. When reading from the electrochemical signal, stronger interaction between the aerolysin nanopore and oligonucleotide represent prolonged duration time, thereby amplifying the hidden but intrinsic signal thus improving the sensitivity. In order to further understand and optimize the performance of the aerolysin nanopore, we focus on the investigation of the hydrogen bond interaction between nanopore, and analytes. Taking advantage of site-direct mutagenesis, single residue is replaced. According to whole protein sequence screening, the region near K238 is one of the key sensing regions. Such a positively charged amino acid is then mutagenized into cysteine and tyrosine denoted as K238C, and K238Y. As (dA)4 traverses the pores, K238C dramatically produces a six times longer duration time than the WT aerolysin nanopore at the voltage of +120 mV. However, K238Y shortens the dwell time which suggests the acceleration of the translocation causing poor sensitivity. Referring to our previous findings in K238G, and K238F, our results suggest that the hydrogen bond does not dominate the dynamic translocation process, but enhances the interaction between pores and analytes confined in such nanopore space. These insights give detailed information for the rational design of the sensing mechanism of the aerolysin nanopore, thereby providing further understanding for the weak interactions between biomolecules and the confined space for nanopore sensing.
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Affiliation(s)
- Meng-Yin Li
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Ya-Qian Wang
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Yao Lu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Yi-Lun Ying
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China.,State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Yi-Tao Long
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China.,State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
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55
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Niu H, Zhang W, Wei L, Liu M, Liu H, Zhao C, Zhang P, Liao Q, Liu Y, Yuan Q, Wu S, Kang M, Geng J. Rapid Nanopore Assay for Carbapenem-Resistant Klebsiella pneumoniae. Front Microbiol 2019; 10:1672. [PMID: 31417504 PMCID: PMC6682601 DOI: 10.3389/fmicb.2019.01672] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 07/08/2019] [Indexed: 02/05/2023] Open
Abstract
The prevalence of carbapenem-resistant Klebsiella pneumoniae (CRKP) is rapidly increasing worldwide in recent decades and poses a challenge for today's clinical practice. Rapid detection of CRKP can avoid inappropriate antimicrobial therapy and save lives. Traditional detection methods for CRKP are extremely time-consuming; PCR and other sequencing methods are too expensive and technologically demanding, making it hard to meet the clinical demands. Nanopore assay has been used for screening biomarkers of diseases recently because of its high sensitivity, real-time detection, and low cost. In this study, we distinguished CRKP from carbapenem-sensitive K. pneumoniae (CSKP) by the detection of increasing amount of extracted 16S ribosomal RNA (16S rRNA) from bacterial culture with antibiotics imipenem, indicating the uninhibited growth of CRKP by the imipenem. Specific signals from single channel recording of 16S rRNA bound with probes by MspA nanopore allowed the ultra-sensitive and fast quantitative detection of 16S rRNA. We proved that only 4 h of CRKP culture time was needed for nanopore assay to distinguish the CRKP and CSKP. The time-cost of the assay is only about 5% of disk diffusion method while reaching the similar accuracy. This new method has the potential application in the fast screening of drug resistance in clinical microorganism samples.
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Affiliation(s)
- Haofu Niu
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
- Department of Microbiology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Weili Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Liangwan Wei
- Department of Microbiology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Meng Liu
- Department of Microbiology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Hao Liu
- Department of Microbiology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Changjian Zhao
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Peng Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Quanfeng Liao
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Ya Liu
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Qingyue Yuan
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Siying Wu
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Mei Kang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
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56
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Liu YM, Fang XY, Fang F, Wu ZY. Investigation of hairpin DNA and chelerythrine interaction by a single bio-nanopore sensing interface. Analyst 2019; 144:4081-4085. [PMID: 31169284 DOI: 10.1039/c9an00113a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Chelerythrine (CHE) is one of the potential drugs for cancer treatments. The interaction between hairpin DNA and CHE has been investigated by spectral and mass spectrometry methods. In this paper, the stability of hairpin DNA with different loop bases and its interaction with CHE were explored with a single α-hemolysin (α-HL) nanopore sensing interface. The results showed that the characteristic current pulses not only relate to the loop composition changes of the hairpin DNA, but also provide interaction information between CHE and the hairpin DNA molecules. The dwell time of current pulses for hairpin DNA was significantly increased (hundreds of ms) due to the addition of CHE, and two characteristic current distributions were recognized for the hairpin with T3 and C3 loops. The two characteristic current groups could be ascribed to the hairpin DNA and the ones with CHE. This study indicates that it is possible to study the interaction between single CHE and single hairpin DNA molecules by the single-nanopore sensing interface as an alternative method to conventional spectrometric methods for therapeutic mechanism and drug screening purposes.
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Affiliation(s)
- Yuan-Min Liu
- Research Center for Analytical Sciences, Chemistry Department, College of Sciences, Northeastern University, Shenyang 110819, China.
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57
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Gao R, Lin Y, Ying YL, Hu YX, Xu SW, Ruan LQ, Yu RJ, Li YJ, Li HW, Cui LF, Long YT. Wireless nanopore electrodes for analysis of single entities. Nat Protoc 2019; 14:2015-2035. [PMID: 31168087 DOI: 10.1038/s41596-019-0171-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 04/02/2019] [Indexed: 11/09/2022]
Abstract
Measurements of a single entity underpin knowledge of the heterogeneity and stochastics in the behavior of molecules, nanoparticles, and cells. Electrochemistry provides a direct and fast method to analyze single entities as it probes electron/charge-transfer processes. However, a highly reproducible electrochemical-sensing nanointerface is often hard to fabricate because of a lack of control of the fabrication processes at the nanoscale. In comparison with conventional micro/nanoelectrodes with a metal wire inside, we present a general and easily implemented protocol that describes how to fabricate and use a wireless nanopore electrode (WNE). Nanoscale metal deposition occurs at the tip of the nanopipette, providing an electroactive sensing interface. The WNEs utilize a dynamic ionic flow instead of a metal wire to sense the interfacial redox process. WNEs provide a highly controllable interface with a 30- to 200-nm diameter. This protocol presents the construction and characterization of two types of WNEs-the open-type WNE and closed-type WNE-which can be used to achieve reproducible electrochemical measurements of single entities. Combined with the related signal amplification mechanisms, we also describe how WNEs can be used to detect single redox molecules/ions, analyze the metabolism of single cells, and discriminate single nanoparticles in a mixture. This protocol is broadly applicable to studies of living cells, nanomaterials, and sensors at the single-entity level. The total time required to complete the protocol is ~10-18 h. Each WNE costs ~$1-$3.
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Affiliation(s)
- Rui Gao
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Yao Lin
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Yi-Lun Ying
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China. .,School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China.
| | - Yong-Xu Hu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Su-Wen Xu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Lin-Qi Ruan
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Ru-Jia Yu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Yuan-Jie Li
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Hao-Wen Li
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Ling-Fei Cui
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Yi-Tao Long
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China.,School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
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58
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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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59
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Furuhata T, Ohshiro T, Akimoto G, Ueki R, Taniguchi M, Sando S. Highly Conductive Nucleotide Analogue Facilitates Base-Calling in Quantum-Tunneling-Based DNA Sequencing. ACS NANO 2019; 13:5028-5035. [PMID: 30888791 DOI: 10.1021/acsnano.9b01250] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Quantum-tunneling-based DNA sequencing is a single molecular technology that has great potential for achieving facile and high-throughput DNA sequencing. In principle, the sequence of DNA could be read out by the time trace of the tunnel current that can be changed according to molecular conductance of nucleobases passing through nanosized gap electrodes. However, efficient base-calling of four genetic alphabets has been seriously impeded due to the similarity of molecular conductance among canonical nucleotides. In this article, we demonstrate that replacement of canonical 2'-deoxyadenosine (dA) with a highly conductive dA analogue, 7-deaza dA, could expand the difference of molecular conductance between four genetic alphabets. Additionally, systematic evaluation of molecular conductance using a series of dA and dG analogues revealed that molecular conductance of the nucleotide is highly dependent on the HOMO level. Thus, the present study demonstrating that signal characteristics of the nucleotide can be modulated based on the HOMO level provides a widely applicable chemical approach and insight for facilitation of single molecular sensing as well as DNA sequencing based on quantum tunneling.
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Affiliation(s)
- Takafumi Furuhata
- Department of Chemistry and Biotechnology, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
| | - Takahito Ohshiro
- The Institute of Scientific and Industrial Research , Osaka University , 8-1 Mihogaoka , Ibaraki , Osaka 567-0047 , Japan
| | - Gaku Akimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
| | - Ryosuke Ueki
- Department of Chemistry and Biotechnology, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
| | - Masateru Taniguchi
- The Institute of Scientific and Industrial Research , Osaka University , 8-1 Mihogaoka , Ibaraki , Osaka 567-0047 , Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
- Department of Bioengineering, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
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60
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Liu L, Fang Z, Zheng X, Xi D. Nanopore-Based Strategy for Sensing of Copper(II) Ion and Real-Time Monitoring of a Click Reaction. ACS Sens 2019; 4:1323-1328. [PMID: 31050287 DOI: 10.1021/acssensors.9b00236] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A straightforward yet efficient, nanopore-based strategy that enables the sensitive detection of copper(II) ion (Cu2+) and real-time monitoring of a click reaction is provided. Two single-stranded DNAs (ssDNAs) are designed to act as the preprobes, one being modified with an azide and the other an alkyne. The presence of Cu2+ induces the ligation of two ssDNAs via click reaction, leading to the formation of a forked DNA which can quantitatively generate characteristic current signatures when interacts with α-hemolysin (α-HL) nanopore. The assay facilitates a highly selective and sensitive measurement of Cu2+ without the need for labels or signal amplification. More importantly, this nanopore platform exhibits excellent performance in real-time monitoring of a copper(I) ion (Cu+)-catalyzed click reaction at the single-molecule level, by recording the current signals of the forked DNA generated by click chemistry. The proposed strategy is believed to play an important role in both nanopore sensing and characterization of chemistry reactions, especially coupling reactions.
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Affiliation(s)
- Liping Liu
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, P. R. China
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Zhen Fang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Xiangjiang Zheng
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Dongmei Xi
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
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61
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Ultrasensitive detection of microRNA using an array of Au nanowires deposited within the channels of a porous anodized alumina membrane. Electrochem commun 2019. [DOI: 10.1016/j.elecom.2019.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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62
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Qiu K, Fato TP, Yuan B, Long YT. Toward Precision Measurement and Manipulation of Single-Molecule Reactions by a Confined Space. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1805426. [PMID: 30924293 DOI: 10.1002/smll.201805426] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/28/2019] [Indexed: 06/09/2023]
Abstract
All chemical reactions can be divided into a series of single molecule reactions (SMRs), the elementary steps that involve only isomerization of, dissociation from, and addition to an individual molecule. Analyzing SMRs is of paramount importance to identify the intrinsic molecular mechanism of a complex chemical reaction, which is otherwise implausible to reveal in an ensemble fashion, owing to the significant static and dynamic heterogeneity of real-world chemical systems. The single-molecule measurement and manipulation methods developed recently are playing an increasingly irreplaceable role to detect and recognize short-lived intermediates, visualize their transient existence, and determinate the kinetics and dynamics of single bond breaking and formation. Notably, none of the above SMRs characterizations can be realized without the aid of a confined space. Therefore, this Review aims to highlight the recent progress in the development of confined space enabled single-molecule sensing, imaging, and tuning methods to study chemical reactions. Future prospects of SMRs research are also included, including a push toward the physical limit on transduction of information to signals and vice versa, transmission and recording of signals, computational modeling and simulation, and rational design of a confined space for precise SMRs.
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Affiliation(s)
- Kaipei Qiu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Tano Patrice Fato
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Bo Yuan
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Yi-Tao Long
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
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63
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Hsu JP, Chen YM, Lin CY, Tseng S. Electrokinetic ion transport in an asymmetric double-gated nanochannel with a pH-tunable zwitterionic surface. Phys Chem Chem Phys 2019; 21:7773-7780. [PMID: 30918928 DOI: 10.1039/c9cp00266a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Bioinspired, artificial functional nanochannels for intelligent molecular and ionic transport control have versatile potential applications in nanofluidics, energy conversion, and controlled drug release. To simulate the gating and rectification functions of biological ion channels, we model the electrokinetic ion transport phenomenon in an asymmetric double-gated nanochannel having a pH-regulated, zwitterionic surface. Taking account of the effect of electroosmotic flow (EOF), the conductance of the nanochannel and its ion current rectification (ICR) behavior are investigated and the associated mechanisms interpreted. In particular, the influences of the solution pH, the bulk salt concentration, and the base opening radius and the surface curvature of the nanochannel on these behaviors are examined. We show that through adjusting the base opening radius and the surface curvature of a nanochannel, its ICR behavior can be tuned effectively. In addition to proposing underlying mechanisms for the phenomena observed, the results gathered in this study also provide necessary information for designing relevant devices.
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Affiliation(s)
- Jyh-Ping Hsu
- Department of Chemical Engineering, National Taiwan University, Taipei, 10617, Taiwan.
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64
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You Y, Zhou K, Guo B, Liu Q, Cao Z, Liu L, Wu HC. Measuring Binding Constants of Cucurbituril-Based Host-Guest Interactions at the Single-Molecule Level with Nanopores. ACS Sens 2019; 4:774-779. [PMID: 30865423 DOI: 10.1021/acssensors.9b00408] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cucurbiturils are one type of widely used macrocyclic host compound in supramolecular chemistry. Their peculiar properties have led to applications in a wide variety of research areas such as fluorescence spectroscopy, drug delivery, catalysis, and nanotechnology. However, the solubilities of cucurbiturils are rather poor in water and many organic solvents, which may cause accuracy problems when measuring binding constants with traditional methods. In this report, we aim to develop an approach to measure the binding constants of cucurbituril-based host-guest interactions at the single-molecule level. First, we covalently attach different guest compounds to the side-chain of DNA molecules. Then, excess cucurbiturils are incubated with DNA probes to form the host-guest complexes. Next, the modified DNA hybrids are threaded through α-hemolysin nanopore to generate highly characteristic current events. Finally, statistical analyses of the obtained events afford the binding constants of cucurbiturils with various molecules. This new approach provides a simple and straightforward method to compare binding strength of different host-guest complexes and may find applications for quantifying other macrocycle-based host-guest interactions.
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Affiliation(s)
- Yi You
- Collaborative Innovation Center of Micro/nano Bio-sensing and Food Safety Inspection, Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha 410114, China
| | - Ke Zhou
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Bingyuan Guo
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Quansheng Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Multidisciplinary Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Zhong Cao
- Collaborative Innovation Center of Micro/nano Bio-sensing and Food Safety Inspection, Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha 410114, China
| | - Lei Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Multidisciplinary Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Hai-Chen Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
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65
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Biomimetic Membranes with Transmembrane Proteins: State-of-the-Art in Transmembrane Protein Applications. Int J Mol Sci 2019; 20:ijms20061437. [PMID: 30901910 PMCID: PMC6472214 DOI: 10.3390/ijms20061437] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/26/2019] [Accepted: 03/13/2019] [Indexed: 12/14/2022] Open
Abstract
In biological cells, membrane proteins are the most crucial component for the maintenance of cell physiology and processes, including ion transportation, cell signaling, cell adhesion, and recognition of signal molecules. Therefore, researchers have proposed a number of membrane platforms to mimic the biological cell environment for transmembrane protein incorporation. The performance and selectivity of these transmembrane proteins based biomimetic platforms are far superior to those of traditional material platforms, but their lack of stability and scalability rule out their commercial presence. This review highlights the development of transmembrane protein-based biomimetic platforms for four major applications, which are biosensors, molecular interaction studies, energy harvesting, and water purification. We summarize the fundamental principles and recent progress in transmembrane protein biomimetic platforms for each application, discuss their limitations, and present future outlooks for industrial implementation.
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66
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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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67
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Yu R, Ying Y, Gao R, Long Y. Confined Nanopipette Sensing: From Single Molecules, Single Nanoparticles, to Single Cells. Angew Chem Int Ed Engl 2019; 58:3706-3714. [DOI: 10.1002/anie.201803229] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 05/25/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Ru‐Jia Yu
- Key Laboratory for Advanced MaterialsSchool of Chemistry & Molecular EngineeringEast China University of Science and Technology Shanghai 200237 P. R. China
| | - Yi‐Lun Ying
- Key Laboratory for Advanced MaterialsSchool of Chemistry & Molecular EngineeringEast China University of Science and Technology Shanghai 200237 P. R. China
| | - Rui Gao
- Key Laboratory for Advanced MaterialsSchool of Chemistry & Molecular EngineeringEast China University of Science and Technology Shanghai 200237 P. R. China
| | - Yi‐Tao Long
- Key Laboratory for Advanced MaterialsSchool of Chemistry & Molecular EngineeringEast China University of Science and Technology Shanghai 200237 P. R. China
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68
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Sui XJ, Li MY, Ying YL, Yan BY, Wang HF, Zhou JL, Gu Z, Long YT. Aerolysin Nanopore Identification of Single Nucleotides Using the AdaBoost Model. JOURNAL OF ANALYSIS AND TESTING 2019. [DOI: 10.1007/s41664-019-00088-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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69
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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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70
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Wang J, Bafna JA, Bhamidimarri SP, Winterhalter M. Permeation von kleinen Molekülen durch Membrankanäle: Chemische Modifikation zur Quantifizierung des Transports über OmpF. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201814489] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jiajun Wang
- Department of Life Sciences und Chemistry Jacobs University Campus Ring 1 28759 Bremen Deutschland
| | - Jayesh Arun Bafna
- Department of Life Sciences und Chemistry Jacobs University Campus Ring 1 28759 Bremen Deutschland
| | | | - Mathias Winterhalter
- Department of Life Sciences und Chemistry Jacobs University Campus Ring 1 28759 Bremen Deutschland
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71
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Wang J, Bafna JA, Bhamidimarri SP, Winterhalter M. Small‐Molecule Permeation across Membrane Channels: Chemical Modification to Quantify Transport across OmpF. Angew Chem Int Ed Engl 2019; 58:4737-4741. [DOI: 10.1002/anie.201814489] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Jiajun Wang
- Department of Life Sciences and Chemistry Jacobs University Campus Ring 1 28759 Bremen Germany
| | - Jayesh Arun Bafna
- Department of Life Sciences and Chemistry Jacobs University Campus Ring 1 28759 Bremen Germany
| | | | - Mathias Winterhalter
- Department of Life Sciences and Chemistry Jacobs University Campus Ring 1 28759 Bremen Germany
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72
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Wang J, Yang J, Ying YL, Long YT. Nanopore-Based Confined Spaces for Single-Molecular Analysis. Chem Asian J 2019; 14:389-397. [PMID: 30548206 DOI: 10.1002/asia.201801648] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/09/2018] [Indexed: 11/07/2022]
Abstract
The field of nanopore sensing at the single-molecular level is in a "boom" period. Such nanopores, which are either composed of biological materials or are fabricated from solid-state substrates, offer a unique confined space that is compatible with the single-molecular scale. Under the influence of an electrical field, such single-biomolecular interfaces can read single-molecular information and, if appropriately fine-tuned, each molecule plays its individual ionic rhythm to compose a "molecular symphony". Over the past few decades, many research groups have worked on nanopore-based single-molecular sensors for a range of thrilling chemical and clinical applications. Furthermore, for the past decade, we have also focused on nanopore-based sensors. In this Minireview, we summarize the recent developments in fundamental research and applications in this area, along with data algorithms and advances in hardware, which act as infrastructure for the electrochemical analysis.
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Affiliation(s)
- Jiajun Wang
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Jie Yang
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
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73
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Yang C, Wang H, Tang H, Zhao D, Li Y. A simple strategy for the fabrication of gold-modified single nanopores and its application for miRNA sensing. Chem Commun (Camb) 2019; 55:10288-10291. [DOI: 10.1039/c9cc04864b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A simple strategy was developed for nanopore modification, and was used for miRNA sensing with good sensitivity and selectivity.
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Affiliation(s)
- Cheng Yang
- Anhui Key Laboratory of Chemo/Biosensing
- College of Chemistry and Materials Science
- Anhui Normal University
- Wuhu
- P. R. China
| | - Hao Wang
- Anhui Key Laboratory of Chemo/Biosensing
- College of Chemistry and Materials Science
- Anhui Normal University
- Wuhu
- P. R. China
| | - Haoran Tang
- Anhui Key Laboratory of Chemo/Biosensing
- College of Chemistry and Materials Science
- Anhui Normal University
- Wuhu
- P. R. China
| | - Dandan Zhao
- Anhui Key Laboratory of Chemo/Biosensing
- College of Chemistry and Materials Science
- Anhui Normal University
- Wuhu
- P. R. China
| | - Yongxin Li
- Anhui Key Laboratory of Chemo/Biosensing
- College of Chemistry and Materials Science
- Anhui Normal University
- Wuhu
- P. R. China
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74
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Chen Z, Sun T, Qing G. cAMP-modulated biomimetic ionic nanochannels based on a smart polymer. J Mater Chem B 2019. [DOI: 10.1039/c9tb00639g] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dynamic gating behaviour of ionic nanochannel is precisely manipulated by cyclic 3′,5′-adenosine monophosphate (cAMP) by taking advantage of reversible conformational transition of the smart polymer chains in response to cAMP specific adsorption, which provides a new idea for developing smart nanochannels regulated by crucial signal-biomolecules.
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Affiliation(s)
- Zhixiang Chen
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing
- Wuhan University of Technology
- Wuhan 430070
- P. R. China
- Key Laboratory of Separation Science for Analytical Chemistry
| | - Taolei Sun
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing
- Wuhan University of Technology
- Wuhan 430070
- P. R. China
| | - Guangyan Qing
- Key Laboratory of Separation Science for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- P. R. China
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75
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Zhang X, Zhang L, Li J. Peptide-modified nanochannel system for carboxypeptidase B activity detection. Anal Chim Acta 2019; 1057:36-43. [DOI: 10.1016/j.aca.2019.01.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 01/08/2019] [Accepted: 01/15/2019] [Indexed: 10/27/2022]
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76
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Yu R, Ying Y, Gao R, Long Y. Detektieren mit Nanopipetten im eingeschränkten Raum: von einzelnen Molekülen über Nanopartikel hin zu der Zelle. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803229] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Ru‐Jia Yu
- Key Laboratory for Advanced MaterialsSchool of Chemistry & Molecular EngineeringEast China University of Science and Technology Shanghai 200237 VR China
| | - Yi‐Lun Ying
- Key Laboratory for Advanced MaterialsSchool of Chemistry & Molecular EngineeringEast China University of Science and Technology Shanghai 200237 VR China
| | - Rui Gao
- Key Laboratory for Advanced MaterialsSchool of Chemistry & Molecular EngineeringEast China University of Science and Technology Shanghai 200237 VR China
| | - Yi‐Tao Long
- Key Laboratory for Advanced MaterialsSchool of Chemistry & Molecular EngineeringEast China University of Science and Technology Shanghai 200237 VR China
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77
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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 2018; 10:1953-1961. [PMID: 30881624 PMCID: PMC6385554 DOI: 10.1039/c8sc04875d] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [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
We adapt a solid-state nanopore for analyzing DNA assembly mixtures, which is usually a tougher task for either traditional characterization methods or nanopores themselves. A trigger induced nucleic acid amplifier, SP-CHA, is designed as a model. We propose an electrophoresis-gel like, but homogeneous, quantitative method that can comprehensively profile the “base-pair distribution” of SP-CHA concatemer mixtures.
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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78
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Liu GC, Gao MJ, Chen W, Hu XY, Song LB, Liu B, Zhao YD. pH-modulated ion-current rectification in a cysteine-functionalized glass nanopipette. Electrochem commun 2018. [DOI: 10.1016/j.elecom.2018.09.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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79
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Zhang D, Zhou S, Liu Y, Fan X, Zhang M, Zhai J, Jiang L. Self-Assembled Porphyrin Nanofiber Membrane-Decorated Alumina Channels for Enhanced Photoelectric Response. ACS NANO 2018; 12:11169-11177. [PMID: 30376291 DOI: 10.1021/acsnano.8b05695] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Photoresponsive nanochannel systems whose ionic transportation properties can be controlled by the photoelectric effect, such as for green chlorophyll pigments in plants, are attracting widespread attention. Herein, we prepared photoresponsive heterogeneous nanochannels by decorating self-assembled tetra(4-sulfonatophenyl)porphyrin (TPPS) nanofiber membranes on a membrane of hourglass-shaped alumina (Al2O3) nanochannels using the diffusion-limited patterning (DLP) method. The close arrangement of large-area nanofibers promoted the photoresponse sensitivity of the heterogeneous nanochannels, which showed the highest ionic transportation current. With illumination comparable to sunlight in intensity, the photoresponsive ionic current was approximately 9.7 μA, demonstrating photoswitching, which could be used to regulate the reversible transformation of ionic currents. Meanwhile, the cooperative effect of the TPPS nanofibers assembled at the entrance to the nanochannels and the TPPS molecules inside the nanochannels allowed the heterogeneous nanochannels to exhibit a good rectifying performance.
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Affiliation(s)
- Dan Zhang
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of the Ministry of Education, School of Chemistry , Beihang University , Beijing 100083 , People's Republic of China
| | - Shuqi Zhou
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of the Ministry of Education, School of Chemistry , Beihang University , Beijing 100083 , People's Republic of China
| | - You Liu
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of the Ministry of Education, School of Chemistry , Beihang University , Beijing 100083 , People's Republic of China
| | - Xia Fan
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of the Ministry of Education, School of Chemistry , Beihang University , Beijing 100083 , People's Republic of China
| | - Mingliang Zhang
- Engineering Research Center for Semiconductor Integrated Technology, Institute of Semiconductors , Chinese Academy of Sciences , Beijing 100083 , People's Republic of China
- College of Materials Science and Optoelectronic Technology , University of Chinese Academy of Sciences , Beijing 101408 , People's Republic of China
| | - Jin Zhai
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of the Ministry of Education, School of Chemistry , Beihang University , Beijing 100083 , People's Republic of China
| | - Lei Jiang
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of the Ministry of Education, School of Chemistry , Beihang University , Beijing 100083 , People's Republic of China
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80
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Yi-Tao Long. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/anie.201806950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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81
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Yi-Tao Long. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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82
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Gao P, Ma Q, Ding D, Wang D, Lou X, Zhai T, Xia F. Distinct functional elements for outer-surface anti-interference and inner-wall ion gating of nanochannels. Nat Commun 2018; 9:4557. [PMID: 30385758 PMCID: PMC6212446 DOI: 10.1038/s41467-018-06873-z] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 10/02/2018] [Indexed: 12/18/2022] Open
Abstract
Over the decades, widespread advances have been achieved on nanochannels, including nanochannel-based DNA sequencing, single-molecule detection, smart sensors, and energy transfer and storage. However, most interest has been focused on the contribution from the functional elements (FEs) at the inner wall (IW) of nanochannels, whereas little attention has been paid to the contribution from the FEs at the nanochannels' outer surface (OS). Herein, we achieve explicit partition of FEOS and FEIW based on accurate regional-modification of OS and IW. The FEIW are served for ionic gating, and the chosen FEOS (hydrophobic or charged) are served for blocking interference molecules into the nanochannels, decreasing the false signals for the ionic gating in complex environments. Furthermore, we define a composite factor, areas of a radar map, to evaluate the FEOS performance for blocking interference molecules.
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Affiliation(s)
- Pengcheng Gao
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences (CUG), 388 lumo Road, 430074, Wuhan, China
| | - Qun Ma
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences (CUG), 388 lumo Road, 430074, Wuhan, China
| | - Defang Ding
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences (CUG), 388 lumo Road, 430074, Wuhan, China
| | - Dagui Wang
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences (CUG), 388 lumo Road, 430074, Wuhan, China
| | - Xiaoding Lou
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences (CUG), 388 lumo Road, 430074, Wuhan, China
| | - Tianyou Zhai
- State Key Laboratory of Material Processing and Die & Mould Technology, School of Material Sciences and Engineering, Huazhong University of Science and Technology (HUST), 430074, Wuhan, China
| | - Fan Xia
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences (CUG), 388 lumo Road, 430074, Wuhan, China.
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83
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Zhang D, Wang Q, Fan X, Zhang M, Zhai J, Jiang L. An Effective Dark-Vis-UV Ternary Biomimetic Switching Based on N3/Spiropyran-Modified Nanochannels. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1804862. [PMID: 30284330 DOI: 10.1002/adma.201804862] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 09/07/2018] [Indexed: 06/08/2023]
Abstract
Many natural photomodulated nanochannels are investigated and are crucial for biological activity. Biomimetic nanochannels with a bistable conductance state under light stimulus are demonstrated. In this system, two molecules, cis-bis-(4,4'-dicarboxy-2,2'-bipyridine) dithiocyanato ruthenium(II) (N3) and spiropyran 1'-(3-carboxypropyl)-3',3'-dimethyl-6-nitro-spiro[2H-1]benzopyran-2,2'-indoline (SP-COOH), each with unique photoresponsive properties, are modified in alumina nanochannels. The two segments of the hourglass-shaped alumina nanochannels are designated to graft a certain molecule. Under ultraviolet (UV) or visible light (vis) irradiation, electrons belonging to N3 are excited, resulting in negatively charged surfaces on the sides of nanochannels modified with N3 molecules. Only under UV stimulus, the conformation change of the SP-COOH molecules leads to positively charged surfaces of nanochannels in the SP-COOH occupied sides. Benefiting from the joint effect of N3 and SP-COOH, low, medium, and high (i.e., "0," "1," and "2") ternary levels of ion conductance are established under the dark-vis-UV alternate stimuli. The multistage current switching containing "0-1-2-0" and "0-1-2-1-0" procedures is stable and robust. Additionally, the diode-like ion transport behavior of the nanochannels could be exploited to support a multivalued logical gating with the management of light signals.
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Affiliation(s)
- Dan Zhang
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of the Ministry of Education, School of Chemistry, Beihang University, Beijing, 100083, P. R. China
| | - Qinqin Wang
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of the Ministry of Education, School of Chemistry, Beihang University, Beijing, 100083, P. R. China
| | - Xia Fan
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of the Ministry of Education, School of Chemistry, Beihang University, Beijing, 100083, P. R. China
| | - Mingliang Zhang
- Engineering Research Center for Semiconductor Integrated Technology, Institute of Semiconductors, Chinese Academy of Sciences, Beijing, 100083, P. R. China
- College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing, 101408, P. R. China
| | - Jin Zhai
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of the Ministry of Education, School of Chemistry, Beihang University, Beijing, 100083, P. R. China
| | - Lei Jiang
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of the Ministry of Education, School of Chemistry, Beihang University, Beijing, 100083, P. R. China
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84
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Chen X, Wang L, Roozbahani GM, Zhang Y, Xiang J, Guan X. Nanopore label-free detection of single-nucleotide deletion in Baxα/BaxΔ2. Electrophoresis 2018; 39:2410-2416. [PMID: 29998460 PMCID: PMC6168411 DOI: 10.1002/elps.201800193] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/14/2018] [Accepted: 07/01/2018] [Indexed: 12/13/2022]
Abstract
Baxα, a key tumor suppressor gene, will not be expressed correctly as a result of single nucleotide mutation in its microsatellite region; Instead, BaxΔ2, an isoform of Baxα, is often produced. In addition, lack of the exon 2 due to an alternative splicing, BaxΔ2 has the same sequence as Baxα except single base deletion from eight continuous guanines (G8) to G7. Most of the currently available methods for Bax∆2 detection are inefficient and time-consuming, and/or require the use of labels or dyes. In this work, we reported a label-free nanopore sensing strategy to differentiate between Baxα and BaxΔ2 with a DNA polymer as a molecular probe based on alternative spliced sequences. Two DNA molecules were designed to selectively detect Baxα and BaxΔ2, respectively. The method was rapid, accurate, and highly sensitive: picomolar concentrations of target nucleic acids could be detected in minutes. Our developed simple and fast nanopore-based detection strategy is not only useful for distinguishing between Baxα and Bax∆2, but also provides a useful tool for detection of other single-base mutations in genetic diagnosis.
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Affiliation(s)
- Xiaohan Chen
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Golbarg M Roozbahani
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Youwen Zhang
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Jialing Xiang
- Department of Biology, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL 60616, USA
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85
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Liu Y, Xu C, Yu P, Chen X, Wang J, Mao L. Counting and Sizing of Single Vesicles/Liposomes by Electrochemical Events. ChemElectroChem 2018. [DOI: 10.1002/celc.201800616] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Yang Liu
- Research Center for Analytical Sciences Department of Chemistry, College of SciencesNortheastern University Box 332 Shenyang 110819 China
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of ChemistryThe Chinese Academy of Sciences (CAS) Beijing 100190 China
| | - Cong Xu
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of ChemistryThe Chinese Academy of Sciences (CAS) Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Ping Yu
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of ChemistryThe Chinese Academy of Sciences (CAS) Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Xuwei Chen
- Research Center for Analytical Sciences Department of Chemistry, College of SciencesNortheastern University Box 332 Shenyang 110819 China
| | - Jianhua Wang
- Research Center for Analytical Sciences Department of Chemistry, College of SciencesNortheastern University Box 332 Shenyang 110819 China
| | - Lanqun Mao
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of ChemistryThe Chinese Academy of Sciences (CAS) Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
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86
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Lin Y, Ying YL, Gao R, Long YT. Single-Molecule Sensing with Nanopore Confinement: From Chemical Reactions to Biological Interactions. Chemistry 2018; 24:13064-13071. [DOI: 10.1002/chem.201800669] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Yao Lin
- Key Laboratory for Advanced Materials & School of, Chemistry and Molecular Engineering; East China University of Science and Technology; Shanghai 200237 P.R. China
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials & School of, Chemistry and Molecular Engineering; East China University of Science and Technology; Shanghai 200237 P.R. China
| | - Rui Gao
- Key Laboratory for Advanced Materials & School of, Chemistry and Molecular Engineering; East China University of Science and Technology; Shanghai 200237 P.R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials & School of, Chemistry and Molecular Engineering; East China University of Science and Technology; Shanghai 200237 P.R. China
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87
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Hiratani M, Kawano R. DNA Logic Operation with Nanopore Decoding To Recognize MicroRNA Patterns in Small Cell Lung Cancer. Anal Chem 2018; 90:8531-8537. [DOI: 10.1021/acs.analchem.8b01586] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Moe Hiratani
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
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88
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Yang Q, Ai T, Lv Y, Huang Y, Geng J, Xiao D, Zhou C. Simultaneous Discrimination of Single-Base Mismatch and Full Match Using a Label-Free Single-Molecule Strategy. Anal Chem 2018; 90:8102-8107. [PMID: 29874049 DOI: 10.1021/acs.analchem.8b01285] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Qiufang Yang
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Tingting Ai
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - You Lv
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Yuqin Huang
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Jia Geng
- Department of Laboratory Medicine, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, P. R. China
| | - Dan Xiao
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Cuisong Zhou
- College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
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89
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LIU Y, YAO XF, WANG HY. Protein Detection Through Single Molecule Nanopore. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2018. [DOI: 10.1016/s1872-2040(18)61093-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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90
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ZHOU S, TANG P, WANG YJ, WANG L, WANG DQ. Applications of Nanopore Sensing in Detection of Toxic Molecules. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2018. [DOI: 10.1016/s1872-2040(18)61089-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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91
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Li S, Cao C, Yang J, Long YT. Detection of Peptides with Different Charges and Lengths by Using the Aerolysin Nanopore. ChemElectroChem 2018. [DOI: 10.1002/celc.201800288] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Shuang Li
- Key Laboratory for Advanced Materials School of Chemistry & Molecular Engineering; East China University of Science and Technology; 130 Meilong Road Shanghai 200237 P.R. China
| | - Chan Cao
- Key Laboratory for Advanced Materials School of Chemistry & Molecular Engineering; East China University of Science and Technology; 130 Meilong Road Shanghai 200237 P.R. China
| | - Jie Yang
- Key Laboratory for Advanced Materials School of Chemistry & Molecular Engineering; East China University of Science and Technology; 130 Meilong Road Shanghai 200237 P.R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials School of Chemistry & Molecular Engineering; East China University of Science and Technology; 130 Meilong Road Shanghai 200237 P.R. China
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92
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Ai T, Yang Q, Lv Y, Huang Y, Li Y, Geng J, Xiao D, Zhou C. Insight into How Telomeric G-Quadruplexes Enhance the Peroxidase Activity of Cellular Hemin. Chem Asian J 2018; 13:1805-1810. [PMID: 29718585 DOI: 10.1002/asia.201800464] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 04/30/2018] [Indexed: 02/05/2023]
Abstract
The toxic oxidative damage of G-quadruplexes (G4), linked to neurodegenerative diseases, may arise from their ability to bind and oxidatively activate cellular hemin. However, there have been no precise studies on how telomeric G4 enhances the low intrinsic peroxidase activity of hemin. Herein, a label-free and nanopore-based strategy was developed to explore the enhancement mechanism of peroxidase activity of hemin induced by telomeric G4 (d(TTAGGG)n ). The nanopore-based strategy demonstrated that there were simultaneously two different binding modes of telomere G4 to hemin. At the single-molecule level, it was found that the hybrid structural telomeric G4 directly binds to hemin (the affinity constant (Ka )≈106 m-1 ) to form a tight complex, and some of them underwent a topological change to a parallel structure with an enhancement of Ka to approximately 107 m-1 . Through detailed analysis of the topology and peroxidase activity and molecular modeling investigations, the parallel telomere G4/hemin DNAzyme structure was proven to be preferable for high peroxidase activity. Upon strong π-π stacking, the parallel structural telomere G4 supplied a key axial ligand to the hemin iron, which accelerated the intermediate compound formation with H2 O2 in the catalytic cycle. Our studies developed a label-free and single-molecule strategy to fundamentally understand the catalytic activity and mechanism of telomeric DNAzyme, which provides some support for utilizing the toxic, oxidative-damage property in cellular oxidative disease and anticancer therapeutics.
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Affiliation(s)
- Tingting Ai
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
| | - Qiufang Yang
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
| | - You Lv
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
| | - Yuqin Huang
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
| | - Yuzhi Li
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
| | - Jia Geng
- Department of Laboratory Medicine, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, P.R. China
| | - Dan Xiao
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
| | - Cuisong Zhou
- College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China
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93
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Cavallo G, Poyer S, Amalian J, Dufour F, Burel A, Carapito C, Charles L, Lutz J. Cleavable Binary Dyads: Simplifying Data Extraction and Increasing Storage Density in Digital Polymers. Angew Chem Int Ed Engl 2018; 57:6266-6269. [DOI: 10.1002/anie.201803027] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Gianni Cavallo
- Université de Strasbourg, CNRS Institut Charles Sadron UPR22 23 rue du Loess 67034 Strasbourg Cedex 2 France
| | - Salomé Poyer
- Aix-Marseille Univ., CNRS, UMR 7273 Institute of Radical Chemistry 13397 Marseille Cedex 20 France
| | - Jean‐Arthur Amalian
- Aix-Marseille Univ., CNRS, UMR 7273 Institute of Radical Chemistry 13397 Marseille Cedex 20 France
| | - Florent Dufour
- Université de Strasbourg, CNRS Institut Charles Sadron UPR22 23 rue du Loess 67034 Strasbourg Cedex 2 France
- Université de Strasbourg, CNRS Institut Pluridisciplinaire Hubert Curien UMR7178 25 Rue Becquerel 67087 Strasbourg France
| | - Alexandre Burel
- Université de Strasbourg, CNRS Institut Pluridisciplinaire Hubert Curien UMR7178 25 Rue Becquerel 67087 Strasbourg France
| | - Christine Carapito
- Université de Strasbourg, CNRS Institut Pluridisciplinaire Hubert Curien UMR7178 25 Rue Becquerel 67087 Strasbourg France
| | - Laurence Charles
- Aix-Marseille Univ., CNRS, UMR 7273 Institute of Radical Chemistry 13397 Marseille Cedex 20 France
| | - Jean‐François Lutz
- Université de Strasbourg, CNRS Institut Charles Sadron UPR22 23 rue du Loess 67034 Strasbourg Cedex 2 France
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94
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Cavallo G, Poyer S, Amalian J, Dufour F, Burel A, Carapito C, Charles L, Lutz J. Cleavable Binary Dyads: Simplifying Data Extraction and Increasing Storage Density in Digital Polymers. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803027] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Gianni Cavallo
- Université de Strasbourg, CNRS Institut Charles Sadron UPR22 23 rue du Loess 67034 Strasbourg Cedex 2 France
| | - Salomé Poyer
- Aix-Marseille Univ., CNRS, UMR 7273 Institute of Radical Chemistry 13397 Marseille Cedex 20 France
| | - Jean‐Arthur Amalian
- Aix-Marseille Univ., CNRS, UMR 7273 Institute of Radical Chemistry 13397 Marseille Cedex 20 France
| | - Florent Dufour
- Université de Strasbourg, CNRS Institut Charles Sadron UPR22 23 rue du Loess 67034 Strasbourg Cedex 2 France
- Université de Strasbourg, CNRS Institut Pluridisciplinaire Hubert Curien UMR7178 25 Rue Becquerel 67087 Strasbourg France
| | - Alexandre Burel
- Université de Strasbourg, CNRS Institut Pluridisciplinaire Hubert Curien UMR7178 25 Rue Becquerel 67087 Strasbourg France
| | - Christine Carapito
- Université de Strasbourg, CNRS Institut Pluridisciplinaire Hubert Curien UMR7178 25 Rue Becquerel 67087 Strasbourg France
| | - Laurence Charles
- Aix-Marseille Univ., CNRS, UMR 7273 Institute of Radical Chemistry 13397 Marseille Cedex 20 France
| | - Jean‐François Lutz
- Université de Strasbourg, CNRS Institut Charles Sadron UPR22 23 rue du Loess 67034 Strasbourg Cedex 2 France
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95
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Chen X, Roozbahani GM, Ye Z, Zhang Y, Ma R, Xiang J, Guan X. Label-Free Detection of DNA Mutations by Nanopore Analysis. ACS APPLIED MATERIALS & INTERFACES 2018; 10:11519-11528. [PMID: 29537824 PMCID: PMC6760912 DOI: 10.1021/acsami.7b19774] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Cancers are caused by mutations to genes that regulate cell normal functions. The capability to rapid and reliable detection of specific target gene variations can facilitate early disease detection and diagnosis and also enables personalized treatment of cancer. Most of the currently available methods for DNA mutation detection are time-consuming and/or require the use of labels or sophisticated instruments. In this work, we reported a label-free enzymatic reaction-based nanopore sensing strategy to detect DNA mutations, including base substitution, deletion, and insertion. The method was rapid and highly sensitive with a detection limit of 4.8 nM in a 10 min electrical recording. Furthermore, the nanopore assay could differentiate among perfect match, one mismatch, and two mismatches. In addition, simulated serum samples were successfully analyzed. Our developed nanopore-based DNA mutation detection strategy should find useful application in genetic diagnosis.
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Affiliation(s)
- Xiaohan Chen
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA
| | - Golbarg M Roozbahani
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA
| | - Zijing Ye
- Department of Biology, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA
| | - Youwen Zhang
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA
| | - Rui Ma
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA
| | - Jialing Xiang
- Department of Biology, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA
- Corresponding author: Tel: 312-567-8922. Fax: 312-567-3494.
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96
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97
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Liu Y, Xu C, Chen X, Wang J, Yu P, Mao L. Voltage-driven counting of phospholipid vesicles with nanopipettes by resistive-pulse principle. Electrochem commun 2018. [DOI: 10.1016/j.elecom.2018.02.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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98
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Abstract
Bioinspired smart asymmetric nanochannel membranes (BSANM) have been explored extensively to achieve the delicate ionic transport functions comparable to those of living organisms. The abiotic system exhibits superior stability and robustness, allowing for promising applications in many fields. In view of the abundance of research concerning BSANM in the past decade, herein, we present a systematic overview of the development of the state-of-the-art BSANM system. The discussion is focused on the construction methodologies based on raw materials with diverse dimensions (i.e. 0D, 1D, 2D, and bulk). A generic strategy for the design and construction of the BSANM system is proposed first and put into context with recent developments from homogeneous to heterogeneous nanochannel membranes. Then, the basic properties of the BSANM are introduced including selectivity, gating, and rectification, which are associated with the particular chemical and physical structures. Moreover, we summarized the practical applications of BSANM in energy conversion, biochemical sensing and other areas. In the end, some personal opinions on the future development of the BSANM are briefly illustrated. This review covers most of the related literature reported since 2010 and is intended to build up a broad and deep knowledge base that can provide a solid information source for the scientific community.
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Affiliation(s)
- Zhen Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Green Printing, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
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99
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Cai H, Zhou C, Yang Q, Ai T, Huang Y, Lv Y, Geng J, Xiao D. Single-molecule investigation of human telomeric G-quadruplex interactions with Thioflavin T. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2017.09.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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100
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Shang J, Li Z, Liu L, Xi D, Wang H. Label-Free Sensing of Human 8-Oxoguanine DNA Glycosylase Activity with a Nanopore. ACS Sens 2018; 3:512-518. [PMID: 29363311 DOI: 10.1021/acssensors.7b00954] [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] [Indexed: 12/27/2022]
Abstract
Human 8-oxoguanine DNA glycosylase (hOGG1) plays a significant role in maintaining the genomic integrity of living organisms for its capability of repairing DNA lesions. Accurate detection of hOGG1 activity would greatly facilitate the screening and early diagnosis of diseases. In this work, we report a nanopore-based sensing strategy to probe the hOGG1 activity by employing the enzyme-catalytic cleavage reaction of DNA substrate. The hOGG1 specifically catalyzed the removal of the 8-hydroxyguanine (8-oxoG) and cleaved the DNA substrates immobilized on magnetic beads, thereby releasing the output DNA which would quantitatively produce the signature current events when subjected to α-hemolysin (α-HL) nanopore test. The approach enables the sensitive detection of hOGG1 activity without the need of any labeling or signal amplification route. Furthermore, the method can be applied to assay the inhibition of hOGG1 and evaluate the activity of endogenous hOGG1 in crude cell extracts. Importantly, since DNAs with specific sequences are the catalytic substrates of a wide variety of enzymes, the proposed strategy should be universally applicable for probing the activities of different types of enzymes with nanopore sensors.
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Affiliation(s)
- Jizhen Shang
- Shandong
Provincial Key Laboratory of Detection Technology for Tumor Makers,
College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
- Institute
of Medicine and Materials Application Technologies, College of Chemistry
and Chemical Engineering, Qufu Normal University, Qufu 273165, P. R. China
| | - Zhi Li
- Shandong
Provincial Key Laboratory of Detection Technology for Tumor Makers,
College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Liping Liu
- Shandong
Provincial Key Laboratory of Detection Technology for Tumor Makers,
College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Dongmei Xi
- Shandong
Provincial Key Laboratory of Detection Technology for Tumor Makers,
College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Hua Wang
- Institute
of Medicine and Materials Application Technologies, College of Chemistry
and Chemical Engineering, Qufu Normal University, Qufu 273165, P. R. China
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