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Wang R, Zhang Y, Ma QDY, Wu L. Recent advances of small molecule detection in nanopore sensing. Talanta 2024; 277:126323. [PMID: 38810384 DOI: 10.1016/j.talanta.2024.126323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/04/2024] [Accepted: 05/23/2024] [Indexed: 05/31/2024]
Abstract
Due to its advantages of label-free and highly sensitive, the resistive pulse sensing with a nanopore has recently become even more potent for the discrimination of analytes in single molecule level. Generally, a transient interruption of ion current originated from the captured molecule passing through a nanopore will provide the rich information on the structure, charge and translocation dynamics of the analytes. Therefore, nanopore sensors have been widely used in the fields of DNA sequencing, protein recognition, and the portable detection of varied macromolecules and particles. However, the conventional nanopore devices are still lack of sufficient selectivity and sensitivity to distinguish more metabolic molecules involving ATP, glucose, amino acids and small molecular drugs because it is hard to receive a large number of identifiable signals with the fabricated pores comparable in size to small molecules for nanopore sensing. For all this, a series of innovative strategies developed in the past decades have been summarized in this review, including host-guest recognition, engineering alteration of protein channel, the introduction of nucleic acid aptamers and various delivery carriers integrating signal amplification sections based on the biological and solid nanopore platforms, to achieve the high resolution for the small molecules sensing in micro-nano environment. These works have greatly enhanced the powerful sensing capabilities and extended the potential application of nanopore sensors.
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Affiliation(s)
- Runyu Wang
- College of Science, Nanjing University of Posts and Telecommunications, Nanjing, 210046, China
| | - Yinuo Zhang
- College of Integrated Circuit Science and Engineering, Nanjing University of Posts and Telecommunications, Nanjing, 210046, China
| | - Qianli D Y Ma
- College of Integrated Circuit Science and Engineering, Nanjing University of Posts and Telecommunications, Nanjing, 210046, China.
| | - Lingzhi Wu
- College of Science, Nanjing University of Posts and Telecommunications, Nanjing, 210046, China.
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2
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de la Torre M, Pomorski A. Investigation of metal ion binding biomolecules one molecule at a time. Front Chem 2024; 12:1378447. [PMID: 38680456 PMCID: PMC11045889 DOI: 10.3389/fchem.2024.1378447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/22/2024] [Indexed: 05/01/2024] Open
Abstract
Metal ions can perform multiple roles ranging from regulatory to structural and are crucial for cell function. While some metal ions like Na+ are ubiquitously present at high concentrations, other ions, especially Ca2+ and transition metals, such as Zn2+ or Cu+/2+ are regulated. The concentrations above or below the physiological range cause severe changes in the behavior of biomolecules that bind them and subsequently affect the cell wellbeing. This has led to the development of specialized protocols to study metal ion binding biomolecules in bulk conditions that mimic the cell environment. Recently, there is growing evidence of influence of post-transcriptional and post-translational modifications on the affinity of the metal ion binding sites. However, such targets are difficult to obtain in amounts required for classical biophysical experiments. Single molecule techniques have revolutionized the field of biophysics, molecular and structural biology. Their biggest advantage is the ability to observe each molecule's interaction independently, without the need for synchronization. An additional benefit is its extremely low sample consumption. This feature allows characterization of designer biomolecules or targets obtained coming from natural sources. All types of biomolecules, including proteins, DNA and RNA were characterized using single molecule methods. However, one group is underrepresented in those studies. These are the metal ion binding biomolecules. Single molecule experiments often require separate optimization, due to extremely different concentrations used during the experiments. In this review we focus on single molecule methods, such as single molecule FRET, nanopores and optical tweezers that are used to study metal ion binding biomolecules. We summarize various examples of recently characterized targets and reported experimental conditions. Finally, we discuss the potential promises and pitfalls of single molecule characterization on metal ion binding biomolecules.
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Affiliation(s)
| | - Adam Pomorski
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
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3
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Laucirica G, Toum-Terrones Y, Cayón VM, Toimil-Molares ME, Azzaroni O, Marmisollé WA. Advances in nanofluidic field-effect transistors: external voltage-controlled solid-state nanochannels for stimulus-responsive ion transport and beyond. Phys Chem Chem Phys 2024; 26:10471-10493. [PMID: 38506166 DOI: 10.1039/d3cp06142f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Ion channels, intricate protein structures facilitating precise ion passage across cell membranes, are pivotal for vital cellular functions. Inspired by the remarkable capabilities of biological ion channels, the scientific community has ventured into replicating these principles in fully abiotic solid-state nanochannels (SSNs). Since the gating mechanisms of SSNs rely on variations in the physicochemical properties of the channel surface, the modification of their internal architecture and chemistry constitutes a powerful strategy to control the transport properties and, consequently, render specific functionalities. In this framework, both the design of the nanofluidic platform and the subsequent selection and attachment of different building blocks gain special attention. Similar to biological ion channels, functional SSNs offer the potential to finely modulate ion transport in response to various stimuli, leading to innovations in a variety of fields. This comprehensive review delves into the intricate world of ion transport across stimuli-responsive SSNs, focusing on the development of external voltage-controlled nanofluidic devices. This kind of field-effect nanofluidic technology has attracted special interest due to the possibility of real-time reconfiguration of the ion transport with a non-invasive strategy. These properties have found interesting applications in drug delivery, biosensing, and nanoelectronics. This document will address the fundamental principles of ion transport through SSNs and the construction, modification, and applications of external voltage-controlled SSNs. It will also address future challenges and prospects, offering a comprehensive perspective on this evolving field.
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Affiliation(s)
- G Laucirica
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET - CC 16 Suc. 4, 1900 La Plata, Argentina.
| | - Y Toum-Terrones
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET - CC 16 Suc. 4, 1900 La Plata, Argentina.
| | - V M Cayón
- Department of Materials- and Geosciences, Technical University of Darmstadt, Darmstadt, Germany
| | - M E Toimil-Molares
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany
- Department of Materials- and Geosciences, Technical University of Darmstadt, Darmstadt, Germany
| | - O Azzaroni
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET - CC 16 Suc. 4, 1900 La Plata, Argentina.
| | - W A Marmisollé
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET - CC 16 Suc. 4, 1900 La Plata, Argentina.
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4
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Zhang X, Dou H, Chen X, Lin M, Dai Y, Xia F. Solid-State Nanopore Sensors with Enhanced Sensitivity through Nucleic Acid Amplification. Anal Chem 2023; 95:17153-17161. [PMID: 37966312 DOI: 10.1021/acs.analchem.3c03806] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Solid-state nanopores have wide applications in DNA sequencing, energy conversion and storage, seawater desalination, sensors, and reactors due to their high stability, controllable geometry, and a variety of pore-forming materials. Solid-state nanopore sensors can be used for qualitative and quantitative analyses of ions, small molecules, proteins, and nucleic acids. The combination of nucleic acid amplification and solid-state nanopores to achieve trace detection of analytes is gradually attracting attention. This review outlines nucleic acid amplification strategies for enhancing the sensitivity of solid-state nanopore sensors by summarizing the articles published in the past 10 years. The future development prospects and challenges of nucleic acid amplification in solid-state nanopore sensors are discussed. This review helps readers better understand the field of solid-state nanopore sensors. We believe that solid-state nanopore sensors will break through the bottleneck of traditional detection and become a powerful single-molecule detection platform.
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Affiliation(s)
- Xiaojin Zhang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Huimin Dou
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Xiaorui Chen
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Meihua Lin
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Yu Dai
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
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5
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Zhou S, Ye J, Zhao X, Zhou Z, Dong Y, Shi Q, Liu N, Wu F. A DNA-Schiff base functional nanopore sensing platform for the highly sensitive detection of Al 3+ and Zn 2+ ions. Dalton Trans 2023; 52:1524-1532. [PMID: 36662484 DOI: 10.1039/d2dt03786f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The combination of DNA nanotechnology and nanopore sensing technology has greatly promoted research on target molecule or ion detection. The large solid-state nanopores/nanochannels show better mechanical stability and reproducibility, but metal ion detection in the large nanopores with diameters of hundreds of nanometers or several micrometers is rarely reported. Hence, it is meaningful and urgent to develop a large nanopore-based sensing platform for the detection of metal ions. Herein, we employed a salicylic aldehyde-modified DNA network in conjunction with a glass nanopipette (GN) with a diameter of hundreds of nanometers as a sensing platform for the detection of target metal ions. Upon the addition of different receptors with the amino group, the salicylic aldehyde could in situ specifically recognize and bind with Zn2+ and Al3, forming Schiff base-metal ion complexes at the four vertices of one face per nanocube unit. The steric hindrance effect of multiple Schiff bases and metal ion complexes leads to the blockage of internal structure and decrease of ion current in the GN. Owing to this signal amplification strategy, the detection limit of the target metal ion reaches a level of fM in the GN with a diameter of about 300 nm. In the future, this functional nanopore sensing platform is expected to realize highly sensitive detection for more biological metal ions by choosing appropriate receptors.
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Affiliation(s)
- Shuailong Zhou
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, China.
| | - Jianhan Ye
- Department of Chemistry, Renmin University of China, Beijing 100872, China.,Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaohuan Zhao
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, China.
| | - Zihao Zhou
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, China.
| | - Yuanchen Dong
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Qian Shi
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, China.
| | - Nannan Liu
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, China.
| | - Fen Wu
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, China.
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6
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Yang Y, Qing Y, Hao X, Fang C, Ouyang P, Li H, Wang Z, Liao Y, Fang H, Du J. APTES-Modified Remote Self-Assembled DNA-Based Electrochemical Biosensor for Human Papillomavirus DNA Detection. BIOSENSORS 2022; 12:bios12070449. [PMID: 35884252 PMCID: PMC9312881 DOI: 10.3390/bios12070449] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 12/24/2022]
Abstract
High-risk human papillomavirus (HPV) infection is an important cause of cervical cancer formation; therefore, being able to detect high-risk HPV (e.g., HPV-16) is important for the early treatment and prevention of cervical cancer. In this study, a combination of a 3-aminopropyltriethoxysilane (APTES) modified gold electrode and a super sandwich structure was creatively developed, resulting in the development of a biosensor that is both sensitive and stable for the detection of HPV-16. The electrochemical biosensor possesses a lower detection limit compared with previous studies with an LOD of 5.475 × 10−16 mol/L and it possesses a wide linear range from 1.0 × 10−13 mol/L to 1.0 × 10−6 mol/L (R2 = 0.9923) for the target DNA. The experimental data show that the sensor has good stability, and there is no significant decrease in the current response value after 7 days in the low-temperature environment. In addition, the sensor proved to be a powerful clinical tool for disease diagnosis because it showed good interference resistance in complex human serum samples.
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7
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Ran XQ, Qian HL, Yan XP. Integrating Ordered Two-Dimensional Covalent Organic Frameworks to Solid-State Nanofluidic Channels for Ultrafast and Sensitive Detection of Mercury. Anal Chem 2022; 94:8533-8538. [PMID: 35653553 DOI: 10.1021/acs.analchem.2c01595] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Grafting specific recognition moieties onto solid-state nanofluidic channels is a promising way for selective and sensitive sensing of analytes. However, the time-consuming interaction between recognition moieties and analytes is the main hindrance to the application of nanofluidic channel-based sensors in rapid detection. Here, we show the integration of ordered two-dimensional covalent organic frameworks (2D COFs) to solid-state nanofluidic channels to achieve rapid, selective, and sensitive detection of contaminants. As a proof of concept, a thiourea-linked 2D COF (JNU-3) as the recognition unit is covalently bonded on the stable artificial anodic aluminum oxide nanochannels (AAO) to fabricate a JNU-3@AAO-based nanofluidic sensor. The rapid and selective interaction of Hg(II) with the highly ordered channels of JNU-3 allows the JNU-3@AAO-based nanofluidic sensor to realize ultrafast and precise determination of Hg(II) (90 s) with a low limit of detection (3.28 fg mL-1), wide linear range (0.01-100 pg mL-1), and good precision (relative standard deviation of 3.8% for 11 replicate determination of 10 pg mL-1). The developed method was successfully applied to the determination of mercury in a certified reference material A072301c (rice powder), real water, and rice samples with recoveries of 90.4-99.8%. This work reveals the great potential of 2D COFs-modified solid-state nanofluidic channels as a sensor for the rapid and precise detection of contaminants in complicated samples.
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Affiliation(s)
- Xu-Qin Ran
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China.,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Hai-Long Qian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China.,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiu-Ping Yan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China.,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, School of Chemical and Material Engineering, Jiangnan University, Wuxi 214122, China
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9
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10
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Gao P, Wang D, Che C, Ma Q, Wu X, Chen Y, Xu H, Li X, Lin Y, Ding D, Lou X, Xia F. Regional and functional division of functional elements of solid-state nanochannels for enhanced sensitivity and specificity of biosensing in complex matrices. Nat Protoc 2021; 16:4201-4226. [PMID: 34321637 DOI: 10.1038/s41596-021-00574-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 05/13/2021] [Indexed: 11/09/2022]
Abstract
Solid-state nanochannels (SSNs) provide a promising approach for biosensing due to the confinement of molecules inside, their great mechanical strength and diversified surface chemical properties; however, until now, their sensitivity and specificity have not satisfied the practical requirements of sensing applications, especially in complex matrices, i.e., media of diverse constitutions. Here, we report a protocol to achieve explicit regional and functional division of functional elements at the outer surface (FEOS) and inner wall (FEIW) of SSNs, which offers a nanochannel-based sensing platform with enhanced specificity and sensitivity. The protocol starts with the fabrication and characterization of the distribution of FEOS and FEIW. Then, the evaluation of the contributions of FEOS and FEIW to ionic gating is described; the FEIW mainly regulate ionic gating, and the FEOS can produce a synergistic effect. Finally, hydrophobic or highly charged FEOS are applied to ward off interference molecules, non-target molecules that may affect the ionic signal of nanochannels, which decreases false signals and helps to achieve the highly specific ionic output in complex matrices. Compared with other methods currently available, this method will contribute to the fundamental understanding of substance transport in SSNs and provide high specificity and sensitivity in SSN-based analyses. The procedure takes 3-6 d to complete.
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Affiliation(s)
- Pengcheng Gao
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences (CUG), Wuhan, P. R. China
| | - Dagui Wang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences (CUG), Wuhan, P. R. China
| | - Cheng Che
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences (CUG), Wuhan, P. R. China
| | - Qun Ma
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences (CUG), Wuhan, P. R. China
| | - Xiaoqing Wu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences (CUG), Wuhan, P. R. China
| | - Yajie Chen
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences (CUG), Wuhan, P. R. China
| | - Hongquan Xu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences (CUG), Wuhan, P. R. China
| | - Xinchun Li
- Pharmaceutical Analysis Division, School of Pharmacy, Guangxi Medical University, Nanning, P. R. China
| | - Yu Lin
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences (CUG), Wuhan, P. R. China
| | - Defang Ding
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences (CUG), Wuhan, P. R. China
| | - Xiaoding Lou
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences (CUG), Wuhan, P. R. China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences (CUG), Wuhan, P. R. China.
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11
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Xi D, Cui M, Zhou X, Zhuge X, Ge Y, Wang Y, Zhang S. Nanopore-Based Single-Molecule Investigation of DNA Sequences with Potential to Form i-Motif Structures. ACS Sens 2021; 6:2691-2699. [PMID: 34237940 DOI: 10.1021/acssensors.1c00712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
i-Motifs are DNA secondary structures present in cytosine-rich sequences. These structures are formed in regulatory regions of the human genome and play key regulatory roles. The investigation of sequences capable of forming i-motif structures at the single-molecule level is highly important. In this study, we used α-hemolysin nanopores to systematically study a series of DNA sequences at the nanometer scale by providing structure-dependent signature current signals to gain in-sights into the i-motif DNA sequence and structural stability. Increasing the length of the cytosine tract in a range of 3-10 nucleobases resulted in a longer translocation time through the pore, indicating improved stability. Changing the loop sequence and length in the sequences did not affect the formation of the i-motif structure but changed its stability. Importantly, the application of all-atom molecular dynamics simulations revealed the structural morphology of all sequences. Based on these results, we postulated a folding rule for i-motif formation, suggesting that thousands of cytosine-rich sequences in the human genome might fold into i-motif structures. Many of these were found in locations where structure formation is likely to play regulatory roles. These findings provide insights into the application of nanopores as a powerful tool for discovering potential i-motif-forming sequences and lay a foundation for future studies exploring the biological roles of i-motifs.
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Affiliation(s)
- Dongmei Xi
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Life Sciences, Linyi University, Linyi 276005, P. R. China
| | - Mengjie Cui
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Xin Zhou
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Xiao Zhuge
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Yaxian Ge
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Ying Wang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Life Sciences, Linyi University, Linyi 276005, P. R. China
| | - Shusheng Zhang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
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12
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Zhang C, Li Q, Xu T, Li W, He Y, Gu H. New DNA-hydrolyzing DNAs isolated from an ssDNA library carrying a terminal hybridization stem. Nucleic Acids Res 2021; 49:6364-6374. [PMID: 34057476 PMCID: PMC8216280 DOI: 10.1093/nar/gkab439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/03/2021] [Accepted: 05/06/2021] [Indexed: 02/07/2023] Open
Abstract
DNA-hydrolyzing DNAs represent an attractive type of DNA-processing catalysts distinctive from the protein-based restriction enzymes. The innate DNA property has enabled them to readily join DNA-based manipulations to promote the development of DNA biotechnology. A major in vitro selection strategy to identify these DNA catalysts relies tightly on the isolation of linear DNAs processed from a circular single-stranded (ss) DNA sequence library by self-hydrolysis. Herein, we report that by programming a terminal hybridization stem in the library, other than the previously reported classes (I & II) of deoxyribozymes, two new classes (III & IV) were identified with the old selection strategy to site-specifically hydrolyze DNA in the presence of Zn2+. Their representatives own a catalytic core consisting of ∼20 conserved nucleotides and a half-life of ∼15 min at neutral pH. In a bimolecular construct, class III exhibits unique broad generality on the enzyme strand, which can be potentially harnessed to engineer DNA-responsive DNA hydrolyzers for detection of any target ssDNA sequence. Besides the new findings, this work should also provide an improved approach to select for DNA-hydrolyzing deoxyribozymes that use various molecules and ions as cofactors.
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Affiliation(s)
- Canyu Zhang
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai 200433, China.,Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai 201399, China
| | - Qingting Li
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai 200433, China
| | - Tianbin Xu
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai 200433, China
| | - Wei Li
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai 200433, China
| | - Yungang He
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai 200433, China
| | - Hongzhou Gu
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai 200433, China.,Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai 201399, China
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13
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Moon WJ, Yang Y, Liu J. Zn 2+ -Dependent DNAzymes: From Solution Chemistry to Analytical, Materials and Therapeutic Applications. Chembiochem 2020; 22:779-789. [PMID: 33007113 DOI: 10.1002/cbic.202000586] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/01/2020] [Indexed: 12/20/2022]
Abstract
Since 1994, deoxyribozymes or DNAzymes have been in vitro selected to catalyze various types of reactions. Metal ions play a critical role in DNAzyme catalysis, and Zn2+ is a very important one among them. Zn2+ has good biocompatibility and can be used for intracellular applications. Chemically, Zn2+ is a Lewis acid and it can bind to both the phosphate backbone and the nucleobases of DNA. Zn2+ undergoes hydrolysis even at neutral pH, and the partially hydrolyzed polynuclear complexes can affect the interactions with DNA. These features have made Zn2+ a unique cofactor for DNAzyme reactions. This review summarizes Zn2+ -dependent DNAzymes with an emphasis on RNA-/DNA-cleaving reactions. A key feature is the sharp Zn2+ concentration and pH-dependent activity for many of the DNAzymes. The applications of these DNAzymes as biosensors for Zn2+ , as therapeutic agents to cleave intracellular RNA, and as chemical biology tools to manipulate DNA are discussed. Future studies can focus on the selection of new DNAzymes with improved performance and detailed biochemical characterizations to understand the role of Zn2+ , which can facilitate practical applications of Zn2+ -dependent DNAzymes.
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Affiliation(s)
- Woohyun J Moon
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Yongjie Yang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada.,Department of Food and Biological Science, College of Agricultural, Yanbian University, Yanbian Chaoxianzuzizhizhou, Yanji, 133002, P. R. China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada.,Centre for Eye and Vision Research, 17W Hong Kong Science Park, Hong Kong, China
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14
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Heaton I, Platt M. DNAzyme Sensor for the Detection of Ca 2+ Using Resistive Pulse Sensing. SENSORS 2020; 20:s20205877. [PMID: 33080851 PMCID: PMC7589696 DOI: 10.3390/s20205877] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/07/2020] [Accepted: 10/10/2020] [Indexed: 12/26/2022]
Abstract
DNAzymes are DNA oligonucleotides that can undergo a specific chemical reaction in the presence of a cofactor. Ribonucleases are a specific form of DNAzymes where a tertiary structure undergoes cleavage at a single ribonuclease site. The cleavage is highly specificity to co-factors, which makes them excellent sensor recognition elements. Monitoring the change in structure upon cleavage has given rise to many sensing strategies; here we present a simple and rapid method of following the reaction using resistive pulse sensors, RPS. To demonstrate this methodology, we present a sensor for Ca2+ ions in solution. A nanoparticle was functionalised with a Ca2+ DNAzyme, and it was possible to follow the cleavage and rearrangement of the DNA as the particles translocate the RPS. The binding of Ca2+ caused a conformation change in the DNAzyme, which was monitored as a change in translocation speed. A 30 min assay produced a linear response for Ca2+ between 1–9 μm, and extending the incubation time to 60 min allowed for a concentration as low as 0.3 μm. We demonstrate that the signal is specific to Ca2+ in the presence of other metal ions, and we can quantify Ca2+ in tap and pond water samples.
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15
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Roozbahani GM, Chen X, Zhang Y, Wang L, Guan X. Nanopore detection of metal ions: Current status and future directions. SMALL METHODS 2020; 4:2000266. [PMID: 33365387 PMCID: PMC7751931 DOI: 10.1002/smtd.202000266] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Indexed: 05/27/2023]
Abstract
In this review, we highlight recent research efforts that aimed at developing nanopore sensors for detection of metal ions, which play a crucial role in environmental safety and human health. Protein pores use three stochastic sensing-based strategies for metal ion detection. The first strategy is to construct engineered nanopores with metal ion binding sites, so that the interaction between the target analytes and the nanopore can slow the movement of metal ions in the nano-channel. Second, large molecules such as nucleic acids and especially peptides could be utilized as external selective molecular probes to detect metal ions based on the conformational change of the ligand molecules induced by the metal ion-ligand chelation / coordination interaction. Third, enzymatic reactions can also be used as an alternative to the molecule probe strategy in the situation that a sensitive and selective probe molecule for the target analyte is difficult to obtain. On the other hand, by taking advantage of steady-state analysis, synthetic nanopores mainly use two strategies (modification and modification-free) to detect metals. Given the advantages of high sensitivity & selectivity, and label-free detection, nanopore-based metal ion sensors should find useful application in many fields, including environmental monitoring, medical diagnosis, and so on.
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Affiliation(s)
| | - Xiaohan Chen
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois, 60616, USA
| | - Youwen Zhang
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois, 60616, USA
| | - Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- The University of Chinese Academy of Science, Beijing, 100049, China
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois, 60616, USA
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16
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High-performance biosensing based on autonomous enzyme-free DNA circuits. Top Curr Chem (Cham) 2020; 378:20. [DOI: 10.1007/s41061-020-0284-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/17/2020] [Indexed: 12/28/2022]
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17
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Pérez-Mitta G, Toimil-Molares ME, Trautmann C, Marmisollé WA, Azzaroni O. Molecular Design of Solid-State Nanopores: Fundamental Concepts and Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1901483. [PMID: 31267585 DOI: 10.1002/adma.201901483] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/16/2019] [Indexed: 06/09/2023]
Abstract
Solid-state nanopores are fascinating objects that enable the development of specific and efficient chemical and biological sensors, as well as the investigation of the physicochemical principles ruling the behavior of biological channels. The great variety of biological nanopores that nature provides regulates not only the most critical processes in the human body, including neuronal communication and sensory perception, but also the most important bioenergetic process on earth: photosynthesis. This makes them an exhaustless source of inspiration toward the development of more efficient, selective, and sophisticated nanopore-based nanofluidic devices. The key point responsible for the vibrant and exciting advance of solid nanopore research in the last decade has been the simultaneous combination of advanced fabrication nanotechnologies to tailor the size, geometry, and application of novel and creative approaches to confer the nanopore surface specific functionalities and responsiveness. Here, the state of the art is described in the following critical areas: i) theory, ii) nanofabrication techniques, iii) (bio)chemical functionalization, iv) construction of nanofluidic actuators, v) nanopore (bio)sensors, and vi) commercial aspects. The plethora of potential applications once envisioned for solid-state nanochannels is progressively and quickly materializing into new technologies that hold promise to revolutionize the everyday life.
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Affiliation(s)
- Gonzalo Pérez-Mitta
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP) - CONICET, Diagonal 113 y 64, 1900, La Plata, Argentina
- Laboratory of Molecular Neurobiology and Biophysics, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | | | - Christina Trautmann
- GSI Helmholtzzentrum für Schwerionenforschung, 64291, Darmstadt, Germany
- Technische Universität Darmstadt, 64287, Darmstadt, Germany
| | - Waldemar A Marmisollé
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP) - CONICET, Diagonal 113 y 64, 1900, La Plata, Argentina
| | - Omar Azzaroni
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP) - CONICET, Diagonal 113 y 64, 1900, La Plata, Argentina
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18
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Ding D, Gao P, Ma Q, Wang D, Xia F. Biomolecule-Functionalized Solid-State Ion Nanochannels/Nanopores: Features and Techniques. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1804878. [PMID: 30756522 DOI: 10.1002/smll.201804878] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/18/2018] [Indexed: 05/12/2023]
Abstract
Solid-state ion nanochannels/nanopores, the biomimetic products of biological ion channels, are promising materials in real-world applications due to their robust mechanical and controllable chemical properties. Functionalizations of solid-state ion nanochannels/nanopores by biomolecules pave a wide way for the introduction of varied properties from biomolecules to solid-state ion nanochannels/nanopores, making them smart in response to analytes or external stimuli and regulating the transport of ions/molecules. In this review, two features for nanochannels/nanopores functionalized by biomolecules are abstracted, i.e., specificity and signal amplification. Both of the two features are demonstrated from three kinds of nanochannels/nanopores: nucleic acid-functionalized nanochannels/nanopores, protein-functionalized nanochannels/nanopores, and small biomolecule-functionalized nanochannels/nanopores, respectively. Meanwhile, the fundamental mechanisms of these combinations between biomolecules and nanochannels/nanopores are explored, providing reasonable constructs for applications in sensing, transport, and energy conversion. And then, the techniques of functionalizations and the basic principle about biomolecules onto the solid-state ion nanochannels/nanopores are summarized. Finally, some views about the future developments of the biomolecule-functionalized nanochannels/nanopores are proposed.
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Affiliation(s)
- 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, Wuhan, 430074, P. R. China
| | - Pengcheng Gao
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences (CUG), 388 Lumo Road, Wuhan, 430074, P. R. 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, Wuhan, 430074, P. R. China
| | - Dagui Wang
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences (CUG), 388 Lumo Road, Wuhan, 430074, P. R. 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, Wuhan, 430074, P. R. China
- State Key Laboratory of Material Processing and Die & Mould Technology, School of Material Sciences and Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074, P. R. China
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19
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Xiong E, Zhen D, Jiang L. Cascade signal amplified assay of nucleic acids based on entropy-driven amplification strategy and Mg2+-dependent DNAzyme cleavage. Talanta 2019; 198:179-184. [DOI: 10.1016/j.talanta.2019.02.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/27/2019] [Accepted: 02/03/2019] [Indexed: 12/15/2022]
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20
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Sun C, Ou X, Cheng Y, Zhai T, Liu B, Lou X, Xia F. Coordination-induced structural changes of DNA-based optical and electrochemical sensors for metal ions detection. Dalton Trans 2019; 48:5879-5891. [PMID: 30681098 DOI: 10.1039/c8dt04733b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Metal ions play a critical role in human health and abnormal levels are closely related to various diseases. Therefore, the detection of metal ions with high selectivity, sensitivity and accuracy is particularly important. This article highlights and comments on the coordination-induced structural changes of DNA-based optical, electrochemical and optical-electrochemical-combined sensors for metal ions detection. Challenges and potential solutions of DNA-based sensors for the simultaneous detection of multiple metal ions are also discussed for further development and exploitation.
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Affiliation(s)
- Chunli Sun
- State Key Laboratory of Material Processing and Die & Mould Technology, School of Materials Science and Engineering; Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering; National Engineering Research Center for Nanomedicine, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
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21
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A protease-free and signal-on electrochemical biosensor for ultrasensitive detection of lead ion based on GR-5 DNAzyme and catalytic hairpin assembly. J Electroanal Chem (Lausanne) 2018. [DOI: 10.1016/j.jelechem.2018.03.036] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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22
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Long Z, Zhan S, Gao P, Wang Y, Lou X, Xia F. Recent Advances in Solid Nanopore/Channel Analysis. Anal Chem 2017; 90:577-588. [DOI: 10.1021/acs.analchem.7b04737] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Zi Long
- Faculty
of Materials Science and Chemistry, China University of Geosciences, Wuhan, Hubei 430074, P. R. China
| | - Shenshan Zhan
- School
of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
| | - Pengcheng Gao
- Faculty
of Materials Science and Chemistry, China University of Geosciences, Wuhan, Hubei 430074, P. R. China
| | - Yongqian Wang
- Faculty
of Materials Science and Chemistry, China University of Geosciences, Wuhan, Hubei 430074, P. R. China
| | - Xiaoding Lou
- Faculty
of Materials Science and Chemistry, China University of Geosciences, Wuhan, Hubei 430074, P. R. China
- School
of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
| | - Fan Xia
- Faculty
of Materials Science and Chemistry, China University of Geosciences, Wuhan, Hubei 430074, P. R. China
- School
of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
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23
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Yin HS, Li BC, Zhou YL, Wang HY, Wang MH, Ai SY. Signal-on fluorescence biosensor for microRNA-21 detection based on DNA strand displacement reaction and Mg 2+ -dependent DNAzyme cleavage. Biosens Bioelectron 2017; 96:106-112. [DOI: 10.1016/j.bios.2017.04.049] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/28/2017] [Accepted: 04/28/2017] [Indexed: 01/09/2023]
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24
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Affiliation(s)
- Wenhu Zhou
- Xiangya
School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Runjhun Saran
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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25
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McGhee CE, Loh KY, Lu Y. DNAzyme sensors for detection of metal ions in the environment and imaging them in living cells. Curr Opin Biotechnol 2017; 45:191-201. [PMID: 28458112 DOI: 10.1016/j.copbio.2017.03.002] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 02/28/2017] [Accepted: 03/02/2017] [Indexed: 12/17/2022]
Abstract
The on-site and real-time detection of metal ions is important for environmental monitoring and for understanding the impact of metal ions on human health. However, developing sensors selective for a wide range of metal ions that can work in the complex matrices of untreated samples and cells presents significant challenges. To meet these challenges, DNAzymes, an emerging class of metal ion-dependent enzymes selective for almost any metal ion, have been functionalized with fluorophores, nanoparticles and other imaging agents and incorporated into sensors for the detection of metal ions in environmental samples and for imaging metal ions in living cells. Herein, we highlight the recent developments of DNAzyme-based fluorescent, colorimetric, SERS, electrochemical and electrochemiluminscent sensors for metal ions for these applications.
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Affiliation(s)
- Claire E McGhee
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Kang Yong Loh
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.
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26
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Abstract
DNAzymes are catalytically active DNA molecules that are obtained via in vitro selection. RNA-cleaving DNAzymes have attracted significant attention for both therapeutic and diagnostic applications due to their excellent programmability, stability, and activity. They can be designed to cleave a specific mRNA to down-regulate gene expression. At the same time, DNAzymes can sense a broad range of analytes. By combining these two functions, theranostic DNAzymes are obtained. This review summarizes the progress of DNAzyme for theranostic applications. First, in vitro selection of DNAzymes is briefly introduced, and some representative DNAzymes related to biological applications are summarized. Then, the applications of DNAzyme for RNA cleaving are reviewed. DNAzymes have been used to cleave RNA for treating various diseases, such as viral infection, cancer, inflammation and atherosclerosis. Several formulations have entered clinical trials. Next, the use of DNAzymes for detecting metal ions, small molecules and nucleic acids related to disease diagnosis is summarized. Finally, the theranostic applications of DNAzyme are reviewed. The challenges to be addressed include poor DNAzyme activity under biological conditions, mRNA accessibility, delivery, and quantification of gene expression. Possible solutions to overcome these challenges are discussed, and future directions of the field are speculated.
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27
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Liu N, Li C, Zhang T, Hou R, Xiong Z, Li Z, Wei B, Yang Z, Gao P, Lou X, Zhang X, Guo W, Xia F. Fabrication of "Plug and Play" Channels with Dual Responses by Host-Guest Interactions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1600287. [PMID: 27158970 DOI: 10.1002/smll.201600287] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 03/22/2016] [Indexed: 06/05/2023]
Abstract
The "Plug and Play" template can be individually or successively grafted by dual-responsive molecules on the α-CD modified channels by host-guest interactions and can be peeled off by UV irradiation. The artificial channels present six kinds of responses cycling among four states responding to three environment stimuli, as light, pH, and temperature.
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Affiliation(s)
- Nannan Liu
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074, P. R. China
| | - Cao Li
- Key Laboratory of Biomedical Polymers, Ministry of Education, Department of Chemistry, Wuhan University, Wuhan, 430072, P. R. China
- Faculty of Materials Science & Engineering, Hubei University, Wuhan, 430062, P. R. China
| | - Tianchi Zhang
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074, P. R. China
| | - Ruizuo Hou
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074, P. R. China
| | - Zhiping Xiong
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074, P. R. China
| | - Zeyong Li
- Key Laboratory of Biomedical Polymers, Ministry of Education, Department of Chemistry, Wuhan University, Wuhan, 430072, P. R. China
| | - Benmei Wei
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074, P. R. China
| | - Zekun Yang
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074, P. R. China
| | - Pengcheng Gao
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074, P. R. China
| | - Xiaoding Lou
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074, P. R. China
| | - Xianzheng Zhang
- Key Laboratory of Biomedical Polymers, Ministry of Education, Department of Chemistry, Wuhan University, Wuhan, 430072, P. R. China
| | - Wei Guo
- Laboratory of Bio-inspired Smart Interface Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Fan Xia
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074, P. R. China
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28
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DNA hybridization chain reaction and DNA supersandwich self-assembly for ultrasensitive detection. Sci China Chem 2016. [DOI: 10.1007/s11426-016-0262-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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