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Lei X, Ding L, Yang X, Xu F, Wu Y, Yu S. PAIT effect: Padlock activator inhibits the trans-cleavage activity of CRISPR/Cas12a. Biosens Bioelectron 2024; 263:116607. [PMID: 39067412 DOI: 10.1016/j.bios.2024.116607] [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: 04/23/2024] [Revised: 07/09/2024] [Accepted: 07/24/2024] [Indexed: 07/30/2024]
Abstract
The CRISPR/Cas12a system is increasingly used in biosensor development. However, high background signal and low sensitivity for the non-nucleic acid targets detection is challenging. Here, a padlock activator which could inhibit the trans-cleavage activity of CRISPR/Cas12a system in the intact form by steric hindrance effect (PAIT effect) was designed for non-nucleic acid targets detection. The PAIT effect disappeared when padlock activator was separated into two split activators. To verify the feasibility of padlock activator, a Ca2+ sensor was developed based on PAIT effect with the assistance of DNAzyme, activity of which was Ca2+ dependent. In the presence of Ca2+, DNAzyme was activated to cleave its substrate, a padlock activator modified with adenine ribonucleotide, into split padlock activators which would trigger the trans-cleavage activity of Cas12a to generate fluorescence. There was a mathematical relationship between the fluorescence intensity and the logarithm of Ca2+ concentration ranging from 10 pM to 1 nM, with a limit of detection of 3.98 pM. The little interference of Mg2+, Mn2+, Cd2+, Cu2+, Na+, Al3+, K+, Fe2+, and Fe3+ indicated high selectivity. Recovery ranged from 93.32% to 103.28% with RSDs from 1.87% to 12.74% showed a good accuracy and reliability. Furthermore, the proposed sensor could be applied to detect Ca2+ in mineral water, milk powder and urine. The results were consistent with that of flame atomic absorption spectroscopy. Thus, PAIT effect is valuable for expanding the application boundary of CRISPR/Cas12a system.
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Affiliation(s)
- Xueying Lei
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Lihua Ding
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Xiaonan Yang
- School of Electrical and Information Engineering, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Feng Xu
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001, PR China
| | - Yongjun Wu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Songcheng Yu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, PR China.
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2
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Morrison K, Tincher M, Rothchild A, Yehl K. Fingerprinting DNAzyme Cross-Reactivity for Pattern-Based Detection of Heavy Metals. Anal Chem 2024; 96:11780-11789. [PMID: 39001810 DOI: 10.1021/acs.analchem.4c01331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2024]
Abstract
Heavy metal contamination in food and water is a major public health concern because heavy metals are toxic in minute amounts. DNAzyme sensors are emerging as a promising tool for rapid onsite detection of heavy metals, which can aid in minimizing exposure. However, DNAzyme activity toward its target metal is not absolute and has cross-reactivity with similar metals, which is a major challenge in the wide-scale application of DNAzyme sensors for environmental monitoring. To address this, we constructed a four DNAzyme array (17E, GR-5, EtNA, and NaA43) and used a pattern-based readout to improve sensor accuracy. We measured cross-reactivity between three metal cofactors (Pb2+, Ca2+, and Na+) and common interferents (Mg2+, Zn2+, Mn2+, UO22+, Li+, K+, and Ag+) and then used t-SNE analysis to identify and quantify the metal ion. We further showed that this method can be used for distinguishing mixtures of metals and detecting Pb2+ in environmental soil samples at micromolar concentrations.
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Affiliation(s)
- Kevin Morrison
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Madeleine Tincher
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Alexis Rothchild
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Kevin Yehl
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
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3
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Xuan J, Wang Z, Huang Y, Liu Y, Han Y, Li M, Xiao M. DNA response element-based smart drug delivery systems for precise drug release. Biomater Sci 2024; 12:3550-3564. [PMID: 38832670 DOI: 10.1039/d4bm00138a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Smart drug delivery systems (DDSs) that respond to, interact with, or are actuated by biological signals or pathological abnormalities (e.g., the tumor microenvironment) for controllable drug release are appealing therapeutic platforms for cancer treatment. Owing to their inherent self-assembled nature, nucleic acids have emerged as programmable materials for the development of multifunctional structures. In response to external environmental stimuli, DNA response elements can serve as switches to trigger conformational changes in DNA structures. Their stimulus-responsive properties make them promising candidates for constructing smart DDSs, and advancements in DNA response element-based DDSs in the field of biomedicine have been made. This review summarizes different types of DNA response elements, including DNA aptamers, DNAzymes, disulfide bond-modified DNA, pH-responsive DNA motifs, and photocleavable DNA building blocks, and highlights the advancements in DNA response element-based smart DDSs for precise drug release. Finally, future challenges and perspectives in this field are discussed.
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Affiliation(s)
- Jinnan Xuan
- Hubei Key Laboratory of Photoelectric Materials and Devices, School of Materials Science and Engineering, Hubei Normal University, 11 Cihu Road, Huangshi 435002, P. R. China
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China.
| | - Zhen Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, P. R. China
| | - Yuting Huang
- Department of Radiotherapy, Chaohu Hospital of Anhui Medical University, 64 Chaohu North Road, Chaohu 238000, P. R. China
| | - Yisi Liu
- Hubei Key Laboratory of Photoelectric Materials and Devices, School of Materials Science and Engineering, Hubei Normal University, 11 Cihu Road, Huangshi 435002, P. R. China
| | - Yuqiang Han
- Hubei Key Laboratory of Photoelectric Materials and Devices, School of Materials Science and Engineering, Hubei Normal University, 11 Cihu Road, Huangshi 435002, P. R. China
| | - Man Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), Shaanxi Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, P. R. China
| | - Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, P. R. China.
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4
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Dantu SC, Khalil M, Bria M, Saint-Pierre C, Orio M, Gasparutto D, Sicoli G. Cleaving DNA with DNA: Cooperative Tuning of Structure and Reactivity Driven by Copper Ions. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306710. [PMID: 38419268 DOI: 10.1002/advs.202306710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/15/2024] [Indexed: 03/02/2024]
Abstract
A copper-dependent self-cleaving DNA (DNAzyme or deoyxyribozyme) previously isolated by in vitro selection has been analyzed by a combination of Molecular Dynamics (MD) simulations and advanced Electron Paramagnetic Resonance (Electron Spin Resonance) EPR/ESR spectroscopy, providing insights on the structural and mechanistic features of the cleavage reaction. The modeled 46-nucleotide deoxyribozyme in MD simulations forms duplex and triplex sub-structures that flank a highly conserved catalytic core. The DNA self-cleaving construct can also form a bimolecular complex that has a distinct substrate and enzyme domains. The highly dynamic structure combined with an oxidative site-specific cleavage of the substrate are two key-aspects to elucidate. By combining EPR/ESR spectroscopy with selectively isotopically labeled nucleotides it has been possible to overcome the major drawback related to the "metal-soup" scenario, also known as "super-stoichiometric" ratios of cofactors versus substrate, conventionally required for the DNA cleavage reaction within those nucleic acids-based enzymes. The focus on the endogenous paramagnetic center (Cu2+) here described paves the way for analysis on mixtures where several different cofactors are involved. Furthermore, the insertion of cleavage reaction within more complex architectures is now a realistic perspective towards the applicability of EPR/ESR spectroscopic studies.
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Affiliation(s)
- Sarath Chandra Dantu
- Department of Computer Science, Brunel University London, Kingston Lane, Uxbridge, UB8 3PH, UK
| | - Mahdi Khalil
- LASIRE, CNRS UMR 8516, University of Lille, C4 building, Avenue Paul Langevin, Villeneuve d'Ascq, F-59655, France
| | - Marc Bria
- Michle-Eugène Chevreul Institute, FR 2638, Avenue Paul Langevin, Villeneuve d'Ascq, F-59655, France
| | - Christine Saint-Pierre
- Université Grenoble Alpes, CEA, CNRS, UMR 5819 SyMMES-CREAB, Avenue des Martyrs, Grenoble, F-38000, France
| | - Maylis Orio
- Aix Marseille Université, CNRS, Centrale Marseille, iSm2, UMR CNRS 7313, Marseille, 13397, France
| | - Didier Gasparutto
- Université Grenoble Alpes, CEA, CNRS, UMR 5819 SyMMES-CREAB, Avenue des Martyrs, Grenoble, F-38000, France
| | - Giuseppe Sicoli
- LASIRE, CNRS UMR 8516, University of Lille, C4 building, Avenue Paul Langevin, Villeneuve d'Ascq, F-59655, France
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Wu Y, Torabi SF, Lake RJ, Hong S, Yu Z, Wu P, Yang Z, Nelson K, Guo W, Pawel GT, Van Stappen J, Shao X, Mirica LM, Lu Y. Simultaneous Fe 2+/Fe 3+ imaging shows Fe 3+ over Fe 2+ enrichment in Alzheimer's disease mouse brain. SCIENCE ADVANCES 2023; 9:eade7622. [PMID: 37075105 PMCID: PMC10115418 DOI: 10.1126/sciadv.ade7622] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Visualizing redox-active metal ions, such as Fe2+ and Fe3+ ions, are essential for understanding their roles in biological processes and human diseases. Despite the development of imaging probes and techniques, imaging both Fe2+ and Fe3+ simultaneously in living cells with high selectivity and sensitivity has not been reported. Here, we selected and developed DNAzyme-based fluorescent turn-on sensors that are selective for either Fe2+ or Fe3+, revealing a decreased Fe3+/Fe2+ ratio during ferroptosis and an increased Fe3+/Fe2+ ratio in Alzheimer's disease mouse brain. The elevated Fe3+/Fe2+ ratio was mainly observed in amyloid plaque regions, suggesting a correlation between amyloid plaques and the accumulation of Fe3+ and/or conversion of Fe2+ to Fe3+. Our sensors can provide deep insights into the biological roles of labile iron redox cycling.
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Affiliation(s)
- Yuting Wu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Seyed-Fakhreddin Torabi
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ryan J. Lake
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shanni Hong
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Zhengxin Yu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Peiwen Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Zhenglin Yang
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Kevin Nelson
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Weijie Guo
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Molecular Bioscience, University of Texas at Austin, Austin, TX 78712, USA
| | - Gregory T. Pawel
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | | | - Xiangli Shao
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Liviu M. Mirica
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Molecular Bioscience, University of Texas at Austin, Austin, TX 78712, USA
- Corresponding author.
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6
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Gao M, Wei D, Chen S, Qin B, Wang Y, Li Z, Yu H. Selection of RNA-Cleaving TNA Enzymes for Cellular Mg 2+ Imaging. Chembiochem 2023; 24:e202200651. [PMID: 36513605 DOI: 10.1002/cbic.202200651] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 12/15/2022]
Abstract
Catalytic DNA-based fluorescent sensors have enabled cellular imaging of metal ions such as Mg2+ . However, natural DNA is prone to nuclease-mediated degradation. Here, we report the in vitro selection of threose nucleic acid enzymes (TNAzymes) with RNA endonuclease activities. One such TNAzyme, T17-22, catalyzes a site-specific RNA cleavage reaction with a kcat of 0.017 min-1 and KM of 675 nM. A fluorescent sensor based on T17-22 responds to an increasing concentration of Mg2+ with a limit of detection at 0.35 mM. This TNAzyme-based sensor also allows cellular imaging of Mg2+ . This work presents the first proof-of-concept demonstration of using a TNA catalyst in cellular metal ion imaging.
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Affiliation(s)
- Mingmei Gao
- State Key Laboratory of Coordination Chemistry Department of Biomedical Engineering College of Engineering and Applied Sciences Chemistry and Biomedicine Innovation Center (ChemBIC) Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Dongying Wei
- State Key Laboratory of Coordination Chemistry Department of Biomedical Engineering College of Engineering and Applied Sciences Chemistry and Biomedicine Innovation Center (ChemBIC) Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Siqi Chen
- State Key Laboratory of Coordination Chemistry Department of Biomedical Engineering College of Engineering and Applied Sciences Chemistry and Biomedicine Innovation Center (ChemBIC) Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Bohe Qin
- State Key Laboratory of Coordination Chemistry Department of Biomedical Engineering College of Engineering and Applied Sciences Chemistry and Biomedicine Innovation Center (ChemBIC) Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Yueyao Wang
- State Key Laboratory of Coordination Chemistry Department of Biomedical Engineering College of Engineering and Applied Sciences Chemistry and Biomedicine Innovation Center (ChemBIC) Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Zhe Li
- State Key Laboratory of Analytical Chemistry for Life Science Department of Biomedical Engineering College of Engineering and Applied Sciences Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Hanyang Yu
- State Key Laboratory of Coordination Chemistry Department of Biomedical Engineering College of Engineering and Applied Sciences Chemistry and Biomedicine Innovation Center (ChemBIC) Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
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7
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Wang Q, Wang Z, He Y, Xiong B, Li Y, Wang F. Chemical and structural modification of RNA-cleaving DNAzymes for efficient biosensing and biomedical applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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8
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Wang H, Chen R, Zhang F, Yu Z, Wang Y, Tang Z, Yang L, Tang X, Xiong B. Superhydrophobic Paper-Based Microfluidic Field-Effect Transistor Biosensor Functionalized with Semiconducting Single-Walled Carbon Nanotube and DNAzyme for Hypocalcemia Diagnosis. Int J Mol Sci 2022; 23:ijms23147799. [PMID: 35887147 PMCID: PMC9318675 DOI: 10.3390/ijms23147799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 02/06/2023] Open
Abstract
Hypocalcemia is caused by a sharp decline in blood calcium concentration after dairy cow calving, which can lead to various diseases or even death. It is necessary to develop an inexpensive, easy-to-operate, reliable sensor to diagnose hypocalcemia. The cellulose-paper-based microfluidic field-effect biosensor is promising for point-of-care, but it has poor mechanical strength and a short service life after exposure to an aqueous solution. Octadecyltrichlorosilane (OTS), as a popular organosilane derivative, can improve the hydrophobicity of cellulose paper to overcome the shortage of cellulose paper. In this work, OTS was used to produce the superhydrophobic cellulose paper that enhances the mechanical strength and short service life of MFB, and a microfluidic field-effect biosensor (MFB) with semiconducting single-walled carbon nanotubes (SWNTs) and DNAzyme was then developed for the Ca2+ determination. Pyrene carboxylic acid (PCA) attached to SWNTs through a non-covalent π-π stacking interaction provided a carboxyl group that can bond with an amino group of DNAzyme. Two DNAzymes with different sensitivities were designed by changing the sequence length and cleavage site, which were functionalized with SPFET/SWNTs-PCA to form Dual-MFB, decreasing the interference of impurities in cow blood. After optimizing the detecting parameters, Dual-MFB could determine the Ca2+ concentration in the range of 25 μM to 5 mM, with a detection limit of 10.7 μM. The proposed Dual-MFB was applied to measure Ca2+ concentration in cow blood, which provided a new method to diagnose hypocalcemia after dairy cow calving.
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Affiliation(s)
- Hui Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.W.); (R.C.); (F.Z.); (Z.Y.); (Y.W.); (Z.T.); (L.Y.)
| | - Ruipeng Chen
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.W.); (R.C.); (F.Z.); (Z.Y.); (Y.W.); (Z.T.); (L.Y.)
| | - Fan Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.W.); (R.C.); (F.Z.); (Z.Y.); (Y.W.); (Z.T.); (L.Y.)
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zhixue Yu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.W.); (R.C.); (F.Z.); (Z.Y.); (Y.W.); (Z.T.); (L.Y.)
| | - Yue Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.W.); (R.C.); (F.Z.); (Z.Y.); (Y.W.); (Z.T.); (L.Y.)
| | - Zhonglin Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.W.); (R.C.); (F.Z.); (Z.Y.); (Y.W.); (Z.T.); (L.Y.)
| | - Liang Yang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.W.); (R.C.); (F.Z.); (Z.Y.); (Y.W.); (Z.T.); (L.Y.)
| | - Xiangfang Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.W.); (R.C.); (F.Z.); (Z.Y.); (Y.W.); (Z.T.); (L.Y.)
- Correspondence: (X.T.); (B.X.)
| | - Benhai Xiong
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.W.); (R.C.); (F.Z.); (Z.Y.); (Y.W.); (Z.T.); (L.Y.)
- Correspondence: (X.T.); (B.X.)
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9
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Zhang Q, Liang Y, Xing H. Caging-Decaging Strategies to Realize Spatiotemporal Control of DNAzyme Activity for Biosensing and Bioimaging. Chem Res Chin Univ 2022. [DOI: 10.1007/s40242-022-2137-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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10
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Electrochemical Biosensor Using Nitrogen-Doped Graphene/Au Nanoparticles/DNAzyme for Ca2+ Determination. BIOSENSORS 2022; 12:bios12050331. [PMID: 35624632 PMCID: PMC9138538 DOI: 10.3390/bios12050331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 12/16/2022]
Abstract
An electrochemical biosensor for detecting Ca2+ concentration was proposed using glass carbon electrodes (GCEs) modified with nitrogen-doped graphene (NGR), gold nanoparticles (AuNPs) and DNAzyme. The resistance signal was amplified through two methods: electrochemical reduction of AuNPs on the NGR surface to increase the specific surface area of the electrode and strengthen the adsorption of DNAzyme; and increasement of the DNAzyme base sequence. The process of electrode modification was characterized by scanning electron microscopy, Raman spectroscopy, cyclic voltammetry (CV), and electrochemical impedance spectroscopy (EIS). Experimental parameters’ influence, such as the deposition time of gold nanoparticles and the detection time, were assessed by electrochemical methods. The linear ranges of the electrochemical biosensor were in the range from 5 × 10−6 to 5 × 10−5 and 5 × 10−5 to 4 × 10−4 M, with a detection limit of 3.8 × 10−6 M. The concentration of Ca2+ in the serum of dairy cows was determined by the biosensor with satisfactory results, which could be potentially used to diagnose subclinical hypocalcemia.
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11
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Zareh MM, Mohamed SF, Elsheikh AM. Polymeric Electrochemical Sensor for Calcium Based on DNA. Polymers (Basel) 2022; 14:polym14091896. [PMID: 35567065 PMCID: PMC9104553 DOI: 10.3390/polym14091896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/18/2021] [Accepted: 12/22/2021] [Indexed: 12/04/2022] Open
Abstract
Plastic membranes containing deoxyribonucleic acid (DNA) as an electroactive material were acting as Ca2+ selective sensors. Diethyl phthalate (DEP), dioctyl Phthalate (DOP), or nitrophenyl octyl ether (NPOE) were used as plasticizers and polyvinyl chloride (PVC) was the membrane matrix. A sensor with a membrane composition of 120 mg PVC, 60 mg DOP plasticizer, and 2 mg DNA ionophore (DNA: DOP: PVC, 1.0:29.2:0.1 mole) was found to have the best performance. The slope of the calibration graph was 30 mV decade−1. The optimum pH range was 5.7–9.5 for 0.01 M Ca2+. The sensor response time was fast (2–3 s) with a long working period (up to 3 weeks). Excellent selectivity for Ca2+ was indicated by the values of selectivity coefficients for different selected interference. The sensor was used effectively for the estimation of calcium in real samples (fruits, calcium syrup, milk, and dairy products).
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12
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13
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Huang Z, Wang X, Wu Z, Jiang JH. Recent Advances on DNAzyme-Based Sensing. Chem Asian J 2022; 17:e202101414. [PMID: 35156764 DOI: 10.1002/asia.202101414] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 02/09/2022] [Indexed: 11/08/2022]
Abstract
DNAzymes are functional nucleic acid with catalytic activity. Owing to the high sensitivity, excellent programmability, and flexible obtainment through in vitro selection, RNA-cleaving DNAzymes have attracted increasing interest in developing DNAzyme-based sensors. In this review, we summarize the recent advances on DNAzyme-based sensing applications. We initially conclude two general strategies to expand the library of DNAzymes, in vitro selection to discover new DNAzymes towards different targets of interest and chemical modifications to endue the existing DNAzymes with new function or properties. We then discuss the recent applications of DNAzyme-based sensors for the detection of a variety of important biomolecules both in vitro and in vivo . Finally, perspectives on the challenges and future directions in the development of DNAzyme-based sensors are provided.
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Affiliation(s)
- Zhimei Huang
- Hunan University, College of Chemistry and Chemical Engineering, CHINA
| | - Xiangnan Wang
- Hunan University of Technology and Business, College of Science, CHINA
| | - Zhenkun Wu
- Hunan University, State Key Laboratory of Chemeo/Bio-Sensing and Chemometrics and College of Chemistry and Chemical Engineering, South of Lushan Road, 410082, Changsha, CHINA
| | - Jian-Hui Jiang
- Hunan University, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics; College of Chemistry and Chemical Engineering, CHINA
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14
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Huang PJJ, Liu J. Sensing Metal Ions with Phosphorothioate-Modified DNAzymes. Methods Mol Biol 2022; 2439:277-289. [PMID: 35226327 DOI: 10.1007/978-1-0716-2047-2_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Phosphorothioate (PS) modification refers to replacing one of the nonbridging oxygen atoms in nucleic acids with sulfur. PS modifications can be easily introduced during solid-phase DNA synthesis. It has been extensively used in ribozyme and DNAzyme research to achieve a bioinorganic understanding of metal binding, bioanalytical applications of metal detection, and chemical biology of DNA modification. It allows for the access of new chemistry, not available to natural DNA. Since each PS modification is accompanied by the production of a chiral phosphorus center, a key technical challenge is to separate the two diastereomers called Rp and Sp. In this chapter, we describe our methods of HPLC-based separation followed by ligation to generate a long and fluorescently modified DNAzyme substrate. Subsequently, the use of the modified substrate for activity assay to understand metal binding and for metal ion detection is also described.
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Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada.
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15
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DNAzyme-Amplified Electrochemical Biosensor Coupled with pH Meter for Ca 2+ Determination at Variable pH Environments. NANOMATERIALS 2021; 12:nano12010004. [PMID: 35009954 PMCID: PMC8746961 DOI: 10.3390/nano12010004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/08/2021] [Accepted: 12/14/2021] [Indexed: 02/07/2023]
Abstract
For more than 50% of multiparous cows, it is difficult to adapt to the sudden increase in calcium demand for milk production, which is highly likely to cause hypocalcemia. An electrochemical biosensor is a portable and efficient method to sense Ca2+ concentrations, but biomaterial is easily affected by the pH of the analyte solution. Here, an electrochemical biosensor was fabricated using a glassy carbon electrode (GCE) and single-walled carbon nanotube (SWNT), which amplified the impedance signal by changing the structure and length of the DNAzyme. Aiming at the interference of the pH, the electrochemical biosensor (GCE/SWNT/DNAzyme) was coupled with a pH meter to form an electrochemical device. It was used to collect data at different Ca2+ concentrations and pH values, and then was processed using different mathematical models, of which GPR showed higher detecting accuracy. After optimizing the detecting parameters, the electrochemical device could determine the Ca2+ concentration ranging from 5 μM to 25 mM, with a detection limit of 4.2 μM at pH values ranging from 4.0 to 7.5. Finally, the electrochemical device was used to determine the Ca2+ concentrations in different blood and milk samples, which can overcome the influence of the pH.
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16
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Zhang SY, Zhou ZR, Qian RC. Recent Progress and Perspectives on Cell Surface Modification. Chem Asian J 2021; 16:3250-3258. [PMID: 34427996 DOI: 10.1002/asia.202100852] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/22/2021] [Indexed: 11/11/2022]
Abstract
The cell membrane is a biological interface consisting of phospholipid bilayer, saccharides and proteins that maintains a stable metabolic intracellular environment as well as regulating and controlling the exchange of substances inside and outside the cell. Cell membranes provide a highly complex biological surface carrying a variety of essential surfaces ligands and receptors for cells to receive various stimuli of external signals, thereby inducing corresponding cell responses regulating the life activities of the cell. These surface receptors can be manipulated via cell surface modification to regulate cellular functions and behaviors Thus, cell surface modification has attracted considerable attention due to its significance in cell fate control, cell engineering and cell therapy. In this minireview, we describe the recent developments and advances of cell surface modification, and summarize the main modification methods with corresponding functions and applications. Finally, the prospect for the future development of the modification of the living cell membrane is discussed.
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Affiliation(s)
- Shi-Yi Zhang
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Ze-Rui Zhou
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Ruo-Can Qian
- 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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17
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Abstract
This article provides a comprehensive review of biosensing with DNAzymes, providing an overview of different sensing applications while highlighting major progress and seminal contributions to the field of portable biosensor devices and point-of-care diagnostics. Specifically, the field of functional nucleic acids is introduced, with a specific focus on DNAzymes. The incorporation of DNAzymes into bioassays is then described, followed by a detailed overview of recent advances in the development of in vivo sensing platforms and portable sensors incorporating DNAzymes for molecular recognition. Finally, a critical perspective on the field, and a summary of where DNAzyme-based devices may make the biggest impact are provided.
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Affiliation(s)
- Erin M McConnell
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
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18
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Li M, Yin F, Song L, Mao X, Li F, Fan C, Zuo X, Xia Q. Nucleic Acid Tests for Clinical Translation. Chem Rev 2021; 121:10469-10558. [PMID: 34254782 DOI: 10.1021/acs.chemrev.1c00241] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Overexpressed or underexpressed as well as mutated nucleic acids have been implicated in many diseases. Therefore, nucleic acid tests (NATs) are extremely important. Inspired by intracellular DNA replication and RNA transcription, in vitro NATs have been extensively developed to improve the detection specificity, sensitivity, and simplicity. The principles of NATs can be in general classified into three categories: nucleic acid hybridization, thermal-cycle or isothermal amplification, and signal amplification. Driven by pressing needs in clinical diagnosis and prevention of infectious diseases, NATs have evolved to be a rapidly advancing field. During the past ten years, an explosive increase of research interest in both basic research and clinical translation has been witnessed. In this review, we aim to provide comprehensive coverage of the progress to analyze nucleic acids, use nucleic acids as recognition probes, construct detection devices based on nucleic acids, and utilize nucleic acids in clinical diagnosis and other important fields. We also discuss the new frontiers in the field and the challenges to be addressed.
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Affiliation(s)
- Min Li
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fangfei Yin
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Lu Song
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fan Li
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Xia
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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19
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XING S, HE M, LIU T, YONG W, ZHANG F. [Research progress of solid phase extraction materials in the application of metal ion pretreatment]. Se Pu 2021; 39:455-462. [PMID: 34227329 PMCID: PMC9421574 DOI: 10.3724/sp.j.1123.2020.07004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Indexed: 11/25/2022] Open
Abstract
Monitoring of trace heavy metal pollutants released during industrial and agricultural processes is essential because of their widespread distribution in the environment and health hazards. Several techniques, including inductively coupled plasma-mass spectrometry (ICP-MS), inductively coupled plasma-optical emission spectrometry (ICP-OES), electrothermal atomic absorption (ETAAS), and flame atomic absorption spectrometry (FAAS), have been proposed for the determination of heavy metals in serum, plasma, whole blood, and food. All these techniques have earned robust recognition in the field of trace heavy metals and have many advantages such as multi-elemental analysis capability, large dynamic linear range, low detection limits, and high productivity. Nevertheless, most of the recommended techniques require digestion of the sample and extraction with an organic solvent for isolation of the metal ion from the sample solution prior to analysis. Despite improvements in the performance of modern analytical instruments, the direct determination of heavy metal ions in real samples is difficult because of their low concentration levels and matrix interference. Thus, extraction and clean-up steps are required for pre-concentration of the analyte, so that detection and elimination of the interfering matrix component are possible. Solid-phase extraction (SPE) is one of the popular metal ion pretreatment methods. The advantages of SPE include easy cartridge/column regeneration, high analytical frequency, and high preconcentration factors for sorbents with high adsorption capacities. On the other hand, when the analytes are extracted from a complex matrix such as serum and meat samples, large amounts of proteins from the samples can be retained on the sorbent surface, obstructing the binding sites on the sorbent and leading to poor precision and accuracy. The key to metal ion detection is the development of new SPE materials with high efficiency and enrichment factors as well as an effective pretreatment technology. Nanomaterials such as restricted-access carbon nanotubes, nanoadsorbents, nanoparticle carriers, and magnetic nanoparticles have shown great promise in advancing biomedical and environmental analysis because of the unique properties originating from their ultrafine dimensions. Nanomaterials can provide large specific surface areas and tunable functional groups to facilitate metal ion absorption. They could also possess superior optical properties and allow for high sensitivity in simple fluorescent or colorimetric detection methods. Owing to their excellent mechanical and chemical stability, polymer materials have been of great interest as adsorbents for the SPE of metal ions from solution. Moreover, a designed polymeric material can show triple functionality such as physical adsorption, chelate formation, and ion exchange for the target metal ions. A dual-functional nanomaterial-DNAzyme platform can simultaneously allow for the sensitive detection and effective removal of heavy metal ions in water. Thus, this platform can serve as a simple, cost-effective tool for rapid and accurate metal quantification in the determination of human metal exposure and inspection of environmental contamination. Furthermore, the new photocaged chelator can uncage and release the combined metal ions into an aqueous solution that is free of the other components of the matrix. In this manner, we can develop diagnostic tests for metal ions that are often difficult to detect using other methods. In this paper, the characteristics of new SPE materials, including nanomaterials, polymer materials, and functional materials as well as advances in their applications to the preparation of complex samples are summarized, and the direction for future development is proposed.
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Affiliation(s)
- Shige XING
- 中国检验检疫科学研究院食品安全研究所, 北京 100176
- Institute of Food Safety, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Muyi HE
- 中国检验检疫科学研究院食品安全研究所, 北京 100176
- Institute of Food Safety, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Tong LIU
- 中国检验检疫科学研究院食品安全研究所, 北京 100176
- Institute of Food Safety, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Wei YONG
- 中国检验检疫科学研究院食品安全研究所, 北京 100176
- Institute of Food Safety, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Feng ZHANG
- 中国检验检疫科学研究院食品安全研究所, 北京 100176
- Institute of Food Safety, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
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20
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Xing S, Lin Y, Cai L, Basa PN, Shigemoto AK, Zheng C, Zhang F, Burdette SC, Lu Y. Detection and Quantification of Tightly Bound Zn 2+ in Blood Serum Using a Photocaged Chelator and a DNAzyme Fluorescent Sensor. Anal Chem 2021; 93:5856-5861. [PMID: 33787228 DOI: 10.1021/acs.analchem.1c00140] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNAzymes have emerged as a powerful class of sensors for metal ions due to their high selectivity over a wide range of metal ions, allowing for on-site and real-time detection. Despite much progress made in this area, detecting and quantifying tightly bound metal ions, such as those in the blood serum, remain a challenge because the DNAzyme sensors reported so far can detect only mobile metal ions that are accessible to bind the DNAzymes. To overcome this major limitation, we report the use of a photocaged chelator, XDPAdeCage to extract the Zn2+ from the blood serum and then release the chelated Zn2+ into a buffer using 365 nm light for quantification by an 8-17 DNAzyme sensor. Protocols to chelate, uncage, extract, and detect metal ions in the serum have been developed and optimized. Because DNAzyme sensors for other metal ions have already been reported and more DNAzyme sensors can be obtained using in vitro selection, the method reported in this work will significantly expand the applications of the DNAzyme sensors from sensing metal ions that are not only free but also bound to other biomolecules in biological and environmental samples.
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Affiliation(s)
- Shige Xing
- Department of Chemistry, Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Institute of Food Safety, Chinese Academy of Inspection & Quarantine, Beijing 100176, China
| | - Yao Lin
- Department of Chemistry, Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Forensic Analytical Toxicology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Liangyuan Cai
- Department of Chemistry, Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Prem N Basa
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Road, Worcester, Massachusetts 01609-2280, United States
| | - Austin K Shigemoto
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Road, Worcester, Massachusetts 01609-2280, United States
| | - Chengbin Zheng
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Feng Zhang
- Institute of Food Safety, Chinese Academy of Inspection & Quarantine, Beijing 100176, China
| | - Shawn C Burdette
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Road, Worcester, Massachusetts 01609-2280, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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21
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Huang PJJ, Liu J. In vitro selection and application of lanthanide-dependent DNAzymes. Methods Enzymol 2021; 651:373-396. [PMID: 33888210 DOI: 10.1016/bs.mie.2021.01.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Highly sensitive and selective detection of lanthanide ions is a major analytical challenge. In recent years, the use of DNA for this purpose has been pursued. For such highly charged cations, it is difficult to select their aptamers due to strong nonspecific binding. On the other hand, the use of catalytic DNA or DNAzymes has an advantage to overcome this problem, especially DNAzymes with RNA-cleaving activity. In this chapter, a few such DNAzymes are introduced and methods for in vitro selection of lanthanide-dependent RNA-cleaving DNAzymes are described in detail, including the selection protocols, the DNA sequences used, the characterization of selected DNAzymes and their conversion into biosensors. All of the experiments use only fluorophore-labeled DNA, and radioisotope labeling is completely avoided. The resulting DNAzymes can distinguish lanthanides from non-lanthanide metals, tell the difference between light and heavy lanthanides, and can be used together to discriminate individual lanthanides.
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Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada.
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22
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Saran R, Huang Z, Liu J. Phosphorothioate nucleic acids for probing metal binding, biosensing and nanotechnology. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2020.213624] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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23
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Wang H, Luo Q, Zhao Y, Nan X, Zhang F, Wang Y, Wang Y, Hua D, Zheng S, Jiang L, Yang L, Xiong B. Electrochemical device based on nonspecific DNAzyme for the high-accuracy determination of Ca 2+ with Pb 2+ interference. Bioelectrochemistry 2020; 140:107732. [PMID: 33465700 DOI: 10.1016/j.bioelechem.2020.107732] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 12/17/2020] [Accepted: 12/19/2020] [Indexed: 12/13/2022]
Abstract
Calcium is one of the most abundant and indispensable elements in biology, as it is a vital component of nerves, bones, and muscles and maintains the excitability of normal neuromuscular muscles. However, it may be harmful to the human body and even damage the organs if the calcium content exceeds the standard value by several times. To evaluate the level of calcium ions (Ca2+), an electrochemical biosensor (FET/SWNTs/Cazyme) was developed using a nonspecific DNAzyme with high stability, which combined the unique advantage of field-effect transistors and single-walled carbon nanotubes, while being easy-to-use and having excellent sensitivity. The incubation time and voltage after optimization were 15 min and +0.02 V. The nonspecific DNAzyme-based biosensor was sensitive to Ca2+, but it was also interfered with by Pb2+, which affected the detection accuracy. To solve this shortcoming, an electrochemical device was proposed, in which FET/SWNTs/Cazyme combined with other specific biosensors for Pb2+, and then established some data processing models were established through support vector machine regression (SVMR) and artificial neural network fitting (ANNF). For the optimal SVMR, the electrochemical device can determine the Ca2+ concentration in the range of 7.5-1000 μM with a detection limit of 5.48 μM. Finally, the prepared electrochemical device was employed to detect the Ca2+ in different milk and water samples.
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Affiliation(s)
- Hui Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Qingyao Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Yiguang Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Xuemei Nan
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Fan Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China; State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, PR China
| | - Yaping Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Yue Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China; College of Animal Science and Technology, Northwest A&F University, Yangling 712100, PR China
| | - Dengke Hua
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Shanshan Zheng
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Linshu Jiang
- School of Animal Science and Technology, Beijing Agricultural University, Beijing Key Laboratory of Dairy Nutrition, Beijing 102206, PR China
| | - Liang Yang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
| | - Benhai Xiong
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
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24
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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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25
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Chakravarthy M, Chen S, Wang T, Veedu RN. Development of Novel Chemically-Modified Nucleic Acid Molecules for Efficient Inhibition of Human MAPT Gene Expression. Genes (Basel) 2020; 11:genes11060667. [PMID: 32575375 PMCID: PMC7349501 DOI: 10.3390/genes11060667] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 12/20/2022] Open
Abstract
The hyperphosphorylation of the microtubule-associated protein tau (MAPT) has been implicated in various neurological diseases, including Alzheimer’s disease. It has been hypothesized that the reduction of MAPT would result in depolymerizing neurofibrillary tangles and could be a potential strategy for the treatment of Alzheimer’s disease and other tauopathies. In this study, we report the development of novel DNAzymes and splice-modulating antisense oligonucleotides (AOs) for the efficient inhibition of MAPT. We designed and synthesized a range of DNAzymes and 2ʹ-O-methyl (2’-OMe)-modified AOs on a phosphorothioate (PS) backbone targeting various exons across the MAPT gene transcript. Our results demonstrated that RNV563, an arm-loop-arm-type DNAzyme targeting exon 13, and an AO candidate AO4, targeting exon 4, efficiently downregulated MAPT RNA expression by 58% and 96%, respectively. In addition, AO4 also reduced the MAPT protein level by 74%. In line with our results, we believe that AO4 could be used as a potential therapeutic molecule for Alzheimer’s disease and other tauopathies.
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Affiliation(s)
- Madhuri Chakravarthy
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth 6150, Australia; (M.C.); (S.C.); (T.W.)
- Perron Institute for Neurological and Translational Science, Perth 6150, Australia
| | - Suxiang Chen
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth 6150, Australia; (M.C.); (S.C.); (T.W.)
- Perron Institute for Neurological and Translational Science, Perth 6150, Australia
| | - Tao Wang
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth 6150, Australia; (M.C.); (S.C.); (T.W.)
- Perron Institute for Neurological and Translational Science, Perth 6150, Australia
| | - Rakesh N. Veedu
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth 6150, Australia; (M.C.); (S.C.); (T.W.)
- Perron Institute for Neurological and Translational Science, Perth 6150, Australia
- Correspondence:
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26
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Photoactivatable fluorescent probes for spatiotemporal-controlled biosensing and imaging. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115811] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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27
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Ma L, Liu J. Catalytic Nucleic Acids: Biochemistry, Chemical Biology, Biosensors, and Nanotechnology. iScience 2020; 23:100815. [PMID: 31954323 PMCID: PMC6962706 DOI: 10.1016/j.isci.2019.100815] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/11/2019] [Accepted: 12/26/2019] [Indexed: 01/06/2023] Open
Abstract
Since the initial discovery of ribozymes in the early 1980s, catalytic nucleic acids have been used in different areas. Compared with protein enzymes, catalytic nucleic acids are programmable in structure, easy to modify, and more stable especially for DNA. We take a historic view to summarize a few main interdisciplinary areas of research on nucleic acid enzymes that may have broader impacts. Early efforts on ribozymes in the 1980s have broken the notion that all enzymes are proteins, supplying new evidence for the RNA world hypothesis. In 1994, the first catalytic DNA (DNAzyme) was reported. Since 2000, the biosensor applications of DNAzymes have emerged and DNAzymes are particularly useful for detecting metal ions, a challenging task for enzymes and antibodies. Combined with nanotechnology, DNAzymes are key building elements for switches allowing dynamic control of materials assembly. The search for new DNAzymes and ribozymes is facilitated by developments in DNA sequencing and computational algorithms, further broadening our fundamental understanding of their biochemistry.
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Affiliation(s)
- Lingzi Ma
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada.
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28
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Huang PJ, Rochambeau D, Sleiman HF, Liu J. Target Self‐Enhanced Selectivity in Metal‐Specific DNAzymes. Angew Chem Int Ed Engl 2020; 59:3573-3577. [PMID: 31867832 DOI: 10.1002/anie.201915675] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Po‐Jung Jimmy Huang
- Department of ChemistryWaterloo Institute for Nanotechnology University of Waterloo 200 University Avenue West Waterloo Ontario N2L 3G1 Canada
| | - Donatien Rochambeau
- Department of ChemistryMcGill University 801 Sherbrooke Street West Montréal Québec H3A 0B8 Canada
| | - Hanadi F. Sleiman
- Department of ChemistryMcGill University 801 Sherbrooke Street West Montréal Québec H3A 0B8 Canada
| | - Juewen Liu
- Department of ChemistryWaterloo Institute for Nanotechnology University of Waterloo 200 University Avenue West Waterloo Ontario N2L 3G1 Canada
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29
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Huang PJ, Rochambeau D, Sleiman HF, Liu J. Target Self‐Enhanced Selectivity in Metal‐Specific DNAzymes. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915675] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Po‐Jung Jimmy Huang
- Department of ChemistryWaterloo Institute for Nanotechnology University of Waterloo 200 University Avenue West Waterloo Ontario N2L 3G1 Canada
| | - Donatien Rochambeau
- Department of ChemistryMcGill University 801 Sherbrooke Street West Montréal Québec H3A 0B8 Canada
| | - Hanadi F. Sleiman
- Department of ChemistryMcGill University 801 Sherbrooke Street West Montréal Québec H3A 0B8 Canada
| | - Juewen Liu
- Department of ChemistryWaterloo Institute for Nanotechnology University of Waterloo 200 University Avenue West Waterloo Ontario N2L 3G1 Canada
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30
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Le Vay K, Salibi E, Song EY, Mutschler H. Nucleic Acid Catalysis under Potential Prebiotic Conditions. Chem Asian J 2020; 15:214-230. [PMID: 31714665 PMCID: PMC7003795 DOI: 10.1002/asia.201901205] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/05/2019] [Indexed: 01/25/2023]
Abstract
Catalysis by nucleic acids is indispensable for extant cellular life, and it is widely accepted that nucleic acid enzymes were crucial for the emergence of primitive life 3.5-4 billion years ago. However, geochemical conditions on early Earth must have differed greatly from the constant internal milieus of today's cells. In order to explore plausible scenarios for early molecular evolution, it is therefore essential to understand how different physicochemical parameters, such as temperature, pH, and ionic composition, influence nucleic acid catalysis and to explore to what extent nucleic acid enzymes can adapt to non-physiological conditions. In this article, we give an overview of the research on catalysis of nucleic acids, in particular catalytic RNAs (ribozymes) and DNAs (deoxyribozymes), under extreme and/or unusual conditions that may relate to prebiotic environments.
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Affiliation(s)
- Kristian Le Vay
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Elia Salibi
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Emilie Y. Song
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Hannes Mutschler
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
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31
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Lake RJ, Yang Z, Zhang J, Lu Y. DNAzymes as Activity-Based Sensors for Metal Ions: Recent Applications, Demonstrated Advantages, Current Challenges, and Future Directions. Acc Chem Res 2019; 52:3275-3286. [PMID: 31721559 PMCID: PMC7103667 DOI: 10.1021/acs.accounts.9b00419] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Metal ions can be beneficial or toxic depending on their identity, oxidation state, and concentration. Therefore, the ability to detect and quantify different types of metal ions using portable sensors or in situ imaging agents is important for better environmental monitoring, in vitro medical diagnostics, and imaging of biological systems. While numerous metal ions in different oxidation states are present in the environment and biological systems, only a limited number of them can be detected effectively using current methods. In this Account, we summarize research results from our group that overcome this limitation by the development of a novel class of activity-based sensors based on metal-dependent DNAzymes, which are DNA molecules with enzymatic activity. First, we have developed an in vitro selection method to obtain DNAzymes from a large DNA library of up to 1015 sequences that can carry out cleavage of an oligonucleotide substrate only in the presence of a specific metal ion with high selectivity. Negative selection steps can further be used to improve the selectivity against potentially competing targets by removing sequences that recognize the competing metal ions. Second, we have developed a patented catalytic beacon method to transform the metal-dependent DNAzyme cleavage reaction into a turn-on fluorescent signal by attaching a fluorophore and quenchers to the DNAzyme complex. Because of the difference in the melting temperatures of DNA hybridization before and after metal-ion-dependent cleavage of the DNAzyme substrate, the fluorophore on the DNA cleavage product can be released from its quenchers to create a turn-on fluorescent signal. Because DNAzymes are easy to conjugate with other signaling moieties, such as gold nanoparticles, lanthanide-doped upconversion nanoparticles, electrochemical agents, and gadolinium complexes, these DNAzymes can also readily be converted into colorimetric sensors, upconversion luminescence sensors, electrochemical sensors, or magnetic resonance contrast agents. In addition to describing recent progress in developing and applying these metal ion sensors for environmental monitoring, point-of-care diagnostics, cellular imaging, and in vivo imaging in zebrafish, we summarize major advantages of this class of activity-based sensors. In addition to advantages common to most activity-based sensors, such as enzymatic turnovers that allow for signal amplification and the use of initial rates instead of absolute signals for quantification to avoid interferences from sample matrices, the DNAzyme-based sensors allow for in vitro selection to expand the method to almost any metal ion under a variety of conditions, negative selection to improve the selectivity against competing targets, and reselection of DNAzymes and combination of active and inactive variants to fine-tune the dynamic range of detection. The use of melting temperature differences to separate target binding from signaling moieties in the catalytic beacon method allows the use of different fluorophores and nanomaterials to extend the versatility and modularity of this sensing platform. Furthermore, sensing and imaging artifacts can be minimized by using an inactive mutant DNAzyme as a negative control, while spatiotemporal control of sensing/imaging can be achieved using optical, photothermal, and endogenous orthogonal caging methods. Finally, current challenges, opportunities, and future perspectives for DNAzymes as activity-based sensors are also discussed.
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Affiliation(s)
- Ryan J. Lake
- Department of Chemistry, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Zhenglin Yang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
- Department of Biochemistry, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - JingJing Zhang
- Department of Chemistry, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
- Department of Biochemistry, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
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32
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Mahapatra M, Dutta A, Roy JSD, Mitra M, Mahalanobish S, Sanfui MDH, Banerjee S, Chattopadhyay PK, Sil PC, Singha NR. Fluorescent Terpolymers via In Situ Allocation of Aliphatic Fluorophore Monomers: Fe(III) Sensor, High-Performance Removals, and Bioimaging. Adv Healthc Mater 2019; 8:e1900980. [PMID: 31664786 DOI: 10.1002/adhm.201900980] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/21/2019] [Indexed: 12/22/2022]
Abstract
Herein, purely aliphatic intrinsically fluorescent terpolymers, i.e., 1 and 2, are synthesized through one-pot solution polymerization via N-H functionalized and multi C-C/C-N coupled in situ protrusion of fluorescent monomers using two nonemissive monomers. These scalable terpolymers are suitable for highly selective Fe(III) sensing, high-performance exclusion of Fe(III), logic function and the imaging of normal mammalian Madin-Darby canine kidney and human osteosarcoma cancer cell lines. The structures of terpolymers, in situ attachment of fluorescent monomers, clusteroluminescence, adsorption-mechanism, and cell-imaging abilities are understood via unadsorbed and/or adsorbed microstructural analyses using 1 H/13 C NMR, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, UV-vis spectroscopy, atomic absorption spectroscopy, thermogravimetric analysis, high-resolution transmission electron microscopy, dynamic light scattering, fluorescence imaging, and fluorescence lifetime. The geometries, electronic structures, location of fluorophores, and singlet-singlet absorption and emission of terpolymers are examined using density functional theory (DFT) and time-dependent DFT. For the precise identification of fluorophores, transition from occupied natural transition orbitals (NTOs) to unoccupied NTOs is computed. For 1/2, limit of detection (LOD) values and adsorption capacities are 6.0 × 10-7 /8.0 × 10-7 m and 147.82/120.56 mg g-1 at pHi = 7.0 and 303 K, respectively. The overall properties of 1 are more advantageous compared to 2 in sensing, cell imaging, and adsorptive exclusion of Fe(III).
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Affiliation(s)
- Manas Mahapatra
- Advanced Polymer LaboratoryDepartment of Polymer Science and TechnologyGovernment College of Engineering and Leather Technology (Post Graduate)Maulana Abul Kalam Azad University of Technology Salt Lake City Kolkata 700106 West Bengal India
| | - Arnab Dutta
- Advanced Polymer LaboratoryDepartment of Polymer Science and TechnologyGovernment College of Engineering and Leather Technology (Post Graduate)Maulana Abul Kalam Azad University of Technology Salt Lake City Kolkata 700106 West Bengal India
| | - Joy Sankar Deb Roy
- Advanced Polymer LaboratoryDepartment of Polymer Science and TechnologyGovernment College of Engineering and Leather Technology (Post Graduate)Maulana Abul Kalam Azad University of Technology Salt Lake City Kolkata 700106 West Bengal India
| | - Madhushree Mitra
- Department of Leather TechnologyGovernment College of Engineering and Leather Technology (Post Graduate)Maulana Abul Kalam Azad University of Technology Salt Lake City Kolkata 700106 West Bengal India
| | - Sushweta Mahalanobish
- Division of Molecular MedicineBose Institute P‐1/12, CIT Scheme VII M Kolkata 700054 West Bengal India
| | - MD Hussain Sanfui
- Advanced Polymer LaboratoryDepartment of Polymer Science and TechnologyGovernment College of Engineering and Leather Technology (Post Graduate)Maulana Abul Kalam Azad University of Technology Salt Lake City Kolkata 700106 West Bengal India
| | - Snehasis Banerjee
- Department of ChemistryGovernment College of Engineering and Leather Technology (Post Graduate)Maulana Abul Kalam Azad University of Technology Salt Lake City Kolkata 700106 West Bengal India
| | - Pijush Kanti Chattopadhyay
- Department of Leather TechnologyGovernment College of Engineering and Leather Technology (Post Graduate)Maulana Abul Kalam Azad University of Technology Salt Lake City Kolkata 700106 West Bengal India
| | - Parames C. Sil
- Division of Molecular MedicineBose Institute P‐1/12, CIT Scheme VII M Kolkata 700054 West Bengal India
| | - Nayan Ranjan Singha
- Advanced Polymer LaboratoryDepartment of Polymer Science and TechnologyGovernment College of Engineering and Leather Technology (Post Graduate)Maulana Abul Kalam Azad University of Technology Salt Lake City Kolkata 700106 West Bengal India
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33
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Du S, Li Y, Chai Z, Shi W, He J. Functionalization of 8-17 DNAzymes modulates catalytic efficiency and divalent metal ion preference. Bioorg Chem 2019; 94:103401. [PMID: 31711763 DOI: 10.1016/j.bioorg.2019.103401] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/17/2019] [Accepted: 10/24/2019] [Indexed: 11/26/2022]
Abstract
8-17 and 17E DNAzyme are being explored as biosensors for metal ions and RNA motifs of interest, more sensitive and efficient DNAzymes are required to meet the practical applications. Their similarity in the catalytic cores and differences in catalytic efficiency and metal ion dependence initiated great interest about the contribution of the catalytic residues. Functionalization of four adenine residues in the catalytic cores of 8-17 DNAzyme and 17E was conducted with amino, guanidinium, and imidazolyl groups. In the bulge loops of 8-17 and 17E, N6-(3-aminopropyl)-2'-deoxyadenosine (residue 1) at A15 led to new DNAzymes 8-17DZ-A15-1 and 17E-A15-1, with much more efficient cleavage ability in the Ca2+-mediated reaction and the greater preference for Ca2+ over Mg2+ than 8-17 DNAzyme and 17E, respectively, especially with a concentration-dependent increase of the selectivity, which is different from most DNAzymes with the similar dependence on both Mg2+ and Ca2+. With this kind of post-selection modification on 8-17 DNAzymes, for the first time, the catalytic efficiency and metal ion selectivity could be positively modulated. It is also helpful for the catalyic mechanistic studies of these DNAzymes, especially, the role of the unconserved A15 should be emphasized.
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Affiliation(s)
- Shanshan Du
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Yang Li
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Zhilong Chai
- School of Pharmaceutical Sciences, Guizhou University, Guizhou 550025, China
| | - Weiguo Shi
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China.
| | - Junlin He
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China.
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34
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Moon WJ, Liu J. Replacing Mg2+by Fe2+for RNA‐Cleaving DNAzymes. Chembiochem 2019; 21:401-407. [DOI: 10.1002/cbic.201900344] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Woohyun J. Moon
- Department of ChemistryWaterloo Institute for NanotechnologyUniversity of Waterloo Waterloo Ontario N2L 3G1 Canada
| | - Juewen Liu
- Department of ChemistryWaterloo Institute for NanotechnologyUniversity of Waterloo Waterloo Ontario N2L 3G1 Canada
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35
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Peng D, Li Y, Huang Z, Liang RP, Qiu JD, Liu J. Efficient DNA-Catalyzed Porphyrin Metalation for Fluorescent Ratiometric Pb 2+ Detection. Anal Chem 2019; 91:11403-11408. [PMID: 31414597 DOI: 10.1021/acs.analchem.9b02759] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Developing biosensors for Pb2+ is an important analytical topic. DNA-based Pb2+ sensors have been designed mainly based on RNA-cleaving DNAzymes and Pb2+-induced folding of G-quadruplex (G4) DNA. Porphyrin metalation is a key reaction in biology and catalysis. Many enzyme mimics have been developed to catalyze this reaction, and some metalation DNAzymes were reported with a G4 structure. Inspired by the excellent G4 binding properties of certain divalent metal ions, we herein screened a few metals and G-rich DNA sequences. The metalation activity of a DNA named T30695 (sequence: (G3T)4) was significantly accelerated by Pb2+. The reaction of Cu2+ insertion into the mesoporphyrin IX had a kcat of 0.89 min-1 and a Km of 9.8 μM, representing a catalytic efficiency similar to that of human ferrochelatase. The reason for the acceleration was attributed to Pb2+ binding of the G4 DNA and the catalytic activity of the large Pb2+ ion for this reaction. A ratiometric sensor for Pb2+ was developed by inserting Zn2+ with a detection limit of 23.5 nM Pb2+. This work has established a new DNA-based reaction that can be used for Pb2+ detection, and it also provides a highly efficient new DNAzyme for porphyrin metalation, which might be used for signal production for other biosensors.
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Affiliation(s)
- Dong Peng
- College of Chemistry , Nanchang University , 999 Xuefu Avenue , Nanchang , 330031 Jiangxi , China.,Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Yuqing Li
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Zhicheng Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Ru-Ping Liang
- College of Chemistry , Nanchang University , 999 Xuefu Avenue , Nanchang , 330031 Jiangxi , China
| | - Jian-Ding Qiu
- College of Chemistry , Nanchang University , 999 Xuefu Avenue , Nanchang , 330031 Jiangxi , China.,Environmental Protection Materials and Equipment Engineering Technology Center of Jiangxi, Department of Materials and Chemical Engineering , Pingxiang University , 211 Pingan North Road , Pingxiang , 337055 Jiangxi , China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
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36
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A Novel Small RNA-Cleaving Deoxyribozyme with a Short Binding Arm. Sci Rep 2019; 9:8224. [PMID: 31160698 PMCID: PMC6546695 DOI: 10.1038/s41598-019-44750-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 04/17/2019] [Indexed: 01/12/2023] Open
Abstract
Deoxyribozymes capable of catalyzing sequence-specific RNA cleavage have found broad applications in biotechnology, DNA computing and environmental sensing. Among these, deoxyribozyme 8–17 is the most common small DNA motif capable of catalyzing RNA cleavage. However, the extent to which other DNA molecules with similar catalytic motifs exist remains elusive. Here we report a novel RNA-cleaving deoxyribozyme called 10–12opt that functions with an equally small catalytic motif and an unusually short binding arm. This deoxyribozyme contains a 14-nucleotide catalytic core that preferentially catalyzes RNA cleavage at UN dinucleotide junctions (kobs = 0.9 h−1 for UU cleavage). Surprisingly, the left binding arm contains only three nucleotides and forms two canonical base pairs with the RNA substrate. Mutational analysis reveals that a riboguanosine residue 3-nucleotide downstream of cleavage site must not form canonical base pairing for the optimal catalysis, and this nucleobase likely participates in catalysis with its carbonyl O6 atom. Furthermore, we demonstrate that deoxyribozyme 10–12opt can be utilized to cleave certain microRNA sequences which are not preferentially cleaved by 8–17. Together, these results suggest that this novel RNA-cleaving deoxyribozyme forms a distinct catalytic structure than 8–17 and that sequence space may contain additional examples of DNA molecules that can cleave RNA at site-specific locations.
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37
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Zhang T, Liu C, Zhou W, Jiang K, Yin C, Liu C, Zhang Z, Li H. Ultrasensitive Detection of Pb 2+ Based on a DNAzyme and Digital PCR. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2019; 2019:3528345. [PMID: 30867973 PMCID: PMC6379836 DOI: 10.1155/2019/3528345] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/30/2018] [Accepted: 10/10/2018] [Indexed: 06/09/2023]
Abstract
In this study, an ultrasensitive detection method for aqueous Pb2+ based on digital polymerase chain reaction (dPCR) technology and a Pb2+-dependent DNAzyme was developed. In the presence of Pb2+, the Gr-5 DNAzyme was activated and catalyzed the hydrolytic cleavage of the substrate strand, resulting in an increase in the amount of template DNA available for dPCR and a resultant change in the number of droplets showing a positive signal. Moreover, the detection system was found to be sensitive and stable in environmental sample detection. In summary, an ultrasensitive quantitative detection method for Pb2+ within environmental substrates was established.
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Affiliation(s)
- Tao Zhang
- Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Cong Liu
- Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Wuping Zhou
- Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Keming Jiang
- Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Chenyu Yin
- Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Cong Liu
- Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
- School of Engineering Science, University of Science and Technology, Hefei, China
| | - Zhiqiang Zhang
- Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Haiwen Li
- Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
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38
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Deng R, Yang H, Dong Y, Zhao Z, Xia X, Li Y, Li J. Temperature-Robust DNAzyme Biosensors Confirming Ultralow Background Detection. ACS Sens 2018; 3:2660-2666. [PMID: 30457325 DOI: 10.1021/acssensors.8b01122] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Catalytic DNA/RNA, such as DNAzyme, has been widely adopted to construct biosensors, especially for metal ion analysis. However, traditional DNAzyme biosensors still suffer from fluctuating and relatively high background. Herein, we proposed a temperature-robust DNAzyme, conferring ultralow background in various temperatures, thus leading to highly sensitive and robust detection of metal ions. Instead of labeling substrate to directly output fluorescence signal, our proposed DNAzyme biosensor utilized a sequential detection process with a couple of proximity fluorescent probes, confirming very low background regardless of the conditions of cleavage reaction. This sequential DNAzyme biosensor conferred a signal to background ratio over 20 when the temperature of the catalytic reaction ranged from 20 to 41 °C. Benefitting from its ultralow background, it could confer a detection limit of 0.22 nM, which ranked as one of the highest sensitivity levels among DNAzyme-based fluorescent biosensors. This DNAzyme biosensor was over 6000 times more selective for Pb2+ against the most active interfering metal ions, Zn2+. Further, it has been successfully applied for analyzing lead pollution in tap water and eggs, with total recoveries ranging from 87% to 114%. This facile, simple, and effective design strategy would significantly improve the detection performance of DNAzyme biosensors, thus facilitating its practical applications for both food safety analysis and environment monitoring.
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Affiliation(s)
- Ruijie Deng
- College of Light Industry, Textile and Food Engineering, Healthy Food Evaluation Research Center and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province, Sichuan University, Chengdu 610065, China
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Hao Yang
- College of Light Industry, Textile and Food Engineering, Healthy Food Evaluation Research Center and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province, Sichuan University, Chengdu 610065, China
| | - Yi Dong
- College of Light Industry, Textile and Food Engineering, Healthy Food Evaluation Research Center and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province, Sichuan University, Chengdu 610065, China
| | - Zhifeng Zhao
- College of Light Industry, Textile and Food Engineering, Healthy Food Evaluation Research Center and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province, Sichuan University, Chengdu 610065, China
| | - Xuhan Xia
- College of Light Industry, Textile and Food Engineering, Healthy Food Evaluation Research Center and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province, Sichuan University, Chengdu 610065, China
| | - Yue Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
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39
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He Y, Zhou Y, Chen D, Liu J. Global Folding of a Na
+
‐Specific DNAzyme Studied by FRET. Chembiochem 2018; 20:385-393. [DOI: 10.1002/cbic.201800548] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Yanping He
- State Key Laboratory of Precision Measurement Technology and InstrumentsUniversity of Tianjin Tianjin 300072 P.R. China
- Department of Chemistry, Waterloo Institute for NanotechnologyUniversity of Waterloo Waterloo Ontario N2L 3G1 Canada
| | - Yibo Zhou
- School of Chemistry and Biological EngineeringChangsha University of Science and Technology Changsha 410114 P.R. China
| | - Da Chen
- State Key Laboratory of Precision Measurement Technology and InstrumentsUniversity of Tianjin Tianjin 300072 P.R. China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for NanotechnologyUniversity of Waterloo Waterloo Ontario N2L 3G1 Canada
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40
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Yang Z, Loh KY, Chu YT, Feng R, Satyavolu NSR, Xiong M, Nakamata Huynh SM, Hwang K, Li L, Xing H, Zhang X, Chemla YR, Gruebele M, Lu Y. Optical Control of Metal Ion Probes in Cells and Zebrafish Using Highly Selective DNAzymes Conjugated to Upconversion Nanoparticles. J Am Chem Soc 2018; 140:17656-17665. [PMID: 30427666 DOI: 10.1021/jacs.8b09867] [Citation(s) in RCA: 175] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Spatial and temporal distributions of metal ions in vitro and in vivo are crucial in our understanding of the roles of metal ions in biological systems, and yet there is a very limited number of methods to probe metal ions with high space and time resolution, especially in vivo. To overcome this limitation, we report a Zn2+-specific near-infrared (NIR) DNAzyme nanoprobe for real-time metal ion tracking with spatiotemporal control in early embryos and larvae of zebrafish. By conjugating photocaged DNAzymes onto lanthanide-doped upconversion nanoparticles (UCNPs), we have achieved upconversion of a deep tissue penetrating NIR 980 nm light into 365 nm emission. The UV photon then efficiently photodecages a substrate strand containing a nitrobenzyl group at the 2'-OH of adenosine ribonucleotide, allowing enzymatic cleavage by a complementary DNA strand containing a Zn2+-selective DNAzyme. The product containing a visible FAM fluorophore that is initially quenched by BHQ1 and Dabcyl quenchers is released after cleavage, resulting in higher fluorescent signals. The DNAzyme-UCNP probe enables Zn2+ sensing by exciting in the NIR biological imaging window in both living cells and zebrafish embryos and detecting in the visible region. In this study, we introduce a platform that can be used to understand the Zn2+ distribution with spatiotemporal control, thereby giving insights into the dynamical Zn2+ ion distribution in intracellular and in vivo models.
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Affiliation(s)
| | | | | | | | | | - Mengyi Xiong
- Institute of Chemical Biology and Nanomedicine, College of Chemistry and Chemical Engineering , Hunan University , Changsha , Hunan 410082 , China
| | | | | | - Lele Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , China
| | - Hang Xing
- Institute of Chemical Biology and Nanomedicine, College of Chemistry and Chemical Engineering , Hunan University , Changsha , Hunan 410082 , China
| | - Xiaobing Zhang
- Institute of Chemical Biology and Nanomedicine, College of Chemistry and Chemical Engineering , Hunan University , Changsha , Hunan 410082 , China
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41
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Gu L, Saran R, Yan W, Huang PJJ, Wang S, Lyu M, Liu J. Reselection Yielding a Smaller and More Active Silver-Specific DNAzyme. ACS OMEGA 2018; 3:15174-15181. [PMID: 31458180 PMCID: PMC6643755 DOI: 10.1021/acsomega.8b02039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/31/2018] [Indexed: 05/11/2023]
Abstract
Ag10c is a recently reported RNA-cleaving DNAzyme obtained from in vitro selection. Its cleavage activity selectively requires Ag+ ions, and thus it has been used as a sensor for Ag+ detection. However, the previous selection yielded very limited information regarding its sequence requirement, since only ∼0.1% of the population in the final library were related to Ag10c and most other sequences were inactive. In this work, we performed a reselection by randomizing the 19 important nucleotides in Ag10c in such a way that a purine has an equal chance of being A or G, whereas a pyrimidine has an equal chance of being T or C. The round 3 library of the reselection was carefully analyzed and a statistic understanding of the relative importance of each nucleotide was obtained. At the same time, a more active mutant was identified, containing two mutated nucleotides. Further analysis indicated new base pairs leading to an enzyme with smaller catalytic loops but with ∼200% activity of the original Ag10c, and also excellent selectivity for Ag+. Therefore, a more active mutant of Ag10c was obtained and further truncations were successfully performed, which might be better candidates for developing new biosensors for silver. A deeper biochemical understanding was also obtained using this reselection method.
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Affiliation(s)
- Lide Gu
- College
of Marine Life and Fisheries and Jiangsu Key Laboratory of Marine
Bioresources and Environment, Huaihai Institute
of Technology, Lianyungang 222005, P. R. China
- Marine
Resources Development Institute of Jiangsu, Lianyungang 222005, P. R. China
- Department
of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Runjhun Saran
- Department
of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Wanli Yan
- College
of Marine Life and Fisheries and Jiangsu Key Laboratory of Marine
Bioresources and Environment, Huaihai Institute
of Technology, Lianyungang 222005, P. R. China
- Marine
Resources Development Institute of Jiangsu, Lianyungang 222005, P. R. China
| | - Po-Jung Jimmy Huang
- Department
of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Shujun Wang
- College
of Marine Life and Fisheries and Jiangsu Key Laboratory of Marine
Bioresources and Environment, Huaihai Institute
of Technology, Lianyungang 222005, P. R. China
- Marine
Resources Development Institute of Jiangsu, Lianyungang 222005, P. R. China
| | - Mingsheng Lyu
- College
of Marine Life and Fisheries and Jiangsu Key Laboratory of Marine
Bioresources and Environment, Huaihai Institute
of Technology, Lianyungang 222005, P. R. China
- Marine
Resources Development Institute of Jiangsu, Lianyungang 222005, P. R. China
- Department
of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- E-mail: (M.L.)
| | - Juewen Liu
- Department
of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- E-mail: (J.L.)
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42
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Ma L, Liu J. An in Vitro-Selected DNAzyme Mutant Highly Specific for Na + under Slightly Acidic Conditions. Chembiochem 2018; 20:537-542. [PMID: 29989277 DOI: 10.1002/cbic.201800322] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Indexed: 12/19/2022]
Abstract
Sodium is one of the most common metal ions in biology; however, DNA-based sodium probes have only been reported recently. A Na+ -specific RNA-cleaving DNAzyme named NaA43 is active with Na+ alone. In this work, we were using Co(NH3 )6 3+ as the intended metal cofactor for in vitro selection, but obtained a mutant of the NaA43 DNAzyme. The mutant was named NaH1, and differs from NaA43 by only two nucleotides. NaA43 has an optimal pH of 7.0, whereas the optimal pH for NaH1 is 6.0. This difference might be due to our selection having been performed at pH 6.0. NaH1 also displays an excellent selectivity for sodium relative to other competing monovalent ions, as well as a fast catalytic rate of (0.11±0.01) min-1 with 50 mm Na+ . At low Na+ concentrations, the selected DNAzyme exhibited a higher cleavage rate than NaA43 and thus a tighter apparent Kd of (12.0±1.6) mm Na+ . Furthermore, the NaH1 DNAzyme was engineered into a fluorescent Na+ biosensor by attaching a fluorophore/quencher pair to the DNAzyme with a detection limit of 223 μm Na+ . Preliminary work on detection of Na+ in serum was demonstrated as well. This study provides a useful mutant that works in a slightly acidic environment, which might be useful for sensing Na+ in acidic in vivo environments.
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Affiliation(s)
- Lingzi Ma
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
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43
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Affiliation(s)
- Tianmeng Yu
- Department of Chemistry and Waterloo Institute for Nanotechnology; University of Waterloo; 200 University Avenue West Waterloo Ontario N2L 3G1 Canada
| | - Wenhu Zhou
- Department of Chemistry and Waterloo Institute for Nanotechnology; University of Waterloo; 200 University Avenue West Waterloo Ontario N2L 3G1 Canada
- Xiangya School of Pharmaceutical Sciences; Central South University; 172 Tongzipo Road Changsha Hunan 410013 China
| | - Juewen Liu
- Department of Chemistry and Waterloo Institute for Nanotechnology; University of Waterloo; 200 University Avenue West Waterloo Ontario N2L 3G1 Canada
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44
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Wang H, Liu Y, Liu G. Electrochemical Biosensor Using DNA Embedded Phosphorothioate Modified RNA for Mercury Ion Determination. ACS Sens 2018; 3:624-631. [PMID: 29489332 DOI: 10.1021/acssensors.7b00892] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Mercury (Hg) and its compounds, originating from a variety of natural and anthropogenic sources, are ubiquitous in the natural environment, and cause severe environmental contamination and pose irreversible harm to human health. A fast and accurate sensing approach is of significant importance for mercury detection. Here, a label-free biosensor using Hg(II)-induced cleavage of phosphorothioate (PS) modified RNA was exploited. We designed a specific single-stranded DNA embedded with four PS-modified RNA (Hg-DPR) to improve the cleavage reaction yield, and then Hg-DPR was covalently linked with single-walled carbon nanotube field effect transistor (SWNTs/FET) via a peptide bond. The Hg-DPR can be efficiently cleaved after exposure to Hg(II), which further causes the conductivity of the SWNTs to change. Using the relative resistance change, the Hg-DPR/SWNTs/FET successfully detected Hg(II) levels as low as 10 pM, and the calibration curves were linear in the range of 50 pM to 100 nM and 100 nM to 10 μM. Additionally, Hg-DPR/SWNTs/FET exhibited excellent sensitivity, portability, and low-cost for Hg(II) detection.
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Affiliation(s)
- Hui Wang
- Key Laboratory of Modern Precision Agriculture System Integration Research, Ministry of Education and Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture, China Agricultural University, Beijing 100083, P.R. China
| | - Yang Liu
- Xi’an Jiaotong University, School of Electronic and Information Engineering, Xi’an 710049, P.R. China
| | - Gang Liu
- Key Laboratory of Modern Precision Agriculture System Integration Research, Ministry of Education and Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture, China Agricultural University, Beijing 100083, P.R. China
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45
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Li L, Ma X, Dong W, Miao P, Tang Y. Electrochemical Determination of Ca 2+ Based On Recycling Formation of Highly Selective DNAzyme and Gold Nanoparticle-Mediated Amplification. Bioconjug Chem 2018. [PMID: 29528621 DOI: 10.1021/acs.bioconjchem.8b00096] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Calcium ion (Ca2+) plays a critical and indispensable role in many physiological and biochemical processes in the human body. In this report, we demonstrate a novel electrochemical method for the determination of the Ca2+ level aided by three functional DNA probes and gold nanoparticles (AuNPs). It affords high selectivity in sensing Ca2+ over other metal cations, which is due to the adoption of the DNAzyme at the electrode interface with exceptionally high binding ability. This method also integrates recycling formation of DNAzyme and AuNPs-mediated amplification; thus, high sensitivity is promised. Therefore, this work provides a favorable way to probe Ca2+ for biomedical applications.
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Affiliation(s)
- Li Li
- Suzhou Institute of Biomedical Engineering and Technology , Chinese Academy of Sciences , Suzhou 215163 , People's Republic of China
| | - Xiaoyi Ma
- Suzhou Institute of Biomedical Engineering and Technology , Chinese Academy of Sciences , Suzhou 215163 , People's Republic of China.,University of Science and Technology of China , Hefei 230026 , People's Republic of China
| | - Wenfei Dong
- Suzhou Institute of Biomedical Engineering and Technology , Chinese Academy of Sciences , Suzhou 215163 , People's Republic of China
| | - Peng Miao
- Suzhou Institute of Biomedical Engineering and Technology , Chinese Academy of Sciences , Suzhou 215163 , People's Republic of China.,University of Science and Technology of China , Hefei 230026 , People's Republic of China
| | - Yuguo Tang
- Suzhou Institute of Biomedical Engineering and Technology , Chinese Academy of Sciences , Suzhou 215163 , People's Republic of China
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46
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Zhou W, Ding J, Liu J. Splitting a DNAzyme enables a Na +-dependent FRET signal from the embedded aptamer. Org Biomol Chem 2018; 15:6959-6966. [PMID: 28792040 DOI: 10.1039/c7ob01709j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Recently, a few Na+-specific RNA-cleaving DNAzymes have been reported, and a Na+ aptamer was identified from the NaA43 and Ce13d DNAzymes. These DNAzymes and the embedded aptamer have been used for Na+ detection. In this work, we studied the Na+-dependent folding of the Ce13d DNAzyme using fluorescence resonance energy transfer (FRET). When a FRET donor and an acceptor were respectively labeled at the ends of the DNAzyme, Na+ failed to induce an obvious end-to-end distance change, suggesting a rigid global structure. To relax this rigidity, the Ce13d DNAzyme was systematically split at various sites on both the enzyme and the substrate strands. The Na+ binding activity of the split structures was characterized by 2-aminopurine fluorescence, enzymatic activity, Tb3+-sensitized luminescence, and DMS footprinting. Among the various constructs, the only one that retained Na+ binding was the split at the cleavage site, and this construct was further labeled with two dyes near the split site. This FRET result showed Na+-dependent folding with a Kd of 26 mM Na+. This study provides important structural information related to Na+ binding to this new aptamer, which might also be useful for future work in biosensor design.
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Affiliation(s)
- Wenhu Zhou
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
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47
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Hu Q, Li H, Wang L, Gu H, Fan C. DNA Nanotechnology-Enabled Drug Delivery Systems. Chem Rev 2018; 119:6459-6506. [PMID: 29465222 DOI: 10.1021/acs.chemrev.7b00663] [Citation(s) in RCA: 559] [Impact Index Per Article: 93.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Over the past decade, we have seen rapid advances in applying nanotechnology in biomedical areas including bioimaging, biodetection, and drug delivery. As an emerging field, DNA nanotechnology offers simple yet powerful design techniques for self-assembly of nanostructures with unique advantages and high potential in enhancing drug targeting and reducing drug toxicity. Various sequence programming and optimization approaches have been developed to design DNA nanostructures with precisely engineered, controllable size, shape, surface chemistry, and function. Potent anticancer drug molecules, including Doxorubicin and CpG oligonucleotides, have been successfully loaded on DNA nanostructures to increase their cell uptake efficiency. These advances have implicated the bright future of DNA nanotechnology-enabled nanomedicine. In this review, we begin with the origin of DNA nanotechnology, followed by summarizing state-of-the-art strategies for the construction of DNA nanostructures and drug payloads delivered by DNA nanovehicles. Further, we discuss the cellular fates of DNA nanostructures as well as challenges and opportunities for DNA nanostructure-based drug delivery.
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Affiliation(s)
- Qinqin Hu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University , Shanghai 200032 , China.,Department of Systems Biology for Medicine , School of Basic Medical Sciences, Fudan University , Shanghai 200032 , China
| | - Hua Li
- Shanghai Institute of Cardiovascular Diseases , Zhongshan Hospital, Fudan University , Shanghai 200032 , China.,Research & Development Center, Shandong Buchang Pharmaceutical Company, Limited, Heze 274000 , China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility Shanghai Institute of Applied Physics , Chinese Academy of Sciences , Shanghai 201800 , China.,School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Hongzhou Gu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University , Shanghai 200032 , China.,Department of Systems Biology for Medicine , School of Basic Medical Sciences, Fudan University , Shanghai 200032 , China.,Shanghai Institute of Cardiovascular Diseases , Zhongshan Hospital, Fudan University , Shanghai 200032 , China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility Shanghai Institute of Applied Physics , Chinese Academy of Sciences , Shanghai 201800 , China.,School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , China
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48
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Abstract
Nucleic acid enzymes require metal ions for activity, and many recently discovered enzymes can use multiple metals, either binding to the scissile phosphate or also playing an allosteric role.
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Affiliation(s)
- Wenhu Zhou
- Xiangya School of Pharmaceutical Sciences
- Central South University
- Changsha
- China
| | - Juewen Liu
- Department of Chemistry
- Water Institute, and Waterloo Institute for Nanotechnology
- University of Waterloo
- Waterloo
- Canada
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49
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Yu T, Zhou W, Liu J. Ultrasensitive DNAzyme-Based Ca 2+ Detection Boosted by Ethanol and a Solvent-Compatible Scaffold for Aptazyme Design. Chembiochem 2017; 19:31-36. [PMID: 29076615 DOI: 10.1002/cbic.201700498] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Indexed: 12/29/2022]
Abstract
Functional DNA includes aptamers and DNAzymes, and metal ions are often important for achieving the chemical functions of such DNA. Biosensors based on functional DNA have mainly been tested in aqueous buffers. By introducing organic solvents with much lower dielectric constants, the interaction between metal ions and DNA can be significantly enhanced, and this might affect the performance of DNA-based biosensors. In this work, the effect of ethanol on the activity of the EtNa DNAzyme was studied for Ca2+ detection. With 30 % ethanol, the sensor has a detection limit of 1.4 μm Ca2+ , which is a 16-fold improvement relative to that in water. This EtNa DNAzyme is unique because other tested DNAzymes are all inhibited by 50 % ethanol. Finally, by using the EtNa DNAzyme as a scaffold, the adenosine monophosphate (AMP) aptamer was inserted to construct an aptazyme, which allowed the measurement of AMP in ethanol. In summary, this study has reported the most sensitive DNA-based sensor for Ca2+ , and its sensitivity and selectivity can approach those of proteins or small-molecule ligands. This work also provides a way to measure aptamer binding in organic solvents.
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Affiliation(s)
- Tianmeng Yu
- Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Wenhu Zhou
- Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada.,School of Pharmaceutical Sciences, Central South University, 172 Tongzipo Road, Changsha, Hunan, 410013, P.R. China
| | - Juewen Liu
- Department of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
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50
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Click chemistry-mediated cyclic cleavage of metal ion-dependent DNAzymes for amplified and colorimetric detection of human serum copper (II). Anal Bioanal Chem 2017; 409:6421-6427. [DOI: 10.1007/s00216-017-0587-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 06/28/2017] [Accepted: 08/14/2017] [Indexed: 12/26/2022]
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