1
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Wang C, Zhang J, Pei Y, Li C, Li Y, Chen S, Wang Z. Visualized electrochemiluminescence detection of trace copper in practical food samples. Food Chem 2024; 451:139461. [PMID: 38701733 DOI: 10.1016/j.foodchem.2024.139461] [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: 02/04/2024] [Revised: 04/09/2024] [Accepted: 04/21/2024] [Indexed: 05/05/2024]
Abstract
Copper as a widely applied element in food supply chain can cause serious contamination issues that threats food safety. In this research, we present a quick and visible method for trace copper ion (Cu2+) quantification in practical food samples. Polymer dots (Pdots) were firstly conjugated with a copper-specific DNA aptamer and then tailored with rhodamine B (RhB) to extinguish the electrochemiluminescence (ECL) signal through a resonance energy transfer process. The selective release of RhB leads to signal restoration when exposed to trace Cu2+ levels, achieving remarkable linearity with the logarithm of Cu2+ concentration within the range of 1 ng/L to 10 μg/L with an impressively low limit of detection at 11.8 pg/L. Most notably, our device was also applicable on visualizing and quantifying trace Cu2+ (∼0.2 μg/g) in practical Glycyrrhiza uralensis Fisch. samples, underscoring its potential as a tool for the early prevention of potential copper contamination in food samples.
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Affiliation(s)
- Cheng Wang
- School of Pharmacy, Changzhou University, No. 21 Middle Gehu Road, Changzhou 213164, PR China.
| | - Jiaxing Zhang
- School of Pharmacy, Changzhou University, No. 21 Middle Gehu Road, Changzhou 213164, PR China
| | - Yang Pei
- Chinese Cultural Teaching Centre, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road, Suzhou 215123, PR China
| | - Chengqi Li
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Soochow University, Suzhou 215123, PR China
| | - Yulin Li
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Soochow University, Suzhou 215123, PR China
| | - Shaoqing Chen
- Department of Radiology, Second People's Hospital of Changzhou, Nanjing Medical University, Changzhou 213004, PR China.
| | - Ziyu Wang
- State Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Soochow University, Suzhou 215123, PR China.
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2
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Ali M, Nair P, Capretta A, Brennan JD. In-vitro Clinical Diagnostics using RNA-Cleaving DNAzymes. Chembiochem 2024; 25:e202400085. [PMID: 38574237 DOI: 10.1002/cbic.202400085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/06/2024]
Abstract
Over the last three decades, significant advancements have been made in the development of biosensors and bioassays that use RNA-cleaving DNAzymes (RCDs) as molecular recognition elements. While early examples of RCDs were primarily responsive to metal ions, the past decade has seen numerous RCDs reported for more clinically relevant targets such as bacteria, cancer cells, small metabolites, and protein biomarkers. Over the past 5 years several RCD-based biosensors have also been evaluated using either spiked biological matrixes or patient samples, including blood, serum, saliva, nasal mucus, sputum, urine, and faeces, which is a critical step toward regulatory approval and commercialization of such sensors. In this review, an overview of the methods used to generate RCDs and the properties of key RCDs that have been utilized for in vitro testing is first provided. Examples of RCD-based assays and sensors that have been used to test either spiked biological samples or patient samples are then presented, highlighting assay performance in different biological matrixes. A summary of current prospects and challenges for development of in vitro diagnostic tests incorporating RCDs and an overview of future directions of the field is also provided.
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Affiliation(s)
- Monsur Ali
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Parameswaran Nair
- Division of Respirology, McMaster University, and, Firestone Institute of Respiratory Health at St. Joseph's Health Care, Hamilton, ON, L8N 4A6, Canada
| | - Alfredo Capretta
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - John D Brennan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
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3
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Zhu X, Xu J, Ling G, Zhang P. Tunable metal-organic frameworks assist in catalyzing DNAzymes with amplification platforms for biomedical applications. Chem Soc Rev 2023; 52:7549-7578. [PMID: 37817667 DOI: 10.1039/d3cs00386h] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2023]
Abstract
Various binding modes of tunable metal organic frameworks (MOFs) and functional DNAzymes (Dzs) synergistically catalyze the emergence of abundant functional nanoplatforms. Given their serial variability in formation, structural designability, and functional controllability, Dzs@MOFs tend to be excellent building blocks for the precise "intelligent" manufacture of functional materials. To present a clear outline of this new field, this review systematically summarizes the progress of Dz integration into MOFs (MOFs@Dzs) through different methods, including various surface infiltration, pore encapsulation, covalent binding, and biomimetic mineralization methods. Atomic-level and time-resolved catalytic mechanisms for biosensing and imaging are made possible by the complex interplay of the distinct molecular structure of Dzs@MOF, conformational flexibility, and dynamic regulation of metal ions. Exploiting the precision of DNAzymes, MOFs@Dzs constructed a combined nanotherapy platform to guide intracellular drug synthesis, photodynamic therapy, catalytic therapy, and immunotherapy to enhance gene therapy in different ways, solving the problems of intracellular delivery inefficiency and insufficient supply of cofactors. MOFs@Dzs nanostructures have become excellent candidates for biosensing, bioimaging, amplification delivery, and targeted cancer gene therapy while emphasizing major advancements and seminal endeavors in the fields of biosensing (nucleic acid, protein, enzyme activity, small molecules, and cancer cells), biological imaging, and targeted cancer gene delivery and gene therapy. Overall, based on the results demonstrated to date, we discuss the challenges that the emerging MOFs@Dzs might encounter in practical future applications and briefly look forward to their bright prospects in other fields.
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Affiliation(s)
- Xiaoguang Zhu
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China.
| | - Jiaqi Xu
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China.
| | - Guixia Ling
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China.
| | - Peng Zhang
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China.
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4
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Yan T, Hou Y, Zuo Q, Jiang D, Zhao H, Xia T, Zhu X, Han X, An R, Liang X. Ultralow background one-pot detection of Lead(II) using a non-enzymatic double-cycle system mediated by a hairpin-involved DNAzyme. Biosens Bioelectron 2023; 237:115534. [PMID: 37527624 DOI: 10.1016/j.bios.2023.115534] [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: 05/10/2023] [Revised: 07/01/2023] [Accepted: 07/13/2023] [Indexed: 08/03/2023]
Abstract
A double-cycle system has been developed for specifically detecting trace amounts of Pb2+ by significantly decreasing the background signal. The detection involves two types of RNA cleavage reactions: one using a Pb2+-specific GR5 DNAzyme (PbDz) and the other utilizing a newly constructed 10-23 DNAzyme with two hairpins embedded in its catalytic center (hpDz). The ring-structured hpDz (c-hpDz) exhibits significantly lower activity compared to the circular 10-23 DNAzyme without hairpin structures, which plays a crucial role in reducing the background signal. When Pb2+ is present, PbDz cleaves c-hpDz to its active form, which then disconnects the molecular beacon to emit the fluorescent signal. The method allows for rapid and sensitive Pb2+ detection within 40 min for 10 fM of Pb2+ and even as short as 10 min for 100 nM of Pb2+. Additionally, visual detection is possible through the non-crosslinking assembly of Au nanoparticles. The entire process can be performed in one pot and even one step, making it highly versatile and suitable for a wide range of applications, including food safety testing and environmental monitoring.
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Affiliation(s)
- Ting Yan
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Yuying Hou
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Qianqian Zuo
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Difei Jiang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Huijie Zhao
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Tongyue Xia
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Xiaoqian Zhu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Xutiange Han
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China.
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
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5
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Xiong M, Wu Y, Kong G, Lewis W, Yang Z, Zhang H, Xu L, Liu Y, Liu Q, Zhao X, Zhang XB, Lu Y. A Semisynthetic Bioluminescence Sensor for Ratiometric Imaging of Metal Ions In Vivo Using DNAzymes Conjugated to An Engineered Nano-Luciferase. Angew Chem Int Ed Engl 2023; 62:e202308086. [PMID: 37548922 PMCID: PMC10527972 DOI: 10.1002/anie.202308086] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Indexed: 08/08/2023]
Abstract
DNA-based probes have gained significant attention as versatile tools for biochemical analysis, benefiting from their programmability and biocompatibility. However, most existing DNA-based probes rely on fluorescence as the signal output, which can be problematic due to issues like autofluorescence and scattering when applied in complex biological materials such as living cells or tissues. Herein, we report the development of bioluminescent nucleic acid (bioLUNA) sensors that offer laser excitation-independent and ratiometric imaging of the target in vivo. The system is based on computational modelling and mutagenesis investigations of a genetic fusion between circular permutated Nano-luciferase (NLuc) and HaloTag, enabling the conjugation of the protein with a DNAzyme. In the presence of Zn2+ , the DNAzyme sensor releases the fluorophore-labelled strand, leading to a reduction in bioluminescent resonance energy transfer (BRET) between the luciferase and fluorophore. Consequently, this process induces ratiometric changes in the bioluminescent signal. We demonstrated that this bioLUNA sensor enabled imaging of both exogenous Zn2+ in vivo and endogenous Zn2+ efflux in normal epithelial prostate and prostate tumors. This work expands the DNAzyme sensors to using bioluminescence and thus has enriched the toolbox of nucleic acid sensors for a broad range of biomedical applications.
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Affiliation(s)
- Mengyi Xiong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, Hunan, P. R. China
| | - Yuting Wu
- Department of Chemistry, University of Texas at Austin, 78712, Austin, TX, USA
| | - Gezhi Kong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, Hunan, P. R. China
| | - Whitney Lewis
- Department of Chemistry, University of Texas at Austin, 78712, Austin, TX, USA
| | - Zhenglin Yang
- Department of Chemistry, University of Texas at Austin, 78712, Austin, TX, USA
| | - Hanxiao Zhang
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, 030001, Taiyuan, Shanxi, P. R. China
| | - Li Xu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, Hunan, P. R. China
| | - Ying Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, Hunan, P. R. China
| | - Qin Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, Hunan, P. R. China
| | - Xuhua Zhao
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, 030001, Taiyuan, Shanxi, P. R. China
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, Hunan, P. R. China
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, 78712, Austin, TX, USA
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6
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Wu Y, Lewis W, Wai JL, Xiong M, Zheng J, Yang Z, Gordon C, Lu Y, New SY, Zhang XB, Lu Y. Ratiometric Detection of Zn 2+ Using DNAzyme-Based Bioluminescence Resonance Energy Transfer Sensors. CHEMISTRY (BASEL, SWITZERLAND) 2023; 5:1745-1759. [PMID: 38371491 PMCID: PMC10874629 DOI: 10.3390/chemistry5030119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
While fluorescent sensors have been developed for monitoring metal ions in health and diseases, they are limited by the requirement of an excitation light source that can lead to photobleaching and a high autofluorescence background. To address these issues, bioluminescence resonance energy transfer (BRET)-based protein or small molecule sensors have been developed; however, most of them are not highly selective nor generalizable to different metal ions. Taking advantage of the high selectivity and generalizability of DNAzymes, we report herein DNAzyme-based ratiometric sensors for Zn2+ based on BRET. The 8-17 DNAzyme was labeled with luciferase and Cy3. The proximity between luciferase and Cy3 permiQed BRET when coelenterazine, the substrate for luciferase, was introduced. Adding samples containing Zn2+ resulted in a cleavage of the substrate strand, causing dehybridization of the DNAzyme construct, thus increasing the distance between Cy3 and luciferase and changing the BRET signals. Using these sensors, we detected Zn2+ in serum samples and achieved Zn2+ detection with a smartphone camera. Moreover, since the BRET pair is not the component that determines the selectivity of the sensors, this sensing platform has the potential to be adapted for the detection of other metal ions with other metal-dependent DNAzymes.
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Affiliation(s)
- Yuting Wu
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Whitney Lewis
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Jing Luen Wai
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- School of Pharmacy, Faculty of Science and Engineering, University of No0ingham Malaysia, Semenyih, Selangor 43500, Malaysia
| | - Mengyi Xiong
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Jiao Zheng
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - 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
| | - Chloe Gordon
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Ying Lu
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Siu Yee New
- School of Pharmacy, Faculty of Science and Engineering, University of No0ingham Malaysia, Semenyih, Selangor 43500, Malaysia
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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7
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Fan H, McGhee CE, Lake RJ, Yang Z, Guo Z, Zhang XB, Lu Y. A Highly Selective Mn(II)-Specific DNAzyme and Its Application in Intracellular Sensing. JACS AU 2023; 3:1615-1622. [PMID: 37388692 PMCID: PMC10302744 DOI: 10.1021/jacsau.3c00062] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/20/2023] [Accepted: 05/01/2023] [Indexed: 07/01/2023]
Abstract
Manganese is an essential trace element in the human body that acts as a cofactor in many enzymes and metabolisms. It is important to develop methods to detect Mn2+ in living cells. While fluorescent sensors have been very effective in detecting other metal ions, Mn2+-specific fluorescent sensors are rarely reported due to nonspecific fluorescence quenching by the paramagnetism of Mn2+ and poor selectivity against other metal ions such as Ca2+ and Mg2+. To address these issues, we herein report in vitro selection of an RNA-cleaving DNAzyme with exceptionally high selectivity for Mn2+. Through converting it into a fluorescent sensor using a catalytic beacon approach, Mn2+ sensing in immune cells and tumor cells has been achieved. The sensor is also used to monitor degradation of manganese-based nanomaterials such as MnOx in tumor cells. Therefore, this work provides an excellent tool to detect Mn2+ in biological systems and monitor the Mn2+-involved immune response and antitumor therapy.
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Affiliation(s)
- Huanhuan Fan
- State
Key Laboratory of Coordination Chemistry, School of Chemistry and
Chemical Engineering, Chemistry and Biomedicine Innovation Center
(ChemBIC), Nanjing University, Nanjing 210023, China
| | - Claire E. McGhee
- Department
of Chemistry, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ryan J. Lake
- Department
of Chemistry, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Zhenglin Yang
- Department
of Chemistry, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Zijian Guo
- State
Key Laboratory of Coordination Chemistry, School of Chemistry and
Chemical Engineering, Chemistry and Biomedicine Innovation Center
(ChemBIC), Nanjing University, Nanjing 210023, China
| | - Xiao-Bing Zhang
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing
and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative
Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, China
| | - Yi Lu
- Department
of Chemistry, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61801, United States
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8
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Etheridge W, Brossard F, Zheng S, Moench S, Pavagada S, Owens RM, Fruk L. Activity-enhanced DNAzyme for design of label-free copper(II) biosensor. NANOSCALE 2023. [PMID: 37325900 DOI: 10.1039/d3nr02169f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Metal ion-driven, DNA-cleaving DNAzymes are characterised by high selectivity and specificity. However, their use for metal ion sensing remains largely unexplored due to long reaction times and poor reaction yields relative to RNA-cleaving DNAzymes and other sensing strategies. Herein we present a study demonstrating a significant rate enhancement of a copper-selective DNA cleaving DNAzyme by both polydopamine (PDA) and gold (Au) nanoparticles (NPs). PDA NPs enhance the reaction through the production of hydrogen peroxide, while for AuNPs the enhancement is aided by the presence of citrate surface moeities, both of which drive the oxidative cleavage of the substrate. A 50-fold enhancement for PDA NPs makes the combination of PDA and DNAzyme suitable for a practical application as a sensitive biosensor for Cu(II) ions. Using DNAzyme deposition onto a gold electrode followed by Polydopamine Assisted DNA Immobilisation (PADI), we achieve a cost-effective, label-free and fast (within 15 min) electrochemical biosensor with a limit of detection of 180 nmol (11 ppm), thus opening a route for the rational design of a new generation of hybrid DNAzyme-based biosensors.
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Affiliation(s)
- William Etheridge
- BioNano Engineering Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, West Cambridge Site, Philippa Fawcett Drive CB3 0AS, Cambridge, UK.
- Hitachi Cambridge Laboratory, Hitachi Europe Ltd, J. J. Thomson Avenue, Cambridge CB3 0HE, UK
| | - Frederic Brossard
- Hitachi Cambridge Laboratory, Hitachi Europe Ltd, J. J. Thomson Avenue, Cambridge CB3 0HE, UK
| | - Sitan Zheng
- BioNano Engineering Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, West Cambridge Site, Philippa Fawcett Drive CB3 0AS, Cambridge, UK.
| | - Svenja Moench
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Suraj Pavagada
- BioNano Engineering Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, West Cambridge Site, Philippa Fawcett Drive CB3 0AS, Cambridge, UK.
| | - Róisín M Owens
- BioNano Engineering Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, West Cambridge Site, Philippa Fawcett Drive CB3 0AS, Cambridge, UK.
| | - Ljiljana Fruk
- BioNano Engineering Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, West Cambridge Site, Philippa Fawcett Drive CB3 0AS, Cambridge, UK.
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9
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Song D, Tian T, Yang X, Wang L, Sun Y, Li Y, Huang H. Smartphone-assisted sensor array constructed by copper-based laccase-like nanozymes for specific identification and discrimination of organophosphorus pesticides. Food Chem 2023; 424:136477. [PMID: 37263094 DOI: 10.1016/j.foodchem.2023.136477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/11/2023] [Accepted: 05/26/2023] [Indexed: 06/03/2023]
Abstract
Accurate pesticide identification is of great importance for regulating food safety. However, the discrimination between organophosphorus pesticides (OPs) and carbamate pesticides (CPs) is still a challenge for existing analytical methods based on cholinesterase inhibition. It mainly because of the similar inhibitory effect of OPs and CPs on cholinesterase. Herein, we found that OPs and CPs differentially affected nanozymes with laccase-like activity, which would be interfered by OPs in different degrees rather than CPs. Thus, we fabricated a nanozyme sensor array and successfully achieved the OPs identification and similar individual discrimination, ignoring the interference from CPs or other potential interferents (antibiotics, ions, other pesticides). On the basis of nanozyme sensor array, a portable method using smartphone was constructed and utilized to determine OPs in fruits and vegetables. This work would contribute to the development of portable sensors and the highly selective identification and discrimination of OPs in complex samples.
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Affiliation(s)
- Donghui Song
- College of Food Science and Engineering, Jilin University, Changchun 130025, China
| | - Tian Tian
- College of Food Science and Engineering, Jilin University, Changchun 130025, China
| | - Xiaoyu Yang
- College of Food Science and Engineering, Jilin University, Changchun 130025, China
| | - Luwei Wang
- College of Food Science and Engineering, Jilin University, Changchun 130025, China
| | - Yue Sun
- Key Lab of Groundwater Resources and Environment of Ministry of Education, Key Lab of Water Resources and Aquatic Environment of Jilin Province, College of New Energy and Environment, Jilin University, Changchun 130021, China
| | - Yongxin Li
- Key Lab of Groundwater Resources and Environment of Ministry of Education, Key Lab of Water Resources and Aquatic Environment of Jilin Province, College of New Energy and Environment, Jilin University, Changchun 130021, China.
| | - Hui Huang
- College of Food Science and Engineering, Jilin University, Changchun 130025, China.
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10
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Zhang H, Dong K, Xiang S, Lin Y, Cha X, Shang Y, Xu W. A Novel Cu2+ Quantitative Detection Nucleic Acid Biosensors Based on DNAzyme and “Blocker” Beacon. Foods 2023; 12:foods12071504. [PMID: 37048325 PMCID: PMC10094606 DOI: 10.3390/foods12071504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/23/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023] Open
Abstract
In this paper, a “turn-off” biosensor for detecting copper (II) ions based on Cu2+-dependent DNAzyme and a “blocker” beacon were developed. Upon the copper ion being added, the Cu2+-dependent DNAzyme substrate strand was irreversibly cleaved, thereby blocking the occurrence of the ligation reaction and PCR, which inhibited the G-rich sequence from forming the G-quadruplex structure, efficiently reducing the detection signal. This method had the characteristics of strong specificity and high sensitivity compared with the existing method due to the application of ligation-dependent probe signal recognition and amplification procedures. Under the optimized conditions, this method proved to be highly sensitive. The signal decreased as the concentration of copper ions increased, exhibiting a linear calibration from 0.03125 μM to 0.5 μM and a limit of detection of 18.25 nM. Subsequently, the selectivity of this biosensor was verified to be excellent by testing different relevant metal ions. Furthermore, this detection system of copper (II) ions was successfully applied to monitor Cu2+ contained in actual water samples, which demonstrated the feasibility of the biosensor.
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Affiliation(s)
- Hanyue Zhang
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China
| | - Kai Dong
- College of Biological Sciences, China Agricultural University, Beijing 100083, China
| | - Shuna Xiang
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China
| | - Yingting Lin
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China
| | - Xiaoyan Cha
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China
| | - Ying Shang
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China
| | - Wentao Xu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
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11
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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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12
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Jarczewska M, Szymczyk A, Zajda J, Olszewski M, Ziółkowski R, Malinowska E. Recent Achievements in Electrochemical and Optical Nucleic Acids Based Detection of Metal Ions. Molecules 2022; 27:7481. [PMID: 36364308 PMCID: PMC9657803 DOI: 10.3390/molecules27217481] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 08/27/2024] Open
Abstract
Recently nucleic acids gained considerable attention as selective receptors of metal ions. This is because of the possibility of adjusting their sequences in new aptamers selection, as well as the convenience of elaborating new detection mechanisms. Such a flexibility allows for easy utilization of newly emerging nanomaterials for the development of detection devices. This, in turn, can significantly increase, e.g., analytical signal intensity, both optical and electrochemical, and the same can allow for obtaining exceptionally low detection limits and fast biosensor responses. All these properties, together with low power consumption, make nucleic acids biosensors perfect candidates as detection elements of fully automatic portable microfluidic devices. This review provides current progress in nucleic acids application in monitoring environmentally and clinically important metal ions in the electrochemical or optical manner. In addition, several examples of such biosensor applications in portable microfluidic devices are shown.
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Affiliation(s)
- Marta Jarczewska
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Stanisława Noakowskiego 3, 00-664 Warsaw, Poland
| | - Anna Szymczyk
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Stanisława Noakowskiego 3, 00-664 Warsaw, Poland
- Doctoral School, Warsaw University of Technology, Plac Politechniki 1, 00-661 Warsaw, Poland
| | - Joanna Zajda
- Chair of Analytical Chemistry, Faculty of Chemistry, Warsaw University of Technology, Stanisława Noakowskiego 3, 00-664 Warsaw, Poland
| | - Marcin Olszewski
- Chair of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University ofTechnology, Koszykowa 75, 00-664 Warsaw, Poland
| | - Robert Ziółkowski
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Stanisława Noakowskiego 3, 00-664 Warsaw, Poland
| | - Elżbieta Malinowska
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Stanisława Noakowskiego 3, 00-664 Warsaw, Poland
- Centre for Advanced Materials and Technologies CEZAMAT, Warsaw University of Technology, Poleczki 19, 02-822 Warsaw, Poland
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13
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Sanford AA, Manuel BA, Romero-Reyes MA, Heemstra JM. Combating small molecule environmental contaminants: detection and sequestration using functional nucleic acids. Chem Sci 2022; 13:7670-7684. [PMID: 35865900 PMCID: PMC9258336 DOI: 10.1039/d2sc00117a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 05/26/2022] [Indexed: 12/05/2022] Open
Abstract
Small molecule contaminants pose a significant threat to the environment and human health. While regulations are in place for allowed limits in many countries, detection and remediation of contaminants in more resource-limited settings and everyday environmental sources remains a challenge. Functional nucleic acids, including aptamers and DNA enzymes, have emerged as powerful options for addressing this challenge due to their ability to non-covalently interact with small molecule targets. The goal of this perspective is to outline recent efforts toward the selection of aptamers for small molecules and describe their subsequent implementation for environmental applications. Finally, we provide an outlook that addresses barriers that hinder these technologies from being widely adopted in field friendly settings and propose a path forward toward addressing these challenges.
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Affiliation(s)
- Aimee A Sanford
- Department of Chemistry, Emory University Atlanta Georgia 30322 USA
| | - Brea A Manuel
- Department of Chemistry, Emory University Atlanta Georgia 30322 USA
| | - Misael A Romero-Reyes
- Department of Chemistry, Emory University Atlanta Georgia 30322 USA
- Department of Chemistry, Hanover College Hanover Indiana 47243 USA
| | - Jennifer M Heemstra
- Department of Chemistry, Emory University Atlanta Georgia 30322 USA
- Department of Biomedical Engineering, Georgia Institute of Technology, Emory University Atlanta GA 30332 USA
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14
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15
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Recent advances in the construction of functional nucleic acids with isothermal amplification for heavy metal ions sensor. Microchem J 2022. [DOI: 10.1016/j.microc.2021.107077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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16
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An RNA-cleaving threose nucleic acid enzyme capable of single point mutation discrimination. Nat Chem 2022; 14:350-359. [PMID: 34916596 DOI: 10.1038/s41557-021-00847-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 10/25/2021] [Indexed: 01/19/2023]
Abstract
Threose nucleic acid has been considered a potential evolutionary progenitor of RNA because of its chemical simplicity, base pairing properties and capacity for higher-order functions such as folding and specific ligand binding. Here we report the in vitro selection of RNA-cleaving threose nucleic acid enzymes. One such enzyme, Tz1, catalyses a site-specific RNA-cleavage reaction with an observed pseudo first-order rate constant (kobs) of 0.016 min-1. The catalytic activity of Tz1 is maximal at 8 mM Mg2+ and remains relatively constant from pH 5.3 to 9.0. Tz1 preferentially cleaves a mutant epidermal growth factor receptor RNA substrate with a single point substitution, while leaving the wild-type intact. We demonstrate that Tz1 mediates selective gene silencing of the mutant epidermal growth factor receptor in eukaryotic cells. The identification of catalytic threose nucleic acids provides further experimental support for threose nucleic acid as an ancestral genetic and functional material. The demonstration of Tz1 mediating selective knockdown of intracellular RNA suggests that functional threose nucleic acids could be developed for future biomedical applications.
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17
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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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18
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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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19
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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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20
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Moon WJ, Huang PJJ, Liu J. Probing Metal-Dependent Phosphate Binding for the Catalysis of the 17E DNAzyme. Biochemistry 2021; 60:1909-1918. [PMID: 34106684 DOI: 10.1021/acs.biochem.1c00091] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The RNA-cleaving 17E DNAzyme exhibits different levels of cleavage activity in the presence of various divalent metal ions, with Pb2+ giving the fastest cleavage. In this study, the metal-phosphate interaction is probed to understand the trend of activity with different metal ions. For the first-row transition metals, the lowest activity shown by Ni2+ correlates with the inhibition by the inorganic phosphate and its water ligand exchange rate, suggesting inner-sphere metal coordination. Cleavage activity with the two stereoisomers of the phosphorothioate-modified substrates, Rp and Sp, indicated that Mg2+, Mn2+, Fe2+, and Co2+ had the highest Sp:Rp activity ratio of >900. Comparatively, the activity was much less affected using the thiophilic metals, including Pb2+, suggesting inner-sphere coordination. The pH-rate profiles showed that Pb2+ was different than the rest of the metal ions in having a smaller slope and a similar fitted apparent pKa and the pKa of metal-bound water. Combining previous reports and our current results, we propose that Pb2+ most likely plays the role of a general acid while the other metal ions are Lewis acid catalysts interacting with the scissile phosphate.
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Affiliation(s)
- Woohyun J Moon
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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21
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Xu X, Xiao L, Gu C, Shang J, Xiang Y. Wavelength-Selective Activation of Photocaged DNAzymes for Metal Ion Sensing in Live Cells. ACS OMEGA 2021; 6:13153-13160. [PMID: 34056465 PMCID: PMC8158819 DOI: 10.1021/acsomega.1c00976] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/28/2021] [Indexed: 05/09/2023]
Abstract
RNA-cleaving DNAzymes are widely applied as sensors for detecting metal ions in environmental samples owing to their high sensitivity and selectivity, but their use for sensing biological metal ions in live cells is challenging because constitutive sensors fail to report the spatiotemporal heterogeneity of biological processes. Photocaged DNAzymes can be activated by light for sensing purposes that need spatial and temporal resolution. Studying complex biological processes requires logic photocontrol, but unfortunately all the literature-reported photocaged DNAzymes working in live cells cannot be selectively controlled by light irradiation at different wavelengths. In this work, we developed photocaged DNAzymes responsive to UV and visible light using a general synthetic method based on phosphorothioate chemistry. Taking the Zn2+-dependent DNAzyme sensor as a model, we achieved wavelength-selective activation of photocaged DNAzymes in live human cells by UV and visible light, laying the groundwork for the logic activation of DNAzyme-based sensors in biological systems.
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22
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Wang G, Wu M, Chu LT, Chen TH. Portable microfluidic device with thermometer-like display for real-time visual quantitation of Cadmium(II) contamination in drinking water. Anal Chim Acta 2021; 1160:338444. [PMID: 33894969 DOI: 10.1016/j.aca.2021.338444] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/12/2021] [Accepted: 03/19/2021] [Indexed: 12/20/2022]
Abstract
Cadmium (Cd2+) is a toxic metal ion widely existing in water, soil and food. Conventional water quality control heavily relies on expensive, bulky and sophisticated instrument such as spectrometry, which is time-consuming and incompatible with on-site, real-time detection. Here, a portable microfluidic device with thermometer-like visual readouts is developed for real-time quantitation of cadmium (II) contamination in drinking water. We use Cd2+-dependent DNAzyme (Cd16), which is cleaved when Cd2+ is present, creating a single strand DNA which triggers catalytic hairpin assembly (CHA) with two hairpins H1 and H2 as the building blocks. Plenty of H1H2 complex, the product after the Cd2+-mediated CHA, are generated, which can connect magnetic microparticles (MMPs) and polystyrene microparticles (PMPs), forming "MMPs-H1H2-PMPs" sandwich structure. To provide visual readout to quantitate the particle connection, the particle solution is loaded into a portable microfluidic chip. A magnetic separator first removes MMPs and the connected PMPs, while free PMPs can continue flowing until accumulating into a bar at the particle dam. Shown as a thermometer-like display, the accumulating length is inversely proportional to the concentration of Cd2+, enabling quantitative detection of Cd2+ by the naked eye. The proposed device exhibits a limit of detection of 11.3 nM of Cd2+, selectivity >200-fold against other metal ions, high tolerance to the interferents present in drinking water and high recovery rate in tap water. With high analytical performance without any sample preparation step, this portable device is highly promising in real-time monitoring in urban drinking water at sites.
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Affiliation(s)
- Gaobo Wang
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong Special Administrative Region, 999077, China
| | - Minghui Wu
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong Special Administrative Region, 999077, China
| | - Lok Ting Chu
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong Special Administrative Region, 999077, China
| | - Ting-Hsuan Chen
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong Special Administrative Region, 999077, China.
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23
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Ultrasensitive detection of total copper with an electrochemical biosensor built on the in cis coupling of hexynyl CLICK-17 DNAzyme with azido self-assembled monolayers. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2021.138125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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24
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Abstract
Aptamers are single-stranded DNA or RNA molecules that can be identified through an iterative in vitro selection–amplification process. Among them, fluorogenic aptamers in response to small molecules have been of great interest in biosensing and bioimaging due to their rapid fluorescence turn-on signals with high target specificity and low background noise. In this review, we report recent advances in fluorogenic aptasensors and their applications to in vitro diagnosis and cellular imaging. These aptasensors modulated by small molecules have been implemented in different modalities that include duplex or molecular beacon-type aptasensors, aptazymes, and fluorogen-activating aptamer reporters. We highlight the working principles, target molecules, modifications, and performance characteristics of fluorogenic aptasensors, and discuss their potential roles in the field of biosensor and bioimaging with future directions and challenges.
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25
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Mukherjee S, Bhattacharyya S, Ghosh K, Pal S, Halder A, Naseri M, Mohammadniaei M, Sarkar S, Ghosh A, Sun Y, Bhattacharyya N. Sensory development for heavy metal detection: A review on translation from conventional analysis to field-portable sensor. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.01.062] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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26
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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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27
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Huang Z, Zhao Y, Liu B, Guan S, Liu J. Stronger Adsorption of Phosphorothioate DNA Oligonucleotides on Graphene Oxide by van der Waals Forces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:13708-13715. [PMID: 33161721 DOI: 10.1021/acs.langmuir.0c02761] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Finding DNA sequences that can adsorb strongly on nanomaterials is critical for bioconjugate and biointerface chemistry. In most previous work, unmodified DNA with a phosphodiester backbone (PO DNA) were screened or selected for adsorption on inorganic surfaces. In this work, the adsorption of phosphorothioate (PS)-modified DNA (PS DNA) on graphene oxide (GO) is studied. By use of fluorescently labeled oligonucleotides as probes, all the tested PS DNA strands are adsorbed more strongly on GO compared to the PO DNA of the same sequence. The adsorption mechanism is probed by washing the adsorbed DNA with proteins, surfactants, and urea. Molecular dynamics simulations show that van der Waals forces are responsible for the tighter adsorption of PS DNA. Polycytosine (poly-C) DNA, in general, has a high affinity for the GO surface, and PS poly-C DNA can adsorb even stronger, making it an ideal anchoring sequence on GO. With this knowledge, noncovalent functionalization of GO with a diblock DNA is demonstrated, where a PS poly-C block is used to anchor on the surface. This conjugate achieves better hybridization than the PO DNA of the same sequence for hybridization with the complementary DNA.
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Affiliation(s)
- Zhicheng Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Yu Zhao
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Biwu Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Shaokang Guan
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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28
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Ochoa S, Milam VT. Modified Nucleic Acids: Expanding the Capabilities of Functional Oligonucleotides. Molecules 2020; 25:E4659. [PMID: 33066073 PMCID: PMC7587394 DOI: 10.3390/molecules25204659] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 12/20/2022] Open
Abstract
In the last three decades, oligonucleotides have been extensively investigated as probes, molecular ligands and even catalysts within therapeutic and diagnostic applications. The narrow chemical repertoire of natural nucleic acids, however, imposes restrictions on the functional scope of oligonucleotides. Initial efforts to overcome this deficiency in chemical diversity included conservative modifications to the sugar-phosphate backbone or the pendant base groups and resulted in enhanced in vivo performance. More importantly, later work involving other modifications led to the realization of new functional characteristics beyond initial intended therapeutic and diagnostic prospects. These results have inspired the exploration of increasingly exotic chemistries highly divergent from the canonical nucleic acid chemical structure that possess unnatural physiochemical properties. In this review, the authors highlight recent developments in modified oligonucleotides and the thrust towards designing novel nucleic acid-based ligands and catalysts with specifically engineered functions inaccessible to natural oligonucleotides.
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Affiliation(s)
- Steven Ochoa
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA;
| | - Valeria T. Milam
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA;
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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29
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Huang PJ, Liu J. In vitro Selection of Chemically Modified DNAzymes. ChemistryOpen 2020; 9:1046-1059. [PMID: 33101831 PMCID: PMC7570446 DOI: 10.1002/open.202000134] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 08/25/2020] [Indexed: 02/06/2023] Open
Abstract
DNAzymes are in vitro selected DNA oligonucleotides with catalytic activities. RNA cleavage is one of the most extensively studied DNAzyme reactions. To expand the chemical functionality of DNA, various chemical modifications have been made during and after selection. In this review, we summarize examples of RNA-cleaving DNAzymes and focus on those modifications introduced during in vitro selection. By incorporating various modified nucleotides via polymerase chain reaction (PCR) or primer extension, a few DNAzymes were obtained that can be specifically activated by metal ions such as Zn2+ and Hg2+. In addition, some modifications were introduced to mimic RNase A that can cleave RNA substrates in the absence of divalent metal ions. In addition, single modifications at the fixed regions of DNA libraries, especially at the cleavage junctions, have been tested, and examples of DNAzymes with phosphorothioate and histidine-glycine modified tertiary amine were successfully obtained specific for Cu2+, Cd2+, Zn2+, and Ni2+. Labeling fluorophore/quencher pair right next to the cleavage junction was also used to obtain signaling DNAzymes for detecting various metal ions and cells. Furthermore, we reviewed work on the cleavage of 2'-5' linked RNA and L-RNA substrates. Finally, applications of these modified DNAzymes as biosensors, RNases, and biochemical probes are briefly described with a few future research opportunities outlined at the end.
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Affiliation(s)
- Po‐Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for NanotechnologyUniversity of WaterlooWaterlooOntario, N2L 3G1Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for NanotechnologyUniversity of WaterlooWaterlooOntario, N2L 3G1Canada
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30
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Ren W, Jimmy Huang PJ, de Rochambeau D, Moon WJ, Zhang J, Lyu M, Wang S, Sleiman H, Liu J. Selection of a metal ligand modified DNAzyme for detecting Ni 2. Biosens Bioelectron 2020; 165:112285. [PMID: 32510338 DOI: 10.1016/j.bios.2020.112285] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/28/2020] [Accepted: 05/07/2020] [Indexed: 12/12/2022]
Abstract
Nickel is a highly important metal, and the detection of Ni2+ using biosensors is a long-stand analytical challenge. DNA has been widely used for metal detection, although no DNA-based sensors were reported for Ni2+. DNAzymes are DNA-based catalysts, and they recruit metal ions for catalysis. In this work, in vitro selection of RNA-cleaving DNAzymes was carried out using a library containing a region of 50 random nucleotides in the presence of Ni2+. To increase Ni2+ binding, a glycyl-histidine-functionalized tertiary amine moiety was inserted at the cleavage junction. A representative DNAzyme named Ni03 showed a high cleavage yield with Ni2+ and it was further studied. After truncation, the optimal sequence of Ni03l could bind one Ni2+ or two Co2+ for catalysis, while other metal ions were inactive. Its cleavage rates for 100 μM Ni2+ reached 0.63 h-1 at pH 8.0. A catalytic beacon biosensor was designed by labeling a fluorophore and a quencher on the Ni03l DNAzyme. Fluorescence enhancement was observed in the presence of Ni2+ with a detection limit of 12.9 μM. The sensor was also tested in spiked Lake Ontario water achieving a similar sensitivity. This is another example of using single-site modified DNAzyme for sensing transition metal ions.
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Affiliation(s)
- Wei Ren
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, 222005, China; Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Po-Jung Jimmy Huang
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Donatien de Rochambeau
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, H3A 0B8, Canada
| | - Woohyun J Moon
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Jinyi Zhang
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Mingsheng Lyu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, Jiangsu, 222005, China
| | - Shujun Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, Jiangsu, 222005, China
| | - Hanadi Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, H3A 0B8, Canada
| | - Juewen Liu
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada.
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31
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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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32
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Electrochemical impedance biosensor array based on DNAzyme-functionalized single-walled carbon nanotubes using Gaussian process regression for Cu(II) and Hg(II) determination. Mikrochim Acta 2020; 187:207. [DOI: 10.1007/s00604-020-4202-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 02/28/2020] [Indexed: 12/12/2022]
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33
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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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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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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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36
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Nucleic acid-cleaving catalytic DNA for sensing and therapeutics. Talanta 2020; 211:120709. [PMID: 32070594 DOI: 10.1016/j.talanta.2019.120709] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 12/28/2019] [Accepted: 12/31/2019] [Indexed: 12/21/2022]
Abstract
DNAzymes with nucleic acid-cleaving catalytic activity are increasing in versatility through concerted efforts to discover new sequences with unique functions, and they are generating excitement in the sensing community as cheap, stable, amplifiable detection elements. This review provides a comprehensive list and detailed descriptions of the DNAzymes identified to date, classified by their associated small molecule or ion needed for catalysis; of note, this classification clarifies conserved regions of various DNAzymes that are not obvious in the literature. Furthermore, we detail the breadth of functionality of these DNA sequences as well as the range of reaction conditions under which they are useful. In addition, the utility of the DNAzymes in a variety of sensing and therapeutic applications is presented, detailing both their advantages and disadvantages.
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Hu L, Fu X, Kong G, Yin Y, Meng HM, Ke G, Zhang XB. DNAzyme–gold nanoparticle-based probes for biosensing and bioimaging. J Mater Chem B 2020; 8:9449-9465. [DOI: 10.1039/d0tb01750g] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The design and applications of DNAzyme–gold nanoparticle-based probes in biosensing and bioimaging are summarized here.
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Affiliation(s)
- Ling Hu
- Molecular Sciences and Biomedicine Laboratory
- State Key Laboratory for Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
| | - Xiaoyi Fu
- Molecular Sciences and Biomedicine Laboratory
- State Key Laboratory for Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
| | - Gezhi Kong
- Molecular Sciences and Biomedicine Laboratory
- State Key Laboratory for Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
| | - Yao Yin
- Molecular Sciences and Biomedicine Laboratory
- State Key Laboratory for Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
| | - Hong-Min Meng
- College of Chemistry
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Guoliang Ke
- Molecular Sciences and Biomedicine Laboratory
- State Key Laboratory for Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
| | - Xiao-Bing Zhang
- Molecular Sciences and Biomedicine Laboratory
- State Key Laboratory for Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha
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39
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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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40
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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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41
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Hwang K, Mou Q, Lake RJ, Xiong M, Holland B, Lu Y. Metal-Dependent DNAzymes for the Quantitative Detection of Metal Ions in Living Cells: Recent Progress, Current Challenges, and Latest Results on FRET Ratiometric Sensors. Inorg Chem 2019; 58:13696-13708. [PMID: 31364355 PMCID: PMC7176321 DOI: 10.1021/acs.inorgchem.9b01280] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Many different metal ions are involved in various biological functions including metallomics and trafficking, and yet there are currently effective sensors for only a few metal ions, despite the first report of metal sensors for calcium more than 40 years ago. To expand upon the number of metal ions that can be probed in biological systems, we and other laboratories employ the in vitro selection method to obtain metal-specific DNAzymes with high specificity for a metal ion and then convert these DNAzymes into fluorescent sensors for these metal ions using a catalytic beacon approach. In this Forum Article, we summarize recent progress made in developing these DNAzyme sensors to probe metal ions in living cells and in vivo, including several challenges that we were able to overcome for this application, such as DNAzyme delivery, spatiotemporal control, and signal amplification. Furthermore, we have identified a key remaining challenge for the quantitative detection of metal ions in living cells and present a new design and the results of a Förster resonance energy transfer (FRET)-based DNAzyme sensor for the ratiometric quantification of Zn2+ in HeLa cells. By converting existing DNAzyme sensors into a ratiometric readout without compromising the fundamental catalytic function of the DNAzymes, this FRET-based ratiometric DNAzyme design can readily be applied to other DNAzyme sensors as a major advance in the field to develop much more quantitative metal-ion probes for biological systems.
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Affiliation(s)
- Kevin Hwang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Quanbing Mou
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Ryan J. Lake
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Mengyi Xiong
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Institute of Chemical Biology and Nanomedicine, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Brandalynn Holland
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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42
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Wang X, Liu G, Qi Y, Yuan Y, Gao J, Luo X, Yang T. Embedded Au Nanoparticles-Based Ratiometric Electrochemical Sensing Strategy for Sensitive and Reliable Detection of Copper Ions. Anal Chem 2019; 91:12006-12013. [PMID: 31433623 DOI: 10.1021/acs.analchem.9b02945] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The ratiometric method allows the measurement of ratio changes between two signals, which can reduce the detection signal fluctuations caused by distinct background conditions and greatly improve the reproducibility and reliability of detection. However, in contrast with the emerging dual excitation or dual emission dyes applied in ratiometric luminescence measurement, only a few internal reference probes have been exploited for ratiometric electrochemical detection. In this paper, a gold nanoparticles@carbonized resin nanospheres composite with thermally reduced graphene oxide as scaffold (AuNPs@CRS-TrGNO) has been fabricated, and the AuNPs embedded in the CRS were first used as an internal reference probe for ratiometric electrochemical detection. The detachment and aggregation of AuNPs is suppressed by embedding in the CRS, so its redox signal is very stable, which provides feasibility for ratiometric detection. Moreover, the embedment of AuNPs, carbonization of resin spheres, and hybridization with TrGNO all have played positive roles in improving the charge transfer rate, which leads to excellent electrochemical performance of the composite. Based on these characteristics of the AuNPs@CRS-TrGNO, a new ratiometric electrochemical detection platform was constructed, and copper ions (Cu2+) in simulated seawater were successfully detected. This ratiometric method has the advantages of simple design and convenient operation, and obviously it improves the reproducibility and reliability of the electrochemical sensor.
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Affiliation(s)
- Xinxing Wang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; Shandong Key Laboratory of Biochemical Analysis; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong; Key Laboratory of Eco-chemical Engineering; College of Chemistry and Molecular Engineering , Qingdao University of Science and Technology , Qingdao 266042 , China
| | - Guangmao Liu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; Shandong Key Laboratory of Biochemical Analysis; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong; Key Laboratory of Eco-chemical Engineering; College of Chemistry and Molecular Engineering , Qingdao University of Science and Technology , Qingdao 266042 , China
| | - Youxiao Qi
- College of Environment and Safety Engineering , Qingdao University of Science and Technology , Qingdao 266042 , China
| | - Yue Yuan
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; Shandong Key Laboratory of Biochemical Analysis; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong; Key Laboratory of Eco-chemical Engineering; College of Chemistry and Molecular Engineering , Qingdao University of Science and Technology , Qingdao 266042 , China
| | - Jian Gao
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; Shandong Key Laboratory of Biochemical Analysis; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong; Key Laboratory of Eco-chemical Engineering; College of Chemistry and Molecular Engineering , Qingdao University of Science and Technology , Qingdao 266042 , China
| | - Xiliang Luo
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; Shandong Key Laboratory of Biochemical Analysis; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong; Key Laboratory of Eco-chemical Engineering; College of Chemistry and Molecular Engineering , Qingdao University of Science and Technology , Qingdao 266042 , China
| | - Tao Yang
- School of Chemical Engineering and Technology , Sun Yat-Sen University , Zhuhai 519082 , China
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43
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Chen C, Chen S, Shiddiky MJA, Chen C, Wu KC. DNA‐Templated Copper Nanoprobes: Overview, Feature, Application, and Current Development in Detection Technologies. CHEM REC 2019; 20:174-186. [DOI: 10.1002/tcr.201900022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/22/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Chung‐An Chen
- Institute of Applied MechanicsNational Taiwan University, No. 1, Sec. 4 Roosevelt Road Taipei 10617 Taiwan
| | - Shih‐Chia Chen
- Institute of Applied MechanicsNational Taiwan University, No. 1, Sec. 4 Roosevelt Road Taipei 10617 Taiwan
| | - Muhammad J. A. Shiddiky
- School of Environment and Science & Queensland Micro- and Nanotechnology CentreNathan campus, Griffith University 170 Kessels Road QLD 4111 Australia
| | - Chien‐Fu Chen
- Institute of Applied MechanicsNational Taiwan University, No. 1, Sec. 4 Roosevelt Road Taipei 10617 Taiwan
| | - Kevin C.‐W. Wu
- Department of Chemical EngineeringNational Taiwan University, No. 1, Sec. 4 Roosevelt Road Taipei 10617 Taiwan
- Division of Medical Engineering Research, National Health
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44
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He Y, Chen D, Huang PJJ, Zhou Y, Ma L, Xu K, Yang R, Liu J. Misfolding of a DNAzyme for ultrahigh sodium selectivity over potassium. Nucleic Acids Res 2019; 46:10262-10271. [PMID: 30215808 PMCID: PMC6212836 DOI: 10.1093/nar/gky807] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 09/08/2018] [Indexed: 02/07/2023] Open
Abstract
Herein, the excellent Na+ selectivity of a few RNA-cleaving DNAzymes was exploited, where Na+ can be around 3000-fold more effective than K+ for promoting catalysis. By using a double mutant based on the Ce13d DNAzyme, and by lowering the temperature, increased 2-aminopurine (2AP) fluorescence was observed with addition of both Na+ and K+. The fluorescence increase was similar for these two metals at below 10 mM, after which K+ took a different pathway. Since 2AP probes its local base stacking environment, K+ can be considered to induce misfolding. Binding of both Na+ and K+ was specific, since single base mutations could fully inhibit 2AP fluorescence for both metals. The binding thermodynamics was measured by temperature-dependent experiments revealing enthalpy-driven binding for both metals and less coordination sites compared to G-quadruplex DNA. Cleavage activity assays indicated a moderate cleavage activity with 10 mM K+, while further increase of K+ inhibited the activity, also supporting its misfolding of the DNAzyme. For comparison, a G-quadruplex DNA was also studied using the same system, where Na+ and K+ led to the same final state with only around 8-fold difference in Kd. This study provides interesting insights into strategies for discriminating Na+ and K+.
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Affiliation(s)
- Yanping He
- State Key Laboratory of Precision Measurement Technology and Instruments, University of Tianjin, Tianjin 300072, China.,Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Da Chen
- State Key Laboratory of Precision Measurement Technology and Instruments, University of Tianjin, Tianjin 300072, China
| | - Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Yibo Zhou
- School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha 410114, P. R. China
| | - Lingzi Ma
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Kexin Xu
- State Key Laboratory of Precision Measurement Technology and Instruments, University of Tianjin, Tianjin 300072, China
| | - Ronghua Yang
- School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha 410114, P. R. China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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45
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Gu L, Yan W, Wu H, Fan S, Ren W, Wang S, Lyu M, Liu J. Selection of DNAzymes for Sensing Aquatic Bacteria: Vibrio Anguillarum. Anal Chem 2019; 91:7887-7893. [DOI: 10.1021/acs.analchem.9b01707] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | | | | | | | - Wei Ren
- Key Laboratory of Marine Biology, Nanjing Agricultural University, Nanjing, Jiangsu 210000, P. R. China
| | | | | | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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46
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Sun C, Ou X, Cheng Y, Zhai T, Liu B, Lou X, Xia F. Coordination-induced structural changes of DNA-based optical and electrochemical sensors for metal ions detection. Dalton Trans 2019; 48:5879-5891. [PMID: 30681098 DOI: 10.1039/c8dt04733b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Metal ions play a critical role in human health and abnormal levels are closely related to various diseases. Therefore, the detection of metal ions with high selectivity, sensitivity and accuracy is particularly important. This article highlights and comments on the coordination-induced structural changes of DNA-based optical, electrochemical and optical-electrochemical-combined sensors for metal ions detection. Challenges and potential solutions of DNA-based sensors for the simultaneous detection of multiple metal ions are also discussed for further development and exploitation.
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Affiliation(s)
- Chunli Sun
- State Key Laboratory of Material Processing and Die & Mould Technology, School of Materials Science and Engineering; Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering; National Engineering Research Center for Nanomedicine, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
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47
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Cao T, Wang Y, Zhao LL, Wang Y, Tao Y, Heyman JA, Weitz DA, Zhou YL, Zhang XX. A simple mix-and-read bacteria detection system based on a DNAzyme and a molecular beacon. Chem Commun (Camb) 2019; 55:7358-7361. [DOI: 10.1039/c9cc03746b] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A simple improved mix-and-read method for the detection of bacteria is developed based on a DNAzyme and a molecular beacon.
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Affiliation(s)
- Ting Cao
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering
- College of Chemistry
- Peking University
- Beijing 100871
| | - Yongcheng Wang
- John A. Paulson School of Engineering and Applied Sciences and Department of Physics
- Harvard University
- Cambridge
- USA
- Wyss Institute for Biologically Inspired Engineering
| | - Ling-Li Zhao
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering
- College of Chemistry
- Peking University
- Beijing 100871
| | - Ye Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering
- College of Chemistry
- Peking University
- Beijing 100871
| | - Ye Tao
- John A. Paulson School of Engineering and Applied Sciences and Department of Physics
- Harvard University
- Cambridge
- USA
| | - John A. Heyman
- John A. Paulson School of Engineering and Applied Sciences and Department of Physics
- Harvard University
- Cambridge
- USA
| | - David A. Weitz
- John A. Paulson School of Engineering and Applied Sciences and Department of Physics
- Harvard University
- Cambridge
- USA
- Wyss Institute for Biologically Inspired Engineering
| | - Ying-Lin Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering
- College of Chemistry
- Peking University
- Beijing 100871
| | - Xin-Xiang Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering
- College of Chemistry
- Peking University
- Beijing 100871
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48
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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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49
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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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Jimmy Huang PJ, Moon WJ, Liu J. Instantaneous Iodine-Assisted DNAzyme Cleavage of Phosphorothioate RNA. Biochemistry 2018; 58:422-429. [PMID: 30272443 DOI: 10.1021/acs.biochem.8b00900] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Metal ions play a critical role in the RNA-cleavage reaction by interacting with the scissile phosphate and stabilizing the highly negatively charged transition state. Many metal-dependent DNAzymes have been selected for RNA cleavage. Herein, we report that the Ce13d DNAzyme can use nonmetallic iodine (I2) to cleave a phosphorothioate (PS)-modified substrate. The cleavage yield exceeded 60% for both the Rp and Sp stereoisomers in 10 s, while the yield without the enzyme strand was only ∼10%. The Ce13d cleavage with I2 also required Na+, consistent with the property of Ce13d and confirming the similar role of I2 as a metal ion. Ce13d had the highest yield among eight tested DNAzymes, with the second highest DNAzyme showing only 20% cleavage. The incomplete cleavage was due to competition from desulfurization and isomerization reactions. This DNAzyme was engineered for fluorescence-based I2 detection. With EDTA for masking metal ions, I2 was selectively detected down to 4.7 nM. Oxidation of I- with Fe3+ produced I2 in situ, allowing detection of Fe3+ down to 78 nM. By harnessing nonelectrostatic interactions, such as the I2/sulfur interaction observed here, more nonmetal species might be discovered to assist DNAzyme-based RNA cleavage.
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Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Woohyun J Moon
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
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