1
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Tao S, Han X, Shi D, Yu T, Long Y, Zou S, Lu S, Song L, Liu G. Portable Device with Nicking Enzyme Enhanced Special RCA on μPADs toward Sensitive Detection of High-Risk HPV Infection. Anal Chem 2024. [PMID: 38912660 DOI: 10.1021/acs.analchem.4c02070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Development of an accurate, rapid, and cost-effective portable device is in high demand for point-of-care molecular diagnosis toward disease screening. Here we report a one-pot homogeneous isothermal assay that leverages nicking endonuclease and minimum secondary structured rolling circle amplification (N-MSSRCA) for fast and sensitive quantification of nucleic acids on distance microfluidic paper-based analytical devices (dμPAD) by a portable custom-made fluorescence detector. Human papillomavirus (HPV) oncogenic E7 mRNA as the biomarker for cervical cancer was used as the model analyte. N-MSSRCA integrates ligase for target recognition, the nicking enzyme for primer generation, and the dual function of the Phi29 DNA polymerase for both on- and off-loop amplification. The proposed method was capable of detecting 1 and 10 fM of the analyte using the microplate reader and portable detector with dμPAD, respectively, with ∼1 h assay time. A cohort study of 40 cervical swab samples shows N-MSSRCA reached positive and negative predictive values of 87.5% and 93.5% using the portable detector with dμPAD, compared to 91.67% and 100% using the microplate reader. N-MSSRCA demonstrates potential in early screening of high-risk HPV infection as a generic strategy to detect various nucleic acids in point-of-care scenarios.
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Affiliation(s)
- Shurui Tao
- Integrated Devices and Intelligent Diagnosis (ID2) Laboratory, CUHK(SZ)-Boyalife Joint Laboratory for Regenerative Medicine Engineering, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Xin Han
- Integrated Devices and Intelligent Diagnosis (ID2) Laboratory, CUHK(SZ)-Boyalife Joint Laboratory for Regenerative Medicine Engineering, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Dongni Shi
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Tian Yu
- Integrated Devices and Intelligent Diagnosis (ID2) Laboratory, CUHK(SZ)-Boyalife Joint Laboratory for Regenerative Medicine Engineering, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Yingxi Long
- Integrated Devices and Intelligent Diagnosis (ID2) Laboratory, CUHK(SZ)-Boyalife Joint Laboratory for Regenerative Medicine Engineering, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Siyi Zou
- Integrated Devices and Intelligent Diagnosis (ID2) Laboratory, CUHK(SZ)-Boyalife Joint Laboratory for Regenerative Medicine Engineering, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Sheng Lu
- Integrated Devices and Intelligent Diagnosis (ID2) Laboratory, CUHK(SZ)-Boyalife Joint Laboratory for Regenerative Medicine Engineering, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Libing Song
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Guozhen Liu
- Integrated Devices and Intelligent Diagnosis (ID2) Laboratory, CUHK(SZ)-Boyalife Joint Laboratory for Regenerative Medicine Engineering, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
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2
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Ashrafi AM, Mukherjee A, Saadati A, Matysik FM, Richtera L, Adam V. Enhancing the substrate selectivity of enzyme mimetics in biosensing and bioassay: Novel approaches. Adv Colloid Interface Sci 2024; 331:103233. [PMID: 38924801 DOI: 10.1016/j.cis.2024.103233] [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: 01/11/2024] [Revised: 06/06/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024]
Abstract
A substantial development in nanoscale materials possessing catalytic activities comparable with natural enzymes has been accomplished. Their advantages were owing to the excellent sturdiness in an extreme environment, possibilities of their large-scale production resulting in higher profitability, and easy manipulation for modification. Despite these advantages, the main challenge for artificial enzyme mimetics is the lack of substrate selectivity where natural enzymes flourish. This review addresses this vital problem by introducing substrate selectivity strategies to three classes of artificial enzymes: molecularly imprinted polymers, nanozymes (NZs), and DNAzymes. These rationally designed strategies enhance the substrate selectivity and are discussed and exemplified throughout the review. Various functional mechanisms associated with applying enzyme mimetics in biosensing and bioassays are also given. Eventually, future directives toward enhancing the substrate selectivity of biomimetics and related challenges are discussed and evaluated based on their efficiency and convenience in biosensing and bioassays.
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Affiliation(s)
- Amir M Ashrafi
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; Institute of Photonics and Electronics, Czech Academy of Sciences, Prague, Czech Republic.
| | - Atripan Mukherjee
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic; ELI Beamlines Facility, The Extreme Light Infrastructure ERIC, Za Radnici 835, 252 41 Dolni Brezany, Czech Republic.
| | - Arezoo Saadati
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ-612 00 Brno, Czech Republic.
| | - Frank-Michael Matysik
- Institute of Analytical Chemistry, Chemo- and Biosensors, University Regensburg, 93053 Regensburg, Germany.
| | - Lukas Richtera
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic.
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic.
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3
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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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4
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Cao X, Tang L, Song J. Circular Single-Stranded DNA: Discovery, Biological Effects, and Applications. ACS Synth Biol 2024; 13:1038-1058. [PMID: 38501391 DOI: 10.1021/acssynbio.4c00040] [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: 03/20/2024]
Abstract
The field of nucleic acid therapeutics has witnessed a significant surge in recent times, as evidenced by the increasing number of approved genetic drugs. However, current platform technologies containing plasmids, lipid nanoparticle-mRNAs, and adeno-associated virus vectors encounter various limitations and challenges. Thus, we are devoted to finding a novel nucleic acid vector and have directed our efforts toward investigating circular single-stranded DNA (CssDNA), an ancient form of nucleic acid. CssDNAs are ubiquitous, but generally ignored. Accumulating evidence suggests that CssDNAs possess exceptional properties as nucleic acid vectors, exhibiting great potential for clinical applications in genetic disorders, gene editing, and immune cell therapy. Here, we comprehensively review the discovery and biological effects of CssDNAs as well as their applications in the field of biomedical research for the first time. Undoubtedly, as an ancient form of DNA, CssDNA holds immense potential and promises novel insights for biomedical research.
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Affiliation(s)
- Xisen Cao
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Linlin Tang
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310022, China
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310022, China
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5
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Chen Z, Liu Z, Liu J, Xiao X. Research progress in the detection of common foodborne hazardous substances based on functional nucleic acids biosensors. Biotechnol Bioeng 2023; 120:3501-3517. [PMID: 37723667 DOI: 10.1002/bit.28555] [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: 06/14/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/20/2023]
Abstract
With the further improvement of food safety requirements, the development of fast, highly sensitive, and portable methods for the determination of foodborne hazardous substances has become a new trend in the food industry. In recent years, biosensors and platforms based on functional nucleic acids, along with a range of signal amplification devices and methods, have been established to enable rapid and sensitive determination of specific substances in samples, opening up a new avenue of analysis and detection. In this paper, functional nucleic acid types including aptamers, deoxyribozymes, and G-quadruplexes which are commonly used in the detection of food source pollutants are introduced. Signal amplification elements include quantum dots, noble metal nanoparticles, magnetic nanoparticles, DNA walkers, and DNA logic gates. Signal amplification technologies including nucleic acid isothermal amplification, hybridization chain reaction, catalytic hairpin assembly, biological barcodes, and microfluidic system are combined with functional nucleic acids sensors and applied to the detection of many foodborne hazardous substances, such as foodborne pathogens, mycotoxins, residual antibiotics, residual pesticides, industrial pollutants, heavy metals, and allergens. Finally, the potential opportunities and broad prospects of functional nucleic acids biosensors in the field of food analysis are discussed.
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Affiliation(s)
- Zijie Chen
- School of Public Health, Hengyang Medical School, University of South China, Hengyang, Hunan, the People's Republic of China
| | - Zhen Liu
- School of Public Health, Hengyang Medical School, University of South China, Hengyang, Hunan, the People's Republic of China
| | - Jingjing Liu
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, Hunan, the People's Republic of China
| | - Xilin Xiao
- School of Public Health, Hengyang Medical School, University of South China, Hengyang, Hunan, the People's Republic of China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, the People's Republic of China
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6
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Gao Y, Fan X, Zhang X, Guan Q, Xing Y, Song W. HCR/DNAzyme-triggered cascaded feedback cycle amplification for self-powered dual-photoelectrode detection of femtomolar HPV16. Biosens Bioelectron 2023; 237:115483. [PMID: 37390640 DOI: 10.1016/j.bios.2023.115483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/05/2023] [Accepted: 06/15/2023] [Indexed: 07/02/2023]
Abstract
For high-performance dual-photoelectrode assay, developing a pair of photoactive materials with well-matched band structure and the design of a powerful sensing strategy are highly desirable. Herein, the Zn-TBAPy pyrene-based MOF and BiVO4/Ti3C2 Schottky junction were employed as photocathode and photoanode to form an efficient dual-photoelectrode system. The integration of the cascaded hybridization chain reaction (HCR)/DNAzyme-assisted feedback amplification with DNA walker-mediated cycle amplification strategy realizes femtomolar HPV16 dual-photoelectrode bioassay. Through the activation of the HCR cascaded with the DNAzyme system in the presence of HPV16, plentiful HPV16 analogs are generated that leads to exponential positive feedback signal amplification. Meanwhile on the Zn-TBAPy photocathode, the NDNA hybridizes with the bipedal DNA walker followed by circular cleavage by Nb.BbvCI NEase, producing a dramatically enhanced PEC readout. The achieved ultralow detection limit of 0.57 fM and a wide linear range of 10-6 nM-103 nM showcase the excellent performance of the developed dual-photoelectrode system.
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Affiliation(s)
- Yao Gao
- College of Chemistry, Jilin University, Changchun, 130012, PR China
| | - Xue Fan
- College of Chemistry, Jilin University, Changchun, 130012, PR China
| | - Xuechen Zhang
- College of Chemistry, Jilin University, Changchun, 130012, PR China
| | - Qinglin Guan
- College of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, PR China
| | - Yongheng Xing
- College of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, PR China
| | - Wenbo Song
- College of Chemistry, Jilin University, Changchun, 130012, PR China.
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7
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Zhand S, Zhu Y, Nazari H, Sadraeian M, Warkiani ME, Jin D. Thiolate DNAzymes on Gold Nanoparticles for Isothermal Amplification and Detection of Mesothelioma-derived Exosomal PD-L1 mRNA. Anal Chem 2023; 95:3228-3237. [PMID: 36624066 DOI: 10.1021/acs.analchem.2c04046] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Catalytic DNAzymes have been used for isothermal amplification and rapid detection of nucleic acids, holding the potential for point-of-care testing applications. However, when Subzymes (universal substrate and DNAzyme) are tethered to the polystyrene magnetic microparticles via biotin-streptavidin bonds, the residual free Subzymes are often detached from the microparticle surface, which causes a significant degree of false positives. Here, we attached dithiol-modified Subzyme to gold nanoparticle and improved the limit of detection (LoD) by 200 times compared to that using magnetic microparticles. As a proof of concept, we applied our new method for the detection of exosomal programed cell-death ligand 1 (PD-L1) RNA. As the classical immune checkpoint, molecule PD-L1, found in small extracellular vesicles (sEVs, traditionally called exosomes), can reflect the antitumor immune response for predicting immunotherapy response. We achieved the LoD as low as 50 fM in detecting both the RNA homologous to the PD-L1 gene and exosomal PD-L1 RNAs extracted from epithelioid and nonepithelioid subtypes of mesothelioma cell lines, which only takes 8 min of reaction time. As the first application of isothermal DNAzymes for detecting exosomal PD-L1 RNA, this work suggests new point-of-care testing potentials toward clinical translations.
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Affiliation(s)
- Sareh Zhand
- Institute for Biomedical Materials and Devices, Faculty of Science, University of Technology Sydney, Sydney, New South Wales 2007, Australia.,School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Ying Zhu
- Institute for Biomedical Materials and Devices, Faculty of Science, University of Technology Sydney, Sydney, New South Wales 2007, Australia.,School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Hojjatollah Nazari
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Mohammad Sadraeian
- Institute for Biomedical Materials and Devices, Faculty of Science, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Majid Ebrahimi Warkiani
- Institute for Biomedical Materials and Devices, Faculty of Science, University of Technology Sydney, Sydney, New South Wales 2007, Australia.,School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia.,Institute of Molecular Medicine, Sechenov First Moscow State University, Moscow 119991, Russia
| | - Dayong Jin
- Institute for Biomedical Materials and Devices, Faculty of Science, University of Technology Sydney, Sydney, New South Wales 2007, Australia
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8
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Bialy RM, Mainguy A, Li Y, Brennan JD. Functional nucleic acid biosensors utilizing rolling circle amplification. Chem Soc Rev 2022; 51:9009-9067. [DOI: 10.1039/d2cs00613h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Functional nucleic acids regulate rolling circle amplification to produce multiple detection outputs suitable for the development of point-of-care diagnostic devices.
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Affiliation(s)
- Roger M. Bialy
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
| | - Alexa Mainguy
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
| | - Yingfu Li
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4O3, Canada
- Department of Biochemistry and Biomedical Sciences, 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 4O3, Canada
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9
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Rolling Circle Amplification as an Efficient Analytical Tool for Rapid Detection of Contaminants in Aqueous Environments. BIOSENSORS-BASEL 2021; 11:bios11100352. [PMID: 34677308 PMCID: PMC8533700 DOI: 10.3390/bios11100352] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/16/2021] [Accepted: 09/21/2021] [Indexed: 12/16/2022]
Abstract
Environmental contaminants are a global concern, and an effective strategy for remediation is to develop a rapid, on-site, and affordable monitoring method. However, this remains challenging, especially with regard to the detection of various contaminants in complex water environments. The application of molecular methods has recently attracted increasing attention; for example, rolling circle amplification (RCA) is an isothermal enzymatic process in which a short nucleic acid primer is amplified to form a long single-stranded nucleic acid using a circular template and special nucleic acid polymerases. Furthermore, this approach can be further engineered into a device for point-of-need monitoring of environmental pollutants. In this paper, we describe the fundamental principles of RCA and the advantages and disadvantages of RCA assays. Then, we discuss the recently developed RCA-based tools for environmental analysis to determine various targets, including heavy metals, organic small molecules, nucleic acids, peptides, proteins, and even microorganisms in aqueous environments. Finally, we summarize the challenges and outline strategies for the advancement of this technique for application in contaminant monitoring.
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10
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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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11
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Li J, Yang F, Jiang B, Zhou W, Xiang Y, Yuan R. The synchronization of multiple signal amplifications for label-free and sensitive aptamer-based sensing of a protein biomarker. Analyst 2021; 145:7858-7863. [PMID: 33020770 DOI: 10.1039/d0an01491e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The abnormal variation of the mucin 1 (MUC1) protein level is associated with the development of multiple cancers, and the monitoring of trace MUC1 can be useful for early disease diagnosis. Here, on the basis of the synchronization of DNA-fueled sequence recycling and dual rolling circle amplification (RCA), the establishment of a non-label and highly sensitive fluorescent aptamer-based detection strategy for the MUC1 protein biomarker is described. The target MUC1 binds the aptamer hairpin probe and causes its structure switching to release an ssDNA tail to trigger the recycling of the complex via two toehold-mediated strand displacement reactions under assistance of a fuel DNA. Such a recycling amplification leads to the formation of a partial dsDNA duplex with two primers at both ends, which cooperatively bind the circular DNA ring template to start the dual RCA to produce many G-quadruplex sequences. The protoporphyrin IX dye further associates with the G-quadruplex structures to show a dramatically elevated fluorescent signal for sensitively detecting MUC1 with a low detection limit of 0.5 pM. The established aptamer-based detecting strategy is also highly selective and can realize assay of MUC1 in diluted human serums, highlighting its potential for the detection of different protein biomarkers at low contents.
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Affiliation(s)
- Jin Li
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, PR China.
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12
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Cozma I, McConnell EM, Brennan JD, Li Y. DNAzymes as key components of biosensing systems for the detection of biological targets. Biosens Bioelectron 2021; 177:112972. [DOI: 10.1016/j.bios.2021.112972] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 01/01/2021] [Accepted: 01/02/2021] [Indexed: 12/11/2022]
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13
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Li H, Tang Y, Song D, Lu B, Guo L, Li B. Establishment of Dual Hairpin Ligation-Induced Isothermal Amplification for Universal, Accurate, and Flexible Nucleic Acid Detection. Anal Chem 2021; 93:3315-3323. [PMID: 33538577 DOI: 10.1021/acs.analchem.1c00007] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Isothermal amplifications have found their potentials in applications of portable nucleic acid diagnostics. However, there are still several certain deficiencies existing in the current amplification methods, including high false-positive signals, limited range of targets, difficult primer design, and so forth. Here, we report an effective solution via the development of dual hairpin ligation-induced isothermal amplification (DHLA) consisting of (1) the formation of a dual hairpin probe (DHP) based on sequence specific hybridization and ligation and (2) exponential isothermal amplification of DHP in the presence of polymerase and primers. Taking both microRNA and virus RNA as model targets, DHLA is proven to be accurate, flexible, and applicable to most deoxyribonucleic acid and ribonucleic acid targets ranging from ∼20 to hundreds of nt. The detection limit is down to the ∼aM level without a false-positive signal. More importantly, the whole detection can be directly applied to a new target via a slight change in the DHP sequence, without redesigning the primer set. This unique property not only simplifies the process for new reaction development but also enables flexible multiprobe strategies to achieve antidegradation analysis.
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Affiliation(s)
- Huan Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China.,Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, P. R. China
| | - Yidan Tang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
| | - Defeng Song
- Department of General Surgery, China-Japan Union Hospital of JiLin University, Changchun, Jilin 130021, P. R. China
| | - Baiyang Lu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
| | - Lulu Guo
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China.,Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, P. R. China
| | - Bingling Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China.,Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, P. R. China
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14
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Sensitive Detection of Nucleic Acids Using Subzyme Feedback Cascades. MOLECULES (BASEL, SWITZERLAND) 2020; 25:molecules25071755. [PMID: 32290237 PMCID: PMC7181152 DOI: 10.3390/molecules25071755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/03/2020] [Accepted: 04/08/2020] [Indexed: 01/14/2023]
Abstract
The development of Subzymes demonstrates how the catalytic activity of DNAzymes can be controlled for detecting nucleic acids; however, Subzymes alone lack the sensitivity required to detect low target concentrations. To improve sensitivity, we developed a feedback system using a pair of cross-catalytic Subzymes. These were individually tethered to microparticles (MP) and separated by a porous membrane rendering them unable to interact. In the presence of a target, active PlexZymes® cleave a first Subzyme, which separates a first DNAzyme from its MP, allowing the DNAzyme to migrate through the membrane, where it can cleave a second Subzyme. This releases a second DNAzyme which can now migrate through the membrane and cleave more of the first Subzyme, thus initiating a cross-catalytic cascade. Activated DNAzymes can additionally cleave fluorescent substrates, generating a signal, and thereby, indicating the presence of the target. The method detected 1 fM of DNA homologous to the ompA gene of Chlamydia trachomatis within 30 min, demonstrating a 10,000-fold increase in sensitivity over PlexZyme detection alone. The Subzyme cascade is universal and can be triggered by any target by modifying the target sensing arms of the PlexZymes. Further, it is isothermal, protein-enzyme-free and shows great potential for rapid and affordable biomarker detection.
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15
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Liu C, Han J, Zhou L, Zhang J, Du J. DNAzyme-Based Target-Triggered Rolling-Circle Amplification for High Sensitivity Detection of microRNAs. SENSORS 2020; 20:s20072017. [PMID: 32260285 PMCID: PMC7180602 DOI: 10.3390/s20072017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 03/29/2020] [Accepted: 04/01/2020] [Indexed: 12/20/2022]
Abstract
MicroRNAs regulate and control the growth and development of cells and can play the role of oncogenes and tumor suppressor genes, which are involved in the occurrence and development of cancers. In this study, DNA fragments obtained by target-induced rolling-circle amplification were constructed to complement with self-cleaving deoxyribozyme (DNAzyme) and release fluorescence biomolecules. This sensing approach can affect multiple signal amplification permitting fluorescence detection of microRNAs at the pmol L−1 level hence affording a simple, highly sensitive, and selective low cost detection platform.
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16
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Li J, Mohammed-Elsabagh M, Paczkowski F, Li Y. Circular Nucleic Acids: Discovery, Functions and Applications. Chembiochem 2020; 21:1547-1566. [PMID: 32176816 DOI: 10.1002/cbic.202000003] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/13/2020] [Indexed: 12/14/2022]
Abstract
Circular nucleic acids (CNAs) are nucleic acid molecules with a closed-loop structure. This feature comes with a number of advantages including complete resistance to exonuclease degradation, much better thermodynamic stability, and the capability of being replicated by a DNA polymerase in a rolling circle manner. Circular functional nucleic acids, CNAs containing at least a ribozyme/DNAzyme or a DNA/RNA aptamer, not only inherit the advantages of CNAs but also offer some unique application opportunities, such as the design of topology-controlled or enabled molecular devices. This article will begin by summarizing the discovery, biogenesis, and applications of naturally occurring CNAs, followed by discussing the methods for constructing artificial CNAs. The exploitation of circular functional nucleic acids for applications in nanodevice engineering, biosensing, and drug delivery will be reviewed next. Finally, the efforts to couple functional nucleic acids with rolling circle amplification for ultra-sensitive biosensing and for synthesizing multivalent molecular scaffolds for unique applications in biosensing and drug delivery will be recapitulated.
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Affiliation(s)
- Jiuxing Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Mostafa Mohammed-Elsabagh
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Freeman Paczkowski
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Yingfu Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
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17
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G-triplex/hemin DNAzyme: An ideal signal generator for isothermal exponential amplification reaction-based biosensing platform. Anal Chim Acta 2019; 1079:139-145. [DOI: 10.1016/j.aca.2019.06.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/11/2019] [Accepted: 06/01/2019] [Indexed: 12/22/2022]
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18
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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: 53] [Impact Index Per Article: 10.6] [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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19
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Li S, Liu S, Xu Y, Zhang R, Zhao Y, Qu X, Wang Y, Huang J, Yu J. Robust and highly specific fluorescence sensing of Salmonella typhimurium based on dual-functional phi29 DNA polymerase-mediated isothermal circular strand displacement polymerization. Analyst 2019; 144:4795-4802. [DOI: 10.1039/c9an00843h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A simple and robust fluorescence sensing strategy has been developed for the detection of pathogenic bacteria by the combination of the dual functionality of phi29 DNA polymerase with isothermal circular strand displacement polymerization (ICSDP).
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Affiliation(s)
- Shasha Li
- College of Biological Sciences and Technology
- University of Jinan
- Jinan 250022
- P. R. China
| | - Su Liu
- School of Water Conservancy and Environment
- University of Jinan
- Jinan 250022
- P. R. China
| | - Yicheng Xu
- College of Biological Sciences and Technology
- University of Jinan
- Jinan 250022
- P. R. China
| | - Rufeng Zhang
- School of Water Conservancy and Environment
- University of Jinan
- Jinan 250022
- P. R. China
| | - Yihan Zhao
- College of Biological Sciences and Technology
- University of Jinan
- Jinan 250022
- P. R. China
| | - Xiaonan Qu
- School of Water Conservancy and Environment
- University of Jinan
- Jinan 250022
- P. R. China
| | - Yu Wang
- College of Biological Sciences and Technology
- University of Jinan
- Jinan 250022
- P. R. China
| | - Jiadong Huang
- College of Biological Sciences and Technology
- University of Jinan
- Jinan 250022
- P. R. China
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong
| | - Jinghua Yu
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong
- College of Chemistry and Chemical Engineering
- University of Jinan
- Jinan 250022
- P. R. China
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