51
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Le ATH, Wang TY, Krylova SM, Beloborodov SS, Krylov SN. Quantitative Characterization of Partitioning in Selection of DNA Aptamers for Protein Targets by Capillary Electrophoresis. Anal Chem 2022; 94:2578-2588. [DOI: 10.1021/acs.analchem.1c04560] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- An T. H. Le
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Tong Ye Wang
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Svetlana M. Krylova
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Stanislav S. Beloborodov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Sergey N. Krylov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
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52
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Zhao F, Xie S, Li B, Zhang X. Functional nucleic acids in glycobiology: A versatile tool in the analysis of disease-related carbohydrates and glycoconjugates. Int J Biol Macromol 2022; 201:592-606. [PMID: 35031315 DOI: 10.1016/j.ijbiomac.2022.01.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/05/2022] [Accepted: 01/07/2022] [Indexed: 12/12/2022]
Abstract
As significant components of the organism, carbohydrates and glycoconjugates play indispensable roles in energy supply, cell signaling, immune modulation, and tumor cell invasion, and function as biomarkers since aberrance of them has been proved to be associated with the emergence and development of certain diseases. Functional nucleic acids (FNAs) have properties including easy-to-synthesize, good stability, good biocompatibility, low cost, and high programmability, they have attracted significant research attention and been incorporated into biosensors for detecting disease-related carbohydrates and glycoconjugates. This review summarizes the construction strategies and biosensing applications of FNAs-based biosensors in glycobiology in terms of target recognition and signal transduction. By illustrating the mechanisms and comparing the performances, the challenges and development opportunities in this area have been critically elaborated. We believe that this review will provide a better understanding of the role of FNAs in the analysis of disease-related carbohydrates and glycoconjugates, and inspire further discovery in fields that include glycobiology, chemical biology, clinical diagnosis, and drug development.
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Affiliation(s)
- Furong Zhao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Siying Xie
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Bingzhi Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China.
| | - Xing Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China.
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53
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Hu C, Zhang J, Jin Y, Ma W, Zhou R, Du H, Yang P, Hou X, Cheng N, Chen J. Protein recognition-initiated exponential amplification reaction (PRIEAR) and its application in clinical diagnosis. Chembiochem 2022; 23:e202100548. [PMID: 34989090 DOI: 10.1002/cbic.202100548] [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: 10/19/2021] [Revised: 01/04/2022] [Indexed: 02/05/2023]
Abstract
The isothermal exponential amplification technology have rarely been fabricated as the universal sensing platform for the detection of various proteins. To broaden its application, we here developed a strategy named protein recognition-initiated exponential amplification reaction (PRIEAR) using protein recognition to induce the DNA assembly which converts protein recognition events into ssDNA amplicons and combining two-stage amplification to achieve exponential amplification technology. Taking advantage of this principle, diverse biomarkers can be quantified at sub-picomolar concentrations in the homogenous manner, making the PRIEAR suitable for clinical practice. Therefore, this strategy can expand the powerful isothermal exponential amplification technology to protein targets and thus provide a new toolbox into the clinical and biomedical applications.
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Affiliation(s)
- Changjia Hu
- Sichuan University, West China hospital, CHINA
| | - Jie Zhang
- Sichuan University, West China hospital, CHINA
| | - Yanwen Jin
- Sichuan University, West China hospital, CHINA
| | - Wenjie Ma
- Sichuan University, West China hospital, CHINA
| | | | - Huan Du
- Sichuan University, College of Chemistry, CHINA
| | - Peng Yang
- Sichuan University, College of Chemistry, CHINA
| | | | | | - Junbo Chen
- Sichuan University, Analytical & Testing Centre, No.29 Wangjiang Road, 610064, Chengdu, CHINA
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54
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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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55
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Liu X, Cheng H, Zhao Y, Wang Y, Li F. Portable electrochemical biosensor based on laser-induced graphene and MnO 2 switch-bridged DNA signal amplification for sensitive detection of pesticide. Biosens Bioelectron 2021; 199:113906. [PMID: 34968952 DOI: 10.1016/j.bios.2021.113906] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 01/18/2023]
Abstract
Developing portable, quantitative, and user-friendly analytical tools for sensitive pesticide assay is of significant importance for guaranteeing food safety. Herein, a novel electrochemical biosensor was constructed by integrating laser-induced graphene (LIG) electrode on polyimide (PI) foil and MnO2 nanosheets loaded on the paper for point-of-care test (POCT) of organophosphorus (OPs) residues. The principle of this biosensor relied on acetylcholinesterase (AChE)-catalyzed hydrolytic product-triggered disintegration of MnO2 nanosheets for releasing assistant DNA to initiate nicking enzyme-aided recycling amplification. In the presence of OPs, the activity of AChE was inhibited and could not initiate the cleavage of the electroactive molecules-labeled hairpin probe on the electrode, resulting in the maintenance of the electrochemical response to realize a "sign-on" determination of OPs. The proposed biosensor exhibited satisfactory analytical performance for OPs assay with a linear range from 3 to 4000 ng/mL and a limit of detection down to 1.2 ng/mL. Moreover, the biosensor was useful for evaluating the residual level of pesticides in the vegetables. Therefore, this novel biosensor holds great promise for OPs assay and opens a new avenue on the development of higher-performance POCT device for sensing applications in the environment and food safety fields.
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Affiliation(s)
- Xiaojuan Liu
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China
| | - Hao Cheng
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China
| | - Yuecan Zhao
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China
| | - Yue Wang
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China
| | - Feng Li
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China.
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56
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Zhao Y, Xiang J, Cheng H, Liu X, Li F. Flexible photoelectrochemical biosensor for ultrasensitive microRNA detection based on concatenated multiplex signal amplification. Biosens Bioelectron 2021; 194:113581. [PMID: 34461568 DOI: 10.1016/j.bios.2021.113581] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/19/2021] [Accepted: 08/22/2021] [Indexed: 12/13/2022]
Abstract
Precise microRNA (miRNA) analysis is significant importance for early disease diagnosis. Herein, a novel flexible photoelectrochemical (PEC) biosensor for miRNA determination was developed by employing CdS NPs-modified carbon cloth (CC) on polyimide (PI) film as photoelectric material to provide the PEC responses and an efficient four-stage reaction system as the target recognition and signal amplification unit to improve the analytical performance. In this PEC biosensor, the presence of target miR-21 would trigger the catalytic hairpin assembly (CHA) and the following hybridization chain reaction (HCR) to produce a long dsDNA labeled with numerous biotins, which would further capture a large amount of alkaline phosphatase (ALP) for catalyzing the generation of ascorbic acid (AA). As an efficient electron donor, AA could be oxidized by the photoelectrode, which would initiate a redox cycling amplification process to regenerate AA, resulting in the enhancement of the photocurrent response. Benefitting from the synergistic nucleic acid-based, enzyme catalytic, and chemical signal amplification strategies, the proposed biosensing strategy enabled ultrasensitive miRNA determination. As expected, the PEC biosensor performed satisfactory analytical performances with a linear range of 1 fM to 1 nM and the detection limit down to 0.41 fM. Furthermore, the PEC biosensing strategy exhibited recommendable selectivity, stability, flexibility, and practical applicability. Therefore, this sensing platform provides promising potential for application in bioassay and early diagnosis of disease.
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Affiliation(s)
- Yuecan Zhao
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Junzhu Xiang
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Hao Cheng
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Xiaojuan Liu
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China.
| | - Feng Li
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China.
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57
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Cao Y, Zhang H, Le XC. Split Locations and Secondary Structures of a DNAzyme Critical to Binding-Assembled Multicomponent Nucleic Acid Enzymes for Protein Detection. Anal Chem 2021; 93:15712-15719. [PMID: 34788018 DOI: 10.1021/acs.analchem.1c03617] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
RNA-cleaving DNAzymes and their multicomponent nucleic acid enzymes (MNAzymes) have been successfully used to detect nucleic acids and proteins. The appropriate split of the catalytic cores of DNAzymes is critical to the formation of MNAzymes with high catalytic activities. However, for protein detection, no systematic investigation has been made on the effects of the split locations and secondary structures of MNAzymes on the catalytic activities of the cleavage reaction. We systematically studied how split locations and secondary structures affect the activity of the MNAzymes that catalyze multiple cleavage steps. We engineered the MNAzymes on the basis of the RNA-cleaving DNAzyme 10-23 as a model system. We designed 28 pairs of MNAzymes, representing 14 different split locations and two secondary structures: the three-arm and the four-arm structures. By comparing the multiple turnover numbers (kobs.m) of the 28 MNAzymes, we showed that the split location between the seventh cytosine and the eighth thymine of the catalytic core region and the four-arm structure resulted in optimum catalytic activity. Binding-induced DNA assembly of the optimized MNAzymes enabled sensitive detection of two model protein targets, demonstrating promising potential of the binding-assembled MNAzymes for protein analysis. The strategy of binding-assembled MNAzymes and systematic studies measuring multiple turnover numbers (kobs.m) provide a new approach to studying other partial (split) DNAzymes and engineering better MNAzymes for the detection of specific proteins.
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Affiliation(s)
- Yiren Cao
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Hongquan Zhang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
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58
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Shang J, Yu S, Chen Y, Gao Y, Hong C, Li F, Wang F. Real-Time Investigation of Intracellular Polynucleotide Kinase Using a Cascaded Amplification Circuit. Anal Chem 2021; 93:15559-15566. [PMID: 34748706 DOI: 10.1021/acs.analchem.1c04033] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polynucleotide kinase (PNK) shows an in-depth correlationship with DNA repair and metabolism processes. The in situ visualization of intracellular PNK revealed an extremely biological significance in supplementing reliable and quantitative information on its spatiotemporal distribution in live cells. Herein, we developed a versatile cascaded DNA amplification circuit through the integration of catalytic DNA assembly and hybridization chain reaction circuits and realized the accurate evaluation of intracellular PNK activity via the Förster resonance energy transfer (FRET) principle. Initially, without PNK, trigger T was firmly caged in the PNK-recognizing hairpin HT, resulting in no disturbance of the concatenated circuit. However, with the introduction of PNK, the 5'-OH terminal of PNK-addressing HT was phosphorylated, then the phosphorylated HT could be subsequently digested by λ exonuclease (λ Exo) to produce trigger T of the cascaded DNA circuit. As a result, the integrated circuit was stimulated to produce an amplified FRET signal for quantitatively monitoring the activity of PNK. Due to the λ Exo-specific digestion of 5'-phosphate DNA and the high signal gain of the cascade circuit, our proposed strategy enables the sensitive analysis of PNK activity in vitro and in complex biological samples. Furthermore, our PNK-sensing platform was extensively explored in HeLa cells for realizing reliable intracellular PNK imaging and thus showed high potential in the future diagnosis and treatment of kinase-related diseases.
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Affiliation(s)
- Jinhua Shang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Shanshan Yu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yingying Chen
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yuhui Gao
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Chen Hong
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Fengzhe Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
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59
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Xu Y, Chen B, He M, Hu B. A homogeneous nucleic acid assay for simultaneous detection of SARS-CoV-2 and influenza A (H3N2) by single-particle inductively coupled plasma mass spectrometry. Anal Chim Acta 2021; 1186:339134. [PMID: 34756259 PMCID: PMC8486417 DOI: 10.1016/j.aca.2021.339134] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/14/2021] [Accepted: 08/28/2021] [Indexed: 12/15/2022]
Abstract
In recent years, single particle inductively coupled plasma mass spectrometry (SP-ICP-MS) has become a powerful tool for biological quantitative analysis. Homogeneous analysis method requires no separation and washing steps, which is suited for the analysis of highly infectious pathogens, so as to reduce the risk of infection during the operation. SARS-CoV-2 spreads all over the world, and its early infection symptoms are similar to influenza, which brings inconvenience to triage. Therefore, developing novel analytical method for simultaneous detection of multiple viral nucleic acids is essential. Taking the advantages of SP-ICP-MS and homogeneous analysis strategy, a SP-ICP-MS homogeneous nucleic acid assay by using gold nanoparticles (Au NPs) and silver nanoparticles (Ag NPs) probes was established for simultaneous sensitive analysis of SARS-CoV-2 and influenza A (H3N2). In the present of target SARS-CoV-2 or H3N2 nucleic acids, corresponding Au NPs or Ag NPs probes form larger aggregates, resulting in increased pulse signal intensity and reduced pulse signal frequency of the corresponding NPs in SP-ICP-MS measurement. In this assay, the reaction system of Au NPs and Ag NPs probes does not interfere with each other, and there was no separation and washing procedure, which facilitates operation, saves the analysis time, and improves the analysis efficiency. The linear range of this method is 5-1000 pmol L-1, with low-level limits of quantification of target nucleic acid. The developed SP-ICP-MS simultaneous homogeneous detection method has a good potential for detecting nucleic acid, protein, cell and other biological samples by changing different modification sequences on the NPs probes.
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60
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Liu H, You Y, Zhu Y, Zheng H. Recent advances in the exonuclease III-assisted target signal amplification strategy for nucleic acid detection. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:5103-5119. [PMID: 34664562 DOI: 10.1039/d1ay01275d] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The detection of nucleic acids has become significantly important in molecular diagnostics, gene therapy, mutation analysis, forensic investigations and biomedical development, and so on. In recent years, exonuclease III (Exo III) as an enzyme in the 3'-5' exonuclease family has evolved as a frequently used technique for signal amplification of low level DNA target detection. Different from the traditional target amplification strategies, the Exo III-assisted amplification strategy has been used for target DNA detection through directly amplifying the amounts of signal reagents. The Exo III-assisted amplification strategy has its unique advantages and characters, because the character of non-specific recognition of Exo III can overcome the limitation of a target-to-probe ratio of 1 : 1 in the traditional nucleic acid hybridization assay and acquire higher sensitivity. In this review, we selectively discuss the recent advances in the Exo III-assisted amplification strategy, including the amplification strategy integrated with nanomaterials, biosensors, hairpin probes and other nucleic acid detection methods. We also discuss the strengths and limitations of each strategy and methods to overcome the limitations.
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Affiliation(s)
- Hongyu Liu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, P. R. China.
| | - Yuhao You
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, P. R. China.
| | - Youzhuo Zhu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, P. R. China.
| | - Heng Zheng
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, P. R. China.
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Tang Y, Gao L, Feng W, Guo C, Yang Q, Li F, Le XC. The CRISPR-Cas toolbox for analytical and diagnostic assay development. Chem Soc Rev 2021; 50:11844-11869. [PMID: 34611682 DOI: 10.1039/d1cs00098e] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) systems have revolutionized biological and biomedical sciences in many ways. The last few years have also seen tremendous interest in deploying the CRISPR-Cas toolbox for analytical and diagnostic assay development because CRISPR-Cas is one of the most powerful classes of molecular machineries for the recognition and manipulation of nucleic acids. In the short period of development, many CRISPR-enabled assays have already established critical roles in clinical diagnostics, biosensing, and bioimaging. We describe in this review the recent advances and design principles of CRISPR mediated analytical tools with an emphasis on the functional roles of CRISPR-Cas machineries as highly efficient binders and molecular scissors. We highlight the diverse engineering approaches for molecularly modifying CRISPR-Cas machineries and for devising better readout platforms. We discuss the potential roles of these new approaches and platforms in enhancing assay sensitivity, specificity, multiplexity, and clinical outcomes. By illustrating the biochemical and analytical processes, we hope this review will help guide the best use of the CRISPR-Cas toolbox in detecting, quantifying and imaging biologically and clinically important molecules and inspire new ideas, technological advances and engineering strategies for addressing real-world challenges such as the on-going COVID-19 pandemic.
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Affiliation(s)
- Yanan Tang
- Analytical & Testing Center, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610064, China.
| | - Lu Gao
- Analytical & Testing Center, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610064, China.
| | - Wei Feng
- Department of Chemistry, Brock University, St. Catharines, Ontario, L2S 3A1, Canada
| | - Chen Guo
- Analytical & Testing Center, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610064, China.
| | - Qianfan Yang
- Analytical & Testing Center, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610064, China.
| | - Feng Li
- Analytical & Testing Center, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610064, China. .,Department of Chemistry, Brock University, St. Catharines, Ontario, L2S 3A1, Canada
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Alberta, T6G 2G3, Canada
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62
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Tan J, Wen Y, Li M. Emerging biosensing platforms for quantitative detection of exosomes as diagnostic biomarkers. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214111] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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63
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Xie Y, Wang H, Yuwen X, Lai G. Exo III-Catalyzed Release of a Zn 2+-Ligation DNAzyme to Drive the Strand Displacement Reaction and Gold Aggregation for the Homogeneous Bioassay of Kanamycin Antibiotics. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:10371-10378. [PMID: 34436884 DOI: 10.1021/acs.jafc.1c04030] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Herein, we combine the exonuclease III (Exo III)-catalyzed release of a Zn2+-dependent ligation DNAzyme with the DNAzyme-driven strand displacement reaction (SDR) to develop a novel homogeneous colorimetric bioassay method for kanamycin (Kana) antibiotic detection. Upon the biorecognition reaction between Kana and a designed hairpin DNA, the DNAzyme-containing strand can be catalytically released by Exo III. Then, this DNAzyme will catalyze the ligation of two oligonucleotides to cause a SDR and the aggregation of gold nanoparticles (Au NPs) labeled by two linker DNA strands. Due to the aggregation of Au NPs for colorimetric signal transduction and the Exo III and SDR-assisted dual signal amplification, this method shows a wide linear range of 5 orders of magnitude and a very low detection limit down to 8.1 fg mL-1. Together with its excellent selectivity, repeatability, reliability, and convenient manipulation, the proposed method shows a great potential for the food quality monitoring application.
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Affiliation(s)
- Yiming Xie
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi 435002, PR China
| | - Haiyan Wang
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi 435002, PR China
| | - Xinyue Yuwen
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi 435002, PR China
| | - Guosong Lai
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, College of Chemistry and Chemical Engineering, Hubei Normal University, Huangshi 435002, PR China
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Abstract
In the past two decades, a DNA-encoded chemical library (DEL or DECL) has emerged and has become a major technology platform for ligand discovery in drug discovery as well as in chemical biology research. Although based on a simple concept, i.e., encoding each compound with a unique DNA tag in a combinatorial chemical library, DEL has been proven to be a powerful tool for interrogating biological targets by accessing vast chemical space at a fraction of the cost of traditional high-throughput screening (HTS). Moreover, the recent technological advances and rapid developments of DEL-compatible reactions have greatly enhanced the chemical diversity of DELs. Today, DELs have been adopted by nearly all major pharmaceutical companies and are also gaining momentum in academia. However, this field is heavily biased toward library encoding and synthesis, and an underexplored aspect of DEL research is the selection methods. Generally, DEL selection is considered to be a massive binding assay conducted over an immobilized protein to identify the physical binders using the typical bind-wash-elute procedure. In recent years, we and other research groups have developed new approaches that can perform DEL selections in the solution phase, which has enabled the selection against complex biological targets beyond purified proteins. On the one hand, these methods have significantly widened the target scope of DELs; on the other hand, they have enabled the functional and potentially phenotypic assays of DELs beyond simple binding. An overview of these methods is provided in this Account.Our laboratory has been using DNA-programmed affinity labeling (DPAL) as the main strategy to develop new DEL selection methods. DPAL is based on DNA-templated synthesis; by using a known ligand to guide the target binding, DPAL is able to specifically establish a stable linkage between the target protein and the ligand. The DNA tag of the target-ligand conjugates serves as a programmable handle for protein characterization or hit compound decoding in the case of DEL selections. DPAL also takes advantage of the fast reaction kinetics of photo-cross-linking to achieve high labeling specificity and fidelity, especially in the selection of DNA-encoded dynamic libraries (DEDLs). DPAL has enabled DEL selections not only in buffer and cell lysates but also with complex biological systems, such as large protein complexes and live cells. Moreover, this strategy has also been employed in other biological applications, such as site-specific protein labeling, protein detection, protein profiling, and target identification. In the Account, we describe these methods, highlight their underlying principles, and conclude with perspectives of the development of the DEL technology.
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Affiliation(s)
- Yinan Song
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Xiaoyu Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission, Units 1503-1511, 15/F, Building 17W, Hong Kong Science and Technology Parks, New
Territories, Hong Kong SAR, China
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Chen J, Zhuang X, Zheng J, Yang R, Wu F, Zhang A, Fang B. Aptamer-based cell-free detection system to detect target protein. Synth Syst Biotechnol 2021; 6:209-215. [PMID: 34466691 PMCID: PMC8374636 DOI: 10.1016/j.synbio.2021.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/21/2021] [Accepted: 07/29/2021] [Indexed: 12/26/2022] Open
Abstract
Biomarkers of disease, especially protein, show great potential for diagnosis and prognosis. For detecting a certain protein, a binding assay implementing antibodies is commonly performed. However, antibodies are not thermally stable and may cause false-positive when the sample composition is complicated. In recent years, a functional nucleic acid named aptamer has been used in many biochemical analysis cases, which is commonly selected from random sequence libraries by using the systematic evolution of ligands by exponential enrichment (SELEX) techniques. Compared to antibodies, the aptamer is more thermal stable, easier to be modified, conjugated, and amplified. Herein, an Aptamer-Based Cell-free Detection (ABCD) system was proposed to detect target protein, using epithelial cell adhesion molecule (EpCAM) as an example. We combined the robustness of aptamer in binding specificity with the signal amplification ability of CRISPR-Cas12a′s trans-cleavage activity in the ABCD system. We also demonstrated that the ABCD system could work well to detect target protein in a relatively low limit of detection (50–100 nM), which lay a foundation for the development of portable detection devices. This work highlights the superiority of the ABCD system in detecting target protein with low abundance and offers new enlightenment for future design and development.
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Affiliation(s)
- Junhong Chen
- XMU-China Team, Xiamen University, Xiamen, 361005, PR China.,College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, PR China
| | - Xiaoyan Zhuang
- XMU-China Team, Xiamen University, Xiamen, 361005, PR China.,College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, PR China
| | - Jiyang Zheng
- XMU-China Team, Xiamen University, Xiamen, 361005, PR China.,College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, PR China
| | - Ruofan Yang
- XMU-China Team, Xiamen University, Xiamen, 361005, PR China.,College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, PR China
| | - Fei Wu
- XMU-China Team, Xiamen University, Xiamen, 361005, PR China
| | - Aihui Zhang
- XMU-China Team, Xiamen University, Xiamen, 361005, PR China.,College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, PR China.,The Key Laboratory for Chemical Biology of Fujian Province, Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, PR China
| | - Baishan Fang
- XMU-China Team, Xiamen University, Xiamen, 361005, PR China.,College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, PR China.,The Key Laboratory for Chemical Biology of Fujian Province, Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, PR China
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66
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Xu Q, Liu K, Jin J, Zhang X. Binding-induced output of catalyst DNA for efficient payload of DNAzyme on magnetic beads by catalyzed hairpin assembly. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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67
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Dziuba D, Didier P, Ciaco S, Barth A, Seidel CAM, Mély Y. Fundamental photophysics of isomorphic and expanded fluorescent nucleoside analogues. Chem Soc Rev 2021; 50:7062-7107. [PMID: 33956014 DOI: 10.1039/d1cs00194a] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are structurally diverse mimics of the natural essentially non-fluorescent nucleosides which have found numerous applications in probing the structure and dynamics of nucleic acids as well as their interactions with various biomolecules. In order to minimize disturbance in the labelled nucleic acid sequences, the FNA chromophoric groups should resemble the natural nucleobases in size and hydrogen-bonding patterns. Isomorphic and expanded FNAs are the two groups that best meet the criteria of non-perturbing fluorescent labels for DNA and RNA. Significant progress has been made over the past decades in understanding the fundamental photophysics that governs the spectroscopic and environmentally sensitive properties of these FNAs. Herein, we review recent advances in the spectroscopic and computational studies of selected isomorphic and expanded FNAs. We also show how this information can be used as a rational basis to design new FNAs, select appropriate sequences for optimal spectroscopic response and interpret fluorescence data in FNA applications.
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Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Stefano Ciaco
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France. and Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Anders Barth
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
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68
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Jiang Y, Yang P, Du L, Xia L, Chen J, Hou X. A signal conversion system using binding-induced strand displacement for disease biomarker assay. LUMINESCENCE 2021; 36:1483-1490. [PMID: 34009741 DOI: 10.1002/bio.4087] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 05/16/2021] [Accepted: 05/17/2021] [Indexed: 11/09/2022]
Abstract
Using the principle of binding-induced DNA strand displacement (BINSD), a DNAzyme-powered nanomachine biosensor for multiple biomarkers via magnetic beads-based signal conversion was designed. This sensor can convert multiple biomarker recognition into release of predesigned output nucleic acids tagged with streptavidin proteins (SA-DNA) for activation of DNA nanomachines. In general, we adopted complementary base pairing rules and affinity ligand specific recognition, and three types of signal conversion systems were constructed that realized universal, sensitive, accurate, and specific detection of multiple biomarkers. Taking the advantage of the strong anti-interference capability of magnetic separation, this strategy could be used for detection of various biomarkers in clinical practice.
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Affiliation(s)
- Yuling Jiang
- College of Chemistry, Sichuan University, Chengdu, China
| | - Peng Yang
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan, China
| | - Lijie Du
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan, China
| | - Lingying Xia
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan, China
| | - Junbo Chen
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan, China
| | - Xiandeng Hou
- College of Chemistry, Sichuan University, Chengdu, China.,Analytical & Testing Center, Sichuan University, Chengdu, Sichuan, China
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69
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Fan W, Chen J, Du H, Hu C, Yang P, Hou X. Activation of catalytic DNAzyme by binding-induced DNA displacement for homogeneous assay. LUMINESCENCE 2021; 36:1498-1506. [PMID: 34014584 DOI: 10.1002/bio.4092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/08/2021] [Accepted: 05/17/2021] [Indexed: 01/14/2023]
Abstract
The sensitive assays for protein, especially for the DNA-based assay, are often dependent on the amplification procedure with assistance of enzyme. Compared with a protein enzyme, deoxyribozyme (DNAzyme) exhibits similar catalytic activity and specificity and better flexibility. In this work, we streamlined the binding induced DNA displacement (BINDD) strategy for the activation of DNAzyme cleavage. Since the intrinsic element of DNAzyme is the nucleic acids, it is easy to join the BINDD by hybridization with an affinity probe. The activity of DNAzyme was initiated by the BINDD reaction mediated by the recognition affinity probe with target proteins. Upon DNAzyme release, it was able to catalyze and cleave the predesigned substrates, generating the enhanced fluorescence signal indicating the protein concentration. Such a constructed homogeneous assay is available and effective in human serum when it was used for detection of platelet derived growth factor-BB (PDGF-BB) and prostate specific antigen (PSA), with detection limits of 100 pM and 200 pM, respectively.
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Affiliation(s)
- Wei Fan
- College of Chemistry, Sichuan University, Chengdu, Sichuan, China
| | - Junbo Chen
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan, China
| | - Huan Du
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan, China
| | - Changjia Hu
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan, China
| | - Peng Yang
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan, China
| | - Xiandeng Hou
- College of Chemistry, Sichuan University, Chengdu, Sichuan, China.,Analytical & Testing Center, Sichuan University, Chengdu, Sichuan, China
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70
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Qi H, Li H, Li F. Aptamer Recognition-Driven Homogeneous Electrochemical Strategy for Simultaneous Analysis of Multiple Pesticides without Interference of Color and Fluorescence. Anal Chem 2021; 93:7739-7745. [PMID: 34009937 DOI: 10.1021/acs.analchem.1c01252] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Credible and simultaneous determination of multiple pesticides is highly desirable for guaranteeing food safety. However, the current methods are limited to significant interference of color and fluorescence or electrode's modification and mainly focus on the analysis of a single pesticide. Herein, we proposed a novel aptamer-based homogeneous electrochemical system for highly sensitive and simultaneous analysis of multiple pesticides based on target pesticide-switched exonuclease III (Exo III)-assisted signal amplification. The recognition of hairpin probes by target pesticides impels the production of pesticide-DNA complexes, which hybridize with electroactive dye-labeled DNA to form double-stranded DNA, subsequently initiating an Exo III-assisted digestion reaction to generate abundant electroactive dye-tagged mononucleotides. In comparison with pesticide deficiency, two higher differential pulse voltammetry (DPV) currents are measured, which rely on the amount of target pesticides. Therefore, simultaneous analysis of two pesticides is realized with limits of detection of 0.0048 and 0.0089 nM, respectively, comparable or superior to those of known methods that focused on a single pesticide. Moreover, the proposed system is successfully employed to simultaneously evaluate the residual level of acetamiprid and profenofos in Brassica chinensis and thus will find more useful applications for pesticide-related food safety.
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Affiliation(s)
- Hongjie Qi
- College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, People's Republic of China.,College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Haiyin Li
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Feng Li
- College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, People's Republic of China.,College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
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71
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Deng J, Tian F, Liu C, Liu Y, Zhao S, Fu T, Sun J, Tan W. Rapid One-Step Detection of Viral Particles Using an Aptamer-Based Thermophoretic Assay. J Am Chem Soc 2021; 143:7261-7266. [PMID: 33944569 DOI: 10.1021/jacs.1c02929] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Rapid and sensitive identification of viral pathogens such as SARS-CoV-2 is a critical step to control the pandemic disease. Viral antigen detection can compete with gold-standard PCR-based nucleic acid diagnostics in terms of better reflection of viral infectivity and reduced risk of contamination from enzymatic amplification. Here, we report the development of a one-step thermophoretic assay using an aptamer and polyethylene glycol (PEG) for direct quantitative detection of viral particles. The assay relies on aptamer binding to the spike protein of SARS-CoV-2 and simultaneous accumulation of aptamer-bound viral particles in laser-induced gradients of temperature and PEG concentration. Using a pseudotyped lentivirus model, a limit of detection of ∼170 particles μL-1 (26 fM of the spike protein) is achieved in 15 min without the need of any pretreatment. As a proof of concept, the one-step thermophoretic assay is used to detect synthetic samples by spiking viral particles into oropharyngeal swabs with an accuracy of 100%. The simplicity, speed, and cost-effectiveness of this thermophoretic assay may expand the diagnostic tools for viral pathogens.
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Affiliation(s)
- Jinqi Deng
- Beijing Engineering Research Center for BioNanotechnology, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China.,Sino-Danish College, Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Tian
- Beijing Engineering Research Center for BioNanotechnology, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China.,Sino-Danish College, Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Liu
- Beijing Engineering Research Center for BioNanotechnology, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China.,Sino-Danish College, Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan Liu
- Beijing Engineering Research Center for BioNanotechnology, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Shuai Zhao
- Beijing Engineering Research Center for BioNanotechnology, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China.,Sino-Danish College, Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ting Fu
- Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China
| | - Jiashu Sun
- Beijing Engineering Research Center for BioNanotechnology, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China.,Sino-Danish College, Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weihong Tan
- Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China.,State Key Laboratory of Chemo/Bio- Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
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72
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Lin B, Tian T, Lu Y, Liu D, Huang M, Zhu L, Zhu Z, Song Y, Yang C. Tracing Tumor‐Derived Exosomal PD‐L1 by Dual‐Aptamer Activated Proximity‐Induced Droplet Digital PCR. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015628] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Bingqian Lin
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation the Key Laboratory of Chemical Biology of Fujian Province State Key Laboratory of Physical Chemistry of Solid Surfaces Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Tian Tian
- Chemistry and Biomedicine Innovation Center (ChemBIC) School of Chemistry and Chemical Engineering Nanjing University Nanjing 210023 China
| | - Yinzhu Lu
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation the Key Laboratory of Chemical Biology of Fujian Province State Key Laboratory of Physical Chemistry of Solid Surfaces Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Dan Liu
- School of Biomedical Sciences College of Chemical Engineering Huaqiao University Xiamen Fujian 362000 China
| | - Mengjiao Huang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation the Key Laboratory of Chemical Biology of Fujian Province State Key Laboratory of Physical Chemistry of Solid Surfaces Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Lin Zhu
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation the Key Laboratory of Chemical Biology of Fujian Province State Key Laboratory of Physical Chemistry of Solid Surfaces Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation the Key Laboratory of Chemical Biology of Fujian Province State Key Laboratory of Physical Chemistry of Solid Surfaces Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Yanling Song
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation the Key Laboratory of Chemical Biology of Fujian Province State Key Laboratory of Physical Chemistry of Solid Surfaces Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation the Key Laboratory of Chemical Biology of Fujian Province State Key Laboratory of Physical Chemistry of Solid Surfaces Department of Chemical Biology College of Chemistry and Chemical Engineering Xiamen University Xiamen 361005 China
- Institute of Molecular Medicine Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
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73
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Wang LJ, Liang L, Liu BJ, Jiang B, Zhang CY. A controlled T7 transcription-driven symmetric amplification cascade machinery for single-molecule detection of multiple repair glycosylases. Chem Sci 2021; 12:5544-5554. [PMID: 34168791 PMCID: PMC8179622 DOI: 10.1039/d1sc00189b] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 02/24/2021] [Indexed: 12/26/2022] Open
Abstract
Genomic oxidation and alkylation are two of the most important forms of cytotoxic damage that may induce mutagenesis, carcinogenicity, and teratogenicity. Human 8-oxoguanine (hOGG1) and alkyladenine DNA glycosylases (hAAG) are responsible for two major forms of oxidative and alkylative damage repair, and their aberrant activities may cause repair deficiencies that are associated with a variety of human diseases, including cancers. Due to their complicated catalytic pathways and hydrolysis mechanisms, simultaneous and accurate detection of multiple repair glycosylases has remained a great challenge. Herein, by taking advantage of unique features of T7-based transcription and the intrinsic superiorities of single-molecule imaging techniques, we demonstrate for the first time the development of a controlled T7 transcription-driven symmetric amplification cascade machinery for single-molecule detection of hOGG1 and hAAG. The presence of hOGG1 and hAAG can remove damaged 8-oxoG and deoxyinosine, respectively, from the dumbbell substrate, resulting in breaking of the dumbbell substrate, unfolding of two loops, and exposure of two T7 promoters simultaneously. The T7 promoters can activate symmetric transcription amplifications with the unfolded loops as the templates, inducing efficient transcription to produce two different single-stranded RNA transcripts (i.e., reporter probes 1 and 2). Reporter probes 1 and 2 hybridize with signal probes 1 and 2, respectively, to initiate duplex-specific nuclease-directed cyclic digestion of the signal probes, liberating large amounts of Cy3 and Cy5 fluorescent molecules. The released Cy3 and Cy5 molecules can be simply measured by total internal reflection fluorescence-based single-molecule detection, with the Cy3 signal indicating the presence of hOGG1 and the Cy5 signal indicating the presence of hAAG. This method exhibits good specificity and high sensitivity with a detection limit of 3.52 × 10-8 U μL-1 for hOGG1 and 3.55 × 10-7 U μL-1 for hAAG, and it can even quantify repair glycosylases at the single-cell level. Moreover, it can be applied for the measurement of kinetic parameters, the screening of potential inhibitors, and the detection of repair glycosylases in human serum, providing a new paradigm for repair enzyme-related biomedical research, drug discovery, and clinical diagnosis.
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Affiliation(s)
- Li-Juan Wang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University Jinan 250014 China
- School of Chemistry and Chemical Engineering, Southeast University Nanjing 211189 China
| | - Le Liang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University Jinan 250014 China
| | - Bing-Jie Liu
- Academy of Medical Sciences, Zhengzhou University Zhengzhou 450000 China
| | - BingHua Jiang
- Academy of Medical Sciences, Zhengzhou University Zhengzhou 450000 China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University Jinan 250014 China
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74
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Lin B, Tian T, Lu Y, Liu D, Huang M, Zhu L, Zhu Z, Song Y, Yang C. Tracing Tumor-Derived Exosomal PD-L1 by Dual-Aptamer Activated Proximity-Induced Droplet Digital PCR. Angew Chem Int Ed Engl 2021; 60:7582-7586. [PMID: 33382182 DOI: 10.1002/anie.202015628] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/17/2020] [Indexed: 12/14/2022]
Abstract
Tumor-derived exosomal proteins have emerged as promising biomarkers for cancer diagnosis, but the quantitation accuracy is hindered by large numbers of normal cell-derived exosomes. Herein, we developed a dual-target-specific aptamer recognition activated in situ connection system on exosome membrane combined with droplet digital PCR (ddPCR) (TRACER) for quantitation of tumor-derived exosomal PD-L1 (Exo-PD-L1 ). Leveraging the high binding affinity of aptamers, excellent selectivity of dual-aptamer recognition, and the high sensitivity of ddPCR, this method exhibits significant sensitivity and selectivity for tracing tumor-derived Exo-PD-L1 in a wash-free manner. Due to the excellent sensitivity, the level of tumor-derived Exo-PD-L1 detected by TRACER can distinguish cancer patients from healthy donors, and for the first time was identified as a more reliable tumor diagnostic marker than total Exo-PD-L1 . The TRACER strategy holds great potential for converting exosomes into reliable clinical indicators and exploring the biological functions of exosomes.
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Affiliation(s)
- Bingqian Lin
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Tian Tian
- Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yinzhu Lu
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Dan Liu
- School of Biomedical Sciences, College of Chemical Engineering, Huaqiao University, Xiamen, Fujian, 362000, China
| | - Mengjiao Huang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Lin Zhu
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Yanling Song
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.,Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
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75
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Zhang Z, Xiang X, Hu Y, Deng Y, Li L, Zhao W, Wu T. A sensitive biomolecules detection device with catalytic hairpin assembly and cationic conjugated polymer-assisted dual signal amplification strategy. Talanta 2021; 223:121716. [PMID: 33303163 DOI: 10.1016/j.talanta.2020.121716] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/16/2020] [Accepted: 09/28/2020] [Indexed: 01/26/2023]
Abstract
A simple, sensitive, selective, and enzyme-free homogeneous fluorescent biosensing device for DNA and protein detection is fabricated based on catalytic hairpin assembly (CHA), cationic conjugated polymer (CCP), and graphene oxide (GO). In this biosensing device, CCP together with CHA, provides dual signal amplification, and GO suppresses the background when the target is absent. Thus, this CHA/CCP/GO-based biosensor shows improved sensitivity compared with conventional CHA-based biosensors. In the biosensor, two 6-carboxyfluorescein (FAM)-labeled hairpin DNA probes (H1 and H2) are designed, and in the initial state, they could absorb on the surface of GO, leading the system to produce a low background fluorescence signal. When the target DNA appears, it continually catalyzes the formation of H1-H2 double-stranded DNA (dsDNA) complex by CHA reaction, which could be regarded as the first-step amplification. At the same time, the H1-H2 dsDNA complex departures from the surface of GO and interacts with CCP through electrostatic interaction. Then, CCP provides the second-step amplification due to its high fluorescence resonance energy transfer (FRET) efficiency from CCP to FAM. The limit of detection (LOD) and the limit of quantification (LOQ) for the target DNA could reach 32 pM and 1 nM, respectively. The linear range was from 0.1 to 40 nM, and relative standard deviation (RSD) for the points on the calibration curve ranged from 2.8% to 13.9%. This strategy could also be applied to protein detection potentially by integrating the aptamer of the target protein into the hairpin DNA. As proof of concept, thrombin was detected, and the LOD and LOQ was 11 pM and 33 pM, respectively. The linear range was from 3 to 54 nM, and RSD ranged from 3.3% to 10.4%. It showed good selectivity for thrombin compared to equal concentrations of interferences. It was also applied to quantify the thrombin (5, 10, 20 nM) in 1% spiked human serum, which showed satisfying recovery in the range of 94.7 ± 5.3 to 103.7 ± 4.9%.
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Affiliation(s)
- Zhen Zhang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xia Xiang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
| | - Yuqiang Hu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yuhan Deng
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Longjie Li
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wenbo Zhao
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China.
| | - Tongbo Wu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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76
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Liu X, Zhao Y, Li F. Nucleic acid-functionalized metal-organic framework for ultrasensitive immobilization-free photoelectrochemical biosensing. Biosens Bioelectron 2021; 173:112832. [DOI: 10.1016/j.bios.2020.112832] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/06/2020] [Accepted: 11/17/2020] [Indexed: 12/20/2022]
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77
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Li Y, Mansour H, Watson CJF, Tang Y, MacNeil AJ, Li F. Amplified detection of nucleic acids and proteins using an isothermal proximity CRISPR Cas12a assay. Chem Sci 2021; 12:2133-2137. [PMID: 34163977 PMCID: PMC8179305 DOI: 10.1039/d0sc06113a] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Herein, we describe an isothermal proximity CRISPR Cas12a assay that harnesses the target-induced indiscrimitive single-stranded DNase activity of Cas12a for the quantitative profiling of gene expression at the mRNA level and detection of proteins with high sensitivity and specificity. The target recognition is achieved through proximity binding rather than recognition by CRISPR RNA (crRNA), which allows for flexible assay design. A binding-induced primer extension reaction is used to generate a predesigned CRISPR-targetable sequence as a barcode for further signal amplification. Through this dual amplification protocol, we were able to detect as low as 1 fM target nucleic acid and 100 fM target protein isothermally. The practical applicability of this assay was successfully demonstrated for the temporal profiling of interleukin-6 gene expression during allergen-mediated mast cell activation.
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Affiliation(s)
- Yongya Li
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Center, Sichuan University 29 Wangjing Road Chengdu Sichuan 610064 China .,Department of Chemistry, Centre for Biotechnology, Brock University St. Catharines Ontario L2S 3A1 Canada
| | - Hayam Mansour
- Department of Chemistry, Centre for Biotechnology, Brock University St. Catharines Ontario L2S 3A1 Canada .,Department of Cell Biology, National Research Center 12622 Egypt
| | - Colton J F Watson
- Department of Health Sciences, Brock University St. Catharines Ontario L2S 3A1 Canada
| | - Yanan Tang
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Center, Sichuan University 29 Wangjing Road Chengdu Sichuan 610064 China
| | - Adam J MacNeil
- Department of Health Sciences, Brock University St. Catharines Ontario L2S 3A1 Canada
| | - Feng Li
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Analytical & Testing Center, Sichuan University 29 Wangjing Road Chengdu Sichuan 610064 China .,Department of Chemistry, Centre for Biotechnology, Brock University St. Catharines Ontario L2S 3A1 Canada
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78
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Shang J, Li C, Li F, Wang Q, Yuan B, Wang F. Construction of an Enzyme-Free Initiator-Replicated Hybridization Chain Reaction Circuit for Amplified Methyltransferase Evaluation and Inhibitor Assay. Anal Chem 2021; 93:2403-2410. [DOI: 10.1021/acs.analchem.0c04356] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Jinhua Shang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Chunxiao Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Fengzhe Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Qing Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Bifeng Yuan
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
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79
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Jia Y, Hu Y. Cofactor-assisted three-way DNA junction-driven strand displacement. RSC Adv 2021; 11:30377-30382. [PMID: 35480263 PMCID: PMC9041134 DOI: 10.1039/d1ra05242j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/27/2021] [Indexed: 11/21/2022] Open
Abstract
Toehold-mediated strand displacement is widely used to construct and operate DNA nanodevices. Cooperative regulation of strand displacement with diverse factors is pivotal in the design and construction of functional and dynamic devices. Herein, a cofactor-assisted three-way DNA junction-driven strand displacement strategy was reported, which could tune the reaction kinetics by the collaboration of DNA and other types of stimulus. This strategy is responsive to various inputs by incorporation of the specific sequence into the three-way junction structure. Specifically, the cooperation of multiple factors changes the conformation of the specific domain and promotes the reaction. To demonstrate the strategy, adenosine triphosphate (ATP), HG2+, and pH were used as cofactors to modulate the displacement reaction. The electrophoresis and fluorescence experiments showed that the cooperative regulation of the strand displacement reaction could be achieved by diverse factors using this strategy. The proposed strategy provides design flexibility for dynamic DNA devices and may have potential in biosensing and biocomputing. Cooperative regulation of strand displacement with diverse factors was achieved by a cofactor-assisted three-way DNA junction-driven strategy. Using this strategy nanodevices reacted to various inputs by incorporating a specific sequence into the three-way junction structure.![]()
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Affiliation(s)
- Yufeng Jia
- School of Economics and Management, Shijiazhuang Tiedao University, Shijiazhuang 050043, P. R. China
| | - Yingxin Hu
- College of Information Science and Technology, Shijiazhuang Tiedao University, Shijiazhuang 050043, P. R. China
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80
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Kučera R, Sčensná A, Miletín M, Zimčík P. The chromatographic behaviour of new double-labelled oligodeoxynucleotide probes containing azaphthalocyanine dye as a quencher with respect to evaluation of their purity. Biomed Chromatogr 2020; 35:e5033. [PMID: 33226652 DOI: 10.1002/bmc.5033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 10/12/2020] [Accepted: 11/19/2020] [Indexed: 11/07/2022]
Abstract
The influence of experimental conditions on chromatographic behaviour of promising oligodeoxynucleotide double-labelled molecular probes containing an azaphthalocyanine macrocycle as a perspective dark quencher was studied. A recently introduced new stationary phase based on styrene-divinylbenzene copolymer was tested. The planar and hydrophobic structure of the azaphthalocyanine is considerably different from those of currently used fluorophores and quenchers. Thus, the most challenging issue was the separation of the double-labelled probe from its main impurity represented by a mono-labelled probe, containing only the azaphthalocyanine macrocycle. The absorbance measurement cannot simply determine this impurity, and its presence fundamentally compromises the biological assay. The commonly used gradient elution was not suitable and isocratic conditions seemed to be more appropriate. The azaphthalocyanine moiety influences the properties of the modified oligodeoxynucleotides substantially, and thus their chromatographic behaviour was determined predominantly by this quencher. Acetonitrile was the preferred organic solvent for the analysis of probes containing the azaphthalocyanine quencher and the effect of ion-pairing reagents was dependent on the probe structure. The temperature seemed to be an effective parameter for fine-tuning of the separation and mass transfer improvement. Generally, our findings could be helpful in method development for purity evaluation of double-labelled oligodeoxynucleotide probes and semipreparative methods.
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Affiliation(s)
- Radim Kučera
- Faculty of Pharmacy in Hradec Králové, Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Hradec Králové, Czech Republic
| | - Anna Sčensná
- Faculty of Pharmacy in Hradec Králové, Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Hradec Králové, Czech Republic
| | - Miroslav Miletín
- Faculty of Pharmacy in Hradec Králové, Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Hradec Králové, Czech Republic
| | - Petr Zimčík
- Faculty of Pharmacy in Hradec Králové, Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Hradec Králové, Czech Republic
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81
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Huang Z, Li Z, Jiang M, Liu R, Lv Y. Homogeneous Multiplex Immunoassay for One-Step Pancreatic Cancer Biomarker Evaluation. Anal Chem 2020; 92:16105-16112. [DOI: 10.1021/acs.analchem.0c03780] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Zili Huang
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Ziyan Li
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Min Jiang
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Rui Liu
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Yi Lv
- Analytical & Testing Center, Sichuan University, Chengdu 610064, China
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82
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Zhu X, Qu B, Ying ZM, Liu JW, Wu Z, Yu RQ, Jiang JH. Cascade Circuits on Self-Assembled DNA Polymers for Targeted RNA Imaging In Vivo. Anal Chem 2020; 92:15953-15958. [PMID: 33275414 DOI: 10.1021/acs.analchem.0c03400] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
DNA molecular probes have emerged as a powerful tool for RNA imaging. Hurdles in cell-specific delivery and other issues such as insufficient stability, limited sensitivity, or slow reaction kinetics, however, hinder the further application of DNA molecular probes in vivo. Herein, we report an aptamer-tethered DNA polymer for cell-specific transportation and amplified imaging of RNA in vivo via a DNA cascade reaction. DNA polymers are constructed through an initiator-triggered hybridization chain reaction using two functional DNA monomers. The prepared DNA polymers show low cytotoxicity and good stability against nuclease degradation and enable cell-specific transportation of DNA circuits via aptamer-receptor binding. Moreover, assembling the reactants of hairpins C1 and C2 on the DNA polymers accelerates the response kinetics and improves the sensitivity of the cascade reaction. We also show that the DNA polymers enable efficient imaging of microRNA-21 in live cells and in vivo via intravenous injection. The DNA polymers provide a valuable platform for targeted and amplified RNA imaging in vivo, which holds great implications for early clinical diagnosis and therapy.
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Affiliation(s)
- Xueli Zhu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, Hunan, China.,Henan Province Function-Oriented Porous Materials Key Laboratory, College of Chemistry and Chemical Engineering, Luoyang Normal University, Luoyang 471934, Henan, China
| | - Bin Qu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, Hunan, China
| | - Zhan-Ming Ying
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, Hunan, China
| | - Jin-Wen Liu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, Hunan, China.,The First Affiliated Hospital of Guangxi Medical University, School of Preclinical Medicine & Centre for Translational Medicine, Guangxi Medical University, Nanning 530021, Guangxi, China
| | - Zhenkun Wu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, Hunan, China
| | - Ru-Qin Yu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, Hunan, China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, Hunan, China
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83
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Gong K, Wu Q, Wang H, He S, Shang J, Wang F. Autocatalytic DNAzyme assembly for amplified intracellular imaging. Chem Commun (Camb) 2020; 56:11410-11413. [PMID: 32940259 DOI: 10.1039/d0cc05257d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The autocatalytic HCR-DNAzyme platform was constructed as a versatile amplification platform for intracellular microRNA imaging by integrating hybridization chain reaction (HCR) circuit with DNAzyme biocatalysis. The HCR-assembled multifunctional DNAzyme nanowires produce new HCR triggers and numerous transducer DNAzyme amplifier, and thus shows great promise in earlier cancer diagnosis.
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Affiliation(s)
- Keke Gong
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei 430072, P. R. China.
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84
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Feng W, Newbigging AM, Le C, Pang B, Peng H, Cao Y, Wu J, Abbas G, Song J, Wang DB, Cui M, Tao J, Tyrrell DL, Zhang XE, Zhang H, Le XC. Molecular Diagnosis of COVID-19: Challenges and Research Needs. Anal Chem 2020; 92:10196-10209. [PMID: 32573207 PMCID: PMC7346719 DOI: 10.1021/acs.analchem.0c02060] [Citation(s) in RCA: 242] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 06/23/2020] [Indexed: 12/15/2022]
Abstract
Molecular diagnosis of COVID-19 primarily relies on the detection of RNA of the SARS-CoV-2 virus, the causative infectious agent of the pandemic. Reverse transcription polymerase chain reaction (RT-PCR) enables sensitive detection of specific sequences of genes that encode the RNA dependent RNA polymerase (RdRP), nucleocapsid (N), envelope (E), and spike (S) proteins of the virus. Although RT-PCR tests have been widely used and many alternative assays have been developed, the current testing capacity and availability cannot meet the unprecedented global demands for rapid, reliable, and widely accessible molecular diagnosis. Challenges remain throughout the entire analytical process, from the collection and treatment of specimens to the amplification and detection of viral RNA and the validation of clinical sensitivity and specificity. We highlight the main issues surrounding molecular diagnosis of COVID-19, including false negatives from the detection of viral RNA, temporal variations of viral loads, selection and treatment of specimens, and limiting factors in detecting viral proteins. We discuss critical research needs, such as improvements in RT-PCR, development of alternative nucleic acid amplification techniques, incorporating CRISPR technology for point-of-care (POC) applications, validation of POC tests, and sequencing of viral RNA and its mutations. Improved assays are also needed for environmental surveillance or wastewater-based epidemiology, which gauges infection on the community level through analyses of viral components in the community's wastewater. Public health surveillance benefits from large-scale analyses of antibodies in serum, although the current serological tests do not quantify neutralizing antibodies. Further advances in analytical technology and research through multidisciplinary collaboration will contribute to the development of mitigation strategies, therapeutics, and vaccines. Lessons learned from molecular diagnosis of COVID-19 are valuable for better preparedness in response to other infectious diseases.
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Affiliation(s)
- Wei Feng
- Division of Analytical and Environmental Toxicology,
Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry,
University of Alberta, Edmonton, Alberta,
Canada T6G 2G3
| | - Ashley M. Newbigging
- Division of Analytical and Environmental Toxicology,
Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry,
University of Alberta, Edmonton, Alberta,
Canada T6G 2G3
| | - Connie Le
- Li Ka Shing Institute of Virology, Department of
Medical Microbiology and Immunology, Faculty of Medicine and Dentistry,
University of Alberta, Edmonton, Alberta,
Canada T6G 2E1
| | - Bo Pang
- Division of Analytical and Environmental Toxicology,
Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry,
University of Alberta, Edmonton, Alberta,
Canada T6G 2G3
| | - Hanyong Peng
- Division of Analytical and Environmental Toxicology,
Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry,
University of Alberta, Edmonton, Alberta,
Canada T6G 2G3
| | - Yiren Cao
- Division of Analytical and Environmental Toxicology,
Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry,
University of Alberta, Edmonton, Alberta,
Canada T6G 2G3
| | - Jinjun Wu
- Division of Analytical and Environmental Toxicology,
Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry,
University of Alberta, Edmonton, Alberta,
Canada T6G 2G3
| | - Ghulam Abbas
- National Laboratory of Biomacromolecules, Institute of
Biophysics, Chinese Academy of Sciences, No. 15 Datun Road,
Beijing, China 100101
| | - Jin Song
- National Laboratory of Biomacromolecules, Institute of
Biophysics, Chinese Academy of Sciences, No. 15 Datun Road,
Beijing, China 100101
| | - Dian-Bing Wang
- National Laboratory of Biomacromolecules, Institute of
Biophysics, Chinese Academy of Sciences, No. 15 Datun Road,
Beijing, China 100101
| | - Mengmeng Cui
- National Laboratory of Biomacromolecules, Institute of
Biophysics, Chinese Academy of Sciences, No. 15 Datun Road,
Beijing, China 100101
| | - Jeffrey Tao
- Division of Analytical and Environmental Toxicology,
Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry,
University of Alberta, Edmonton, Alberta,
Canada T6G 2G3
| | - D. Lorne Tyrrell
- Li Ka Shing Institute of Virology, Department of
Medical Microbiology and Immunology, Faculty of Medicine and Dentistry,
University of Alberta, Edmonton, Alberta,
Canada T6G 2E1
| | - Xian-En Zhang
- National Laboratory of Biomacromolecules, Institute of
Biophysics, Chinese Academy of Sciences, No. 15 Datun Road,
Beijing, China 100101
| | - Hongquan Zhang
- Division of Analytical and Environmental Toxicology,
Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry,
University of Alberta, Edmonton, Alberta,
Canada T6G 2G3
| | - X. Chris Le
- Division of Analytical and Environmental Toxicology,
Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry,
University of Alberta, Edmonton, Alberta,
Canada T6G 2G3
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85
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He L, Chen F, Zhang D, Xie S, Xu S, Wang Z, Zhang L, Cui C, Liu Y, Tan W. Transducing Complex Biomolecular Interactions by Temperature-Output Artificial DNA Signaling Networks. J Am Chem Soc 2020; 142:14234-14239. [DOI: 10.1021/jacs.0c05453] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Lei He
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Fengming Chen
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Dailiang Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Sitao Xie
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Shujuan Xu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Zhimin Wang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Lili Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Cheng Cui
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Yanlan Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
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86
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Zhang Y, Zhang Y, Zhang X, Li Y, He Y, Liu Y, Ju H. A photo zipper locked DNA nanomachine with an internal standard for precise miRNA imaging in living cells. Chem Sci 2020; 11:6289-6296. [PMID: 32874516 PMCID: PMC7448525 DOI: 10.1039/d0sc00394h] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 05/26/2020] [Indexed: 12/28/2022] Open
Abstract
DNA nanomachines are capable of converting tiny triggers into autonomous accelerated cascade hybridization reactions and they have been used as a signal amplification strategy for intracellular imaging. However, the "always active" property of most DNA nanomachines with an "absolute intensity-dependent" signal acquisition mode results in "false positive signal amplification" by extracellular analytes and impairs detection accuracy. Here we design a photo zipper locked miRNA responsive DNA nanomachine (PZ-DNA nanomachine) based on upconversion nanoparticles (UCNPs) with a photo-cleavable DNA strand to block the miRNA recognition region, which provided sufficient protection to the DNA nanomachine against nonspecific extracellular activation and allowed satisfactory signal amplification for sensitive miRNA imaging after intracellular photoactivation. Multiple emissions from the UCNPs were also utilized as an internal standard to self-calibrate the intracellular miRNA responsive fluorescence signal. The presented PZ-DNA nanomachine demonstrated the sensitive imaging of intracellular miRNA from different cell lines, which resulted in good accordance with qRT-PCR measurements, providing a universal platform for precise imaging in living cells with high spatial-temporal specificity.
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Affiliation(s)
- Yue Zhang
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
| | - Yue Zhang
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
| | - Xiaobo Zhang
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
| | - Yuyi Li
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
| | - Yuling He
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
| | - Ying Liu
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
- Chemistry and Biomedicine Innovation Center , Nanjing University , Nanjing 210023 , China .
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
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87
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Wei J, Wang H, Gong X, Wang Q, Wang H, Zhou Y, Wang F. A proteinase-free DNA replication machinery for in vitro and in vivo amplified MicroRNA imaging. Nucleic Acids Res 2020; 48:e60. [PMID: 32347938 PMCID: PMC7261173 DOI: 10.1093/nar/gkaa250] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 03/05/2020] [Accepted: 04/01/2020] [Indexed: 12/13/2022] Open
Abstract
The construction of robust, modular and compact DNA machinery facilitates us to build more intelligent and ingenious sensing strategies in complex biological systems. However, the performance of conventional DNA amplifiers is always impeded by their limited in-depth amplifications and miscellaneously enzymatic requirements. Here, a proteinase-free reciprocal DNA replication machinery is developed by exploiting the synergistic cross-activation between hybridization chain reaction (HCR) and DNAzyme. The DNAzyme provides an efficient way to simplify the sophisticated design of HCR machinery and simultaneously to promote the amplification capacity. And the HCR-assembled tandem DNAzyme nanowires produce numerous new triggers for reversely stimulating HCR amplifier as systematically explored by experiments and computer-aided simulations. The reciprocal amplifier can be executed as a versatile and powerful sensing platform for analyzing miRNA in living cells and even in mice, originating from the inherent reaction accelerations and multiple-guaranteed recognitions. The reciprocal catalytic DNA machine holds great potential in clinical diagnosis and assessment.
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Affiliation(s)
- Jie Wei
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430000, P. R. China
| | - Huimin Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430000, P. R. China
| | - Xue Gong
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430000, P. R. China
| | - Qing Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430000, P. R. China
| | - Hong Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430000, P. R. China
| | - Yangjie Zhou
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430000, P. R. China
| | - Fuan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430000, P. R. China
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88
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Aparin IO, Sergeeva OV, Mishin AS, Khaydukov EV, Korshun VA, Zatsepin TS. Excimer-FRET Cascade in Dual DNA Probes: Open Access to Large Stokes Shift, Enhanced Acceptor Light up, and Robust RNA Sensing. Anal Chem 2020; 92:7028-7036. [DOI: 10.1021/acs.analchem.0c00270] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ilya O. Aparin
- Skolkovo Institute of Science and Technology, 143026 Skolkovo, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - Olga V. Sergeeva
- Skolkovo Institute of Science and Technology, 143026 Skolkovo, Russia
| | - Alexander S. Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - Evgeny V. Khaydukov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- Federal Scientific Research Centre “Crystallography and Photonics” RAS, 119333 Moscow, Russia
- Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Vladimir A. Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- Gause Institute of New Antibiotics, 119021 Moscow, Russia
- Department of Biology and Biotechnology, National Research University Higher School of Economics, 117312 Moscow, Russia
| | - Timofei S. Zatsepin
- Skolkovo Institute of Science and Technology, 143026 Skolkovo, Russia
- Department of Chemistry, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
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89
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Sensors design based on hybrid gold-silica nanostructures. Biosens Bioelectron 2020; 153:112054. [DOI: 10.1016/j.bios.2020.112054] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 01/11/2020] [Accepted: 01/25/2020] [Indexed: 12/14/2022]
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90
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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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91
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A novel electrochemical biosensor with molecularly imprinted polymers and aptamer-based sandwich assay for determining amyloid-β oligomer. J Electroanal Chem (Lausanne) 2020. [DOI: 10.1016/j.jelechem.2020.114017] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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92
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Hassan EM, DeRosa MC. Recent advances in cancer early detection and diagnosis: Role of nucleic acid based aptasensors. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115806] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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93
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Shang J, Wei J, Wang Q, Wang J, Zhou Y, Yu S, Liu X, Wang F. Adaption of an autonomously cascade DNA circuit for amplified detection and intracellular imaging of polynucleotide kinase with ultralow background. Biosens Bioelectron 2020; 152:111994. [DOI: 10.1016/j.bios.2019.111994] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/15/2019] [Accepted: 12/23/2019] [Indexed: 12/20/2022]
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94
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Zhou R, Li Y, Dong T, Tang Y, Li F. A sequence-specific plasmonic loop-mediated isothermal amplification assay with orthogonal color readouts enabled by CRISPR Cas12a. Chem Commun (Camb) 2020; 56:3536-3538. [PMID: 32103228 DOI: 10.1039/d0cc00397b] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Herein, we introduce a sequence-specific plasmonic loop-mediated isothermal amplification (LAMP) assay with dual, complementary color readouts enabled by CRISPR Cas12a. Using this assay, any double-stranded LAMP amplicon containing a 5'-TTN PAM sequence can be recognized by Cas12a through a specific CRISPR RNA. The signal transduction is achieved using two orthogonal plasmonic systems mediated by Cas12a.
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Affiliation(s)
- Rongxing Zhou
- Biliary Surgical Department of West China Hospital, Sichuan University, Chengdu, Sichuan, China
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95
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Wang JR, Xia C, Yang L, Li YF, Li CM, Huang CZ. DNA Nanofirecrackers Assembled through Hybridization Chain Reaction for Ultrasensitive SERS Immunoassay of Prostate Specific Antigen. Anal Chem 2020; 92:4046-4052. [PMID: 32048509 DOI: 10.1021/acs.analchem.9b05648] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Isothermal nucleic acid amplification technology has been widely adopted for analytical chemistry with the purpose of sensitivity improvement. Herein we present an ultrasensitive concatenated hybridization chain reaction (C-HCR) based surface-enhanced Raman scattering (SERS) immunoassay by forming antibody-antigen-aptamer heterosandwich structures with the model analyte of total prostate specific antigens (tPSA). In the C-HCR, two HCRs, one proceeds with two hairpins and the other with four biotin-modified hairpins, are coupled, making the formation of DNA nanofirecrackers with the lengths longer than 200 nm and more than four hundred million binding sites of streptavidin modified enzymes. These types of DNA nanofirecrackers through the aptamer encoded linker strand to form heterosandwich structures could provide a general signal application platform such as enzyme catalysis with high amplification efficiency. As a proof of concept, the Au@Ag core-shell nanostructure based SERS immunoassay with excellent signal amplification has been developed by employing the streptavidin modified alkaline phosphatase (SA-ALP) through its catalysis of 2-phospho-l-ascorbic acid trisodium salt (AAP) to form Au@Ag core-shell nanostructures via the formation of ascorbic acid (AA) to reduce AgNO3 and deposition of silver element on gold nanorods (AuNRs). The newly developed method has a detection limit as low as 0.94 fg/mL and has successfully achieved the detection of serum samples from clinical patients, which was consistent with the clinical test results, showing that this C-HCR strategy to form DNA nanofirecrackers has great potential in clinical applications.
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Affiliation(s)
- Jia Ru Wang
- Key Laboratory of Luminescent and Real-Time Analytical System (Southwest University), Chongqing Science and Technology Bureau, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Chang Xia
- Key Laboratory of Luminescent and Real-Time Analytical System (Southwest University), Chongqing Science and Technology Bureau, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Lin Yang
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Yuan Fang Li
- Key Laboratory of Luminescent and Real-Time Analytical System (Southwest University), Chongqing Science and Technology Bureau, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Chun Mei Li
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Cheng Zhi Huang
- Key Laboratory of Luminescent and Real-Time Analytical System (Southwest University), Chongqing Science and Technology Bureau, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.,College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
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96
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Ma K, Dong P, Liang M, Yu S, Chen Y, Wang F. Facile Assembly of Multifunctional Antibacterial Nanoplatform Leveraging Synergistic Sensitization between Silver Nanostructure and Vancomycin. ACS APPLIED MATERIALS & INTERFACES 2020; 12:6955-6965. [PMID: 31977179 DOI: 10.1021/acsami.9b22043] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The emergence of antibiotic-resistant bacterial strains renders the conventional antibiotic therapy less efficient. The integration of two distinct bactericides into one compact platform provides a promising strategy to realize a combinational antimicrobial therapy. In this work, an efficient chemo-Ag nanohybrid antibacterial platform was facilely developed based on the integration of vancomycin-carrying polydopamine with silver nanoparticles (PDA@Van-Ag). The as-synthesized antibacterial nanohybrid inherited the intrinsic properties of both bactericides to achieve a synergistic antibacterial performance against both Staphylococcus aureus and Escherichia coli strains by attacking bacteria from two distinct fronts. Through this combinational therapy, the efficiency of antibiotic against S. aureus was significantly improved by reducing drug dosage with less opportunity for imparting drug resistance. In addition, this antibacterial nanohybrid, with innate photothermal properties, could achieve auxiliary hyperthermia-assisted bacterial inactivation in the meantime. Furthermore, the outstanding in vivo bacteria-killing activity and wound-healing acceleration were demonstrated in a S. aureus-infected mouse skin defect model. Taken together, this bactericidal nanohybrid could achieve sustained antibiotic release and wipe out bacteria more effectively in a synergistic way, thus reducing the emergence of antibiotic resistance. This work holds great potential to advance the development of novel antibacterial agents and combinational strategies as a promising supplement of antibiotics in the near future.
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Affiliation(s)
- Kang Ma
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , P. R. China
| | - Pei Dong
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , P. R. China
| | - Meijuan Liang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , P. R. China
| | - Shanshan Yu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , P. R. China
| | - Yingying Chen
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , P. R. China
| | - Fuan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , P. R. China
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97
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One-pot synthesized AuNPs/MoS2/rGO nanocomposite as sensitive electrochemical aptasensing platform for nucleolin detection. J Electroanal Chem (Lausanne) 2020. [DOI: 10.1016/j.jelechem.2020.113868] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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98
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Huang Z, Wang C, Liu R, Su Y, Lv Y. Self-Validated Homogeneous Immunoassay by Single Nanoparticle in-Depth Scrutinization. Anal Chem 2020; 92:2876-2881. [PMID: 31910615 DOI: 10.1021/acs.analchem.9b05596] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The most convenient method for the clinical routine analysis of disease biomarkers is homogeneous immunoassay, which minimizes the requirements for automation and time-/lab-consumption. Despite great success, because sample constituents are not removed by a separation or washing step, a major challenge in conducting homogeneous immunoassays for the practical application is the matrix effect-related inaccuracy. Herein, to guarantee an accurate quantification, a self-validated homogeneous immunoassay was proposed, by simultaneously scrutinizing both frequency and intensity of single gold nanoparticles. The two analytical modes of single particle inductively coupled plasma mass spectrometry (ICPMS) correlated well with each other, resulting in a self-validation mechanism for the accurate immunoassay. Both two modes of the proposed method provided linear ranges of 2 orders of magnitude and LODs of pM level. Thanks to the self-validated strategy and the high tolerance of the matrix effect of ICPMS, the proposed homogeneous immunoassay was successfully demonstrated in a series of human serum samples, with results in good accordance with clinical routine methods.
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Affiliation(s)
- Zili Huang
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry , Sichuan University , Chengdu , Sichuan 610064 , China
| | - Chaoqun Wang
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry , Sichuan University , Chengdu , Sichuan 610064 , China
| | - Rui Liu
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry , Sichuan University , Chengdu , Sichuan 610064 , China
| | - Yingying Su
- Analytical & Testing Center , Sichuan University , Chengdu 610064 , China
| | - Yi Lv
- Analytical & Testing Center , Sichuan University , Chengdu 610064 , China
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99
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Gao L, Yang Q, Wu P, Li F. Recent advances in nanomaterial-enhanced enzyme-linked immunosorbent assays. Analyst 2020; 145:4069-4078. [DOI: 10.1039/d0an00597e] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This review highlights functional roles of nanomaterials for advancing conventional ELISA assays by serving as substrate-alternatives, enzyme-alternatives, or non-enzyme amplifiers.
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Affiliation(s)
- Lu Gao
- Key laboratory of Green Chemistry & Technology of Ministry of Education
- College of chemistry
- Analytical & Testing Center
- Sichuan University
- Chengdu
| | - Qianfan Yang
- Key laboratory of Green Chemistry & Technology of Ministry of Education
- College of chemistry
- Analytical & Testing Center
- Sichuan University
- Chengdu
| | - Peng Wu
- Key laboratory of Green Chemistry & Technology of Ministry of Education
- College of chemistry
- Analytical & Testing Center
- Sichuan University
- Chengdu
| | - Feng Li
- Key laboratory of Green Chemistry & Technology of Ministry of Education
- College of chemistry
- Analytical & Testing Center
- Sichuan University
- Chengdu
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100
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Wu J, Ren N, Lu Y, Jia M, Wang R, Zhang J. A poly (diallyldimethylammonium chloride)-mediated R-phycoerythrin/DNA hybrid system as a fluorescent biosensor for DNA detection. Microchem J 2020. [DOI: 10.1016/j.microc.2019.104314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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