1
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Yuan H, Hu J, Ge QQ, Liu WJ, Ma F, Zhang CY. Construction of a Spatial-Confined Self-Stacking Catalytic Circuit for Rapid and Sensitive Imaging of Piwi-Interacting RNA in Living Cells. NANO LETTERS 2024; 24:8732-8740. [PMID: 38958407 DOI: 10.1021/acs.nanolett.4c02230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
Piwi-interacting RNAs (piRNAs) are small noncoding RNAs that repress transposable elements to maintain genome integrity. The canonical catalytic hairpin assembly (CHA) circuit relies on random collisions of free-diffused reactant probes, which substantially slow down reaction efficiency and kinetics. Herein, we demonstrate the construction of a spatial-confined self-stacking catalytic circuit for rapid and sensitive imaging of piRNA in living cells based on intramolecular and intermolecular hybridization-accelerated CHA. We rationally design a 3WJ probe that not only accelerates the reaction kinetics by increasing the local concentration of reactant probes but also eliminates background signal leakage caused by cross-entanglement of preassembled probes. This strategy achieves high sensitivity and good specificity with shortened assay time. It can quantify intracellular piRNA expression at a single-cell level, discriminate piRNA expression in tissues of breast cancer patients and healthy persons, and in situ image piRNA in living cells, offering a new approach for early diagnosis and postoperative monitoring.
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Affiliation(s)
- Huimin Yuan
- School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing 211189, China
| | - Jinping Hu
- School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing 211189, China
| | - Qi-Qin Ge
- School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing 211189, China
| | - Wen-Jing Liu
- School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing 211189, China
| | - Fei Ma
- School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing 211189, China
| | - Chun-Yang Zhang
- School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing 211189, China
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2
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Zhang X, Li Y, Wang Q, Jiang C, Shan Y, Liu Y, Ma C, Guo Q, Shi C. Three-way junction structure-mediated reverse transcription-free exponential amplification reaction for pathogen RNA detection. Anal Bioanal Chem 2024; 416:3161-3171. [PMID: 38558309 DOI: 10.1007/s00216-024-05264-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/27/2024] [Accepted: 03/22/2024] [Indexed: 04/04/2024]
Abstract
Since RNA is an important biomarker of many infectious pathogens, RNA detection of pathogenic organisms is crucial for disease diagnosis and environmental and food safety. By simulating the base mismatch during DNA replication, this study presents a novel three-way junction structure-mediated reverse transcription-free exponential amplification reaction (3WJ-RTF-EXPAR) for the rapid and sensitive detection of pathogen RNA. The target RNA served as a switch to initiate the reaction by forming a three-way junction (3WJ) structure with the ex-trigger strand and the ex-primer strand. The generated trigger strand could be significantly amplified through EXPAR to open the stem-loop structure of the molecular beacon to emit fluorescence signal. The proofreading activity of Vent DNA polymerase, in combination with the unique structure of 2+1 bases at the 3'-end of the ex-primer strand, could enhance the role of target RNA as a reaction switch to reduce non-specific amplification and ensure excellent specificity to differentiate target pathogen from those causing similar symptoms. Furthermore, detection of target RNA showed a detection limit of 1.0×104 copies/mL, while the time consumption was only 20 min, outperforming qRT-LAMP and qRT-PCR, the most commonly used RNA detection methods in clinical practice. All those indicates the great application prospects of this method in clinical diagnostic.
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Affiliation(s)
- Xinguang Zhang
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Qingdao University, Qingdao, 266071, People's Republic of China
| | - Yang Li
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Qingdao University, Qingdao, 266071, People's Republic of China
| | - Qing Wang
- Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, People's Republic of China
| | - Chao Jiang
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Qingdao University, Qingdao, 266071, People's Republic of China
| | - Yuting Shan
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Qingdao University, Qingdao, 266071, People's Republic of China
| | - Yao Liu
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Qingdao University, Qingdao, 266071, People's Republic of China
| | - Cuiping Ma
- Shandong Provincial Key Laboratory of Biochemical Engineering, Key Laboratory of Nucleic Acid Rapid Detection, Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, College of Biological Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao University of Science and Technology, QingdaoQingdao, 266042, China
| | - Qunqun Guo
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Qingdao University, Qingdao, 266071, People's Republic of China.
| | - Chao Shi
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Qingdao University, Qingdao, 266071, People's Republic of China.
- Department of Pathogenic Biology, School of Basic Medicine, Qingdao University, Qingdao, 266071, People's Republic of China.
- Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, People's Republic of China.
- Qingdao JianMa Gene Technology Co., Ltd, Qingdao, 266114, People's Republic of China.
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3
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Chen MM, Kopittke PM, Zhao FJ, Wang P. Applications and opportunities of click chemistry in plant science. TRENDS IN PLANT SCIENCE 2024; 29:167-178. [PMID: 37612212 DOI: 10.1016/j.tplants.2023.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 06/29/2023] [Accepted: 07/19/2023] [Indexed: 08/25/2023]
Abstract
The Nobel Prize in Chemistry for 2022 was awarded to the pioneers of Lego-like 'click chemistry': combinatorial chemistry with remarkable modularity and diversity. It has been applied to a wide variety of biological systems, from microorganisms to plants and animals, including humans. Although click chemistry is a powerful chemical biology tool, comparatively few studies have examined its potential in plant science. Here, we review click chemistry reactions and their applications in plant systems, highlighting the activity-based probes and metabolic labeling strategies combined with bioorthogonal click chemistry to visualize plant biological processes. These applications offer new opportunities to explore and understand the underlying molecular mechanisms regulating plant composition, growth, metabolism, defense, and immune responses.
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Affiliation(s)
- Ming-Ming Chen
- Centre of Agriculture and Health, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peter M Kopittke
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peng Wang
- Centre of Agriculture and Health, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China; State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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4
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Qin X, Wang X, Xu K, Zhang Y, Tian H, Li Y, Qi B, Yang X. Quantitative analysis of miRNAs using SplintR ligase-mediated ligation of complementary-pairing probes enhanced by RNase H (SPLICER)-qPCR. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 31:241-255. [PMID: 36700047 PMCID: PMC9842969 DOI: 10.1016/j.omtn.2022.12.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022]
Abstract
Here, a method using SplintR ligase-mediated ligation of complementary-pairing probes enhanced by RNase H (SPLICER) for miRNAs quantification was established. The strategy has two steps: (1) ligation of two DNA probes specifically hybridize to target miRNA and (2) qPCR amplifying the ligated probe. The miRNA-binding regions of the probes are stem-looped, a motif significantly reduces nonspecific ligation at high ligation temperature (65°C). The ends of the probes are designed complementary to form a paired probe, facilitating the recognition of target miRNAs with low concentrations. RNase H proved to be able to stabilize the heteroduplex formed by the probe and target miRNA, contributing to enhanced sensitivity (limit of detection = 60 copies). High specificity (discriminating homology miRNAs differing only one nucleotide), wide dynamic range (seven orders of magnitude) and ability to accurately detect plant miRNAs (immune to hindrance of 2'-O-methyl moiety) enable SPLICER comparable with the commercially available TaqMan and miRCURY assays. SYBR green I, rather than expensive hydrolysis or locked nucleic acid probes indispensable to TaqMan and miRCURY assays, is adequate for SPLICER. The method was efficient (<1 h), economical ($7 per sample), and robust (able to detect xeno-miRNAs in mammalian bodies), making it a powerful tool for molecular diagnosis and corresponding therapy.
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Affiliation(s)
- Xinshu Qin
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang’an Avenue, Xi’an 710062, Shaanxi, China
| | - Xingyu Wang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang’an Avenue, Xi’an 710062, Shaanxi, China,Corresponding author: Xingyu Wang, College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang’an Avenue, Xi’an 710054, Shaanxi, China.
| | - Ke Xu
- Department of Joint Surgery, Hong Hui Hospital, Xi’an Jiaotong University, Xi’an 710054, Shaanxi, China
| | - Yi Zhang
- Department of Food Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - Hongye Tian
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang’an Avenue, Xi’an 710062, Shaanxi, China
| | - Yinglei Li
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang’an Avenue, Xi’an 710062, Shaanxi, China
| | - Bangran Qi
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang’an Avenue, Xi’an 710062, Shaanxi, China
| | - Xingbin Yang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang’an Avenue, Xi’an 710062, Shaanxi, China,Corresponding author: Xingbin Yang, College of Food Engineering and Nutritional Science, Shaanxi Normal University, No. 620 West Chang’an Avenue, Xi’an 710054, Shaanxi, China.
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5
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Liu X, Xiang J, Cheng H, Wang Y, Li F. Engineering Multipedal
DNA
Walker on Paper for Sensitive Electrochemical Detection of Plant
MicroRNA. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202200368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Xiaojuan Liu
- College of Chemistry and Pharmaceutical Sciences Qingdao Agricultural University Qingdao 266109 People's Republic of China
| | - Junzhu Xiang
- College of plant health & medicine Qingdao Agricultural University Qingdao 266109 People's Republic of China
| | - Hao Cheng
- College of plant health & medicine Qingdao Agricultural University Qingdao 266109 People's Republic of China
| | - Yuying Wang
- College of plant health & medicine 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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6
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Yang H, Chen J, Yang S, Zhang T, Xia X, Zhang K, Deng S, He G, Gao H, He Q, Deng R. CRISPR/Cas14a-Based Isothermal Amplification for Profiling Plant MicroRNAs. Anal Chem 2021; 93:12602-12608. [PMID: 34506121 DOI: 10.1021/acs.analchem.1c02137] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
MicroRNAs (miRNAs) play key roles in biological processes in plants, such as stress resistance, yet can hardly be quantified by an enzyme-involved terminal polymerization process due to their 2'-O-methyl modifications at the 3'-terminal. Herein, we proposed a CRISPR/Cas14a-based rolling circle amplification (termed Cas14R) assay, allowing reverse transcription-free and demethylation-free detection of plant miRNAs with single-nucleotide resolution. The employment of target-templated rolling circle amplification circumvents the extension of the unaccessible 2'-O-methyl group at the 3'-terminal. Particularly, the activated Cas14a confers the trans-cleavage activity for identifying target single-stranded DNA sequences without the necessity of the protospacer adjacent motif, generalizing the detection of miRNA sequences and the integration of different isothermal amplification techniques. Ultimately, the Cas14R assay has been applied to profile miR156a to evaluate the ripeness process of banana, indicating its feasibility in analyzing the roles of miRNAs in biological processes of plants.
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Affiliation(s)
- Hao Yang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Junbo Chen
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, China
| | - Sen Yang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Ting Zhang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Xuhan Xia
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Kaixiang Zhang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University, Zhengzhou 450001, China
| | - Sha Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Guiping He
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Hong Gao
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Qiang He
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
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7
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Chai H, Wang M, Tang L, Miao P. Ultrasensitive electrochemical detection of miRNA coupling tetrahedral DNA modified gold nanoparticles tags and catalyzed hairpin assembly. Anal Chim Acta 2021; 1165:338543. [PMID: 33975698 DOI: 10.1016/j.aca.2021.338543] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/02/2021] [Accepted: 04/17/2021] [Indexed: 12/22/2022]
Abstract
MicroRNAs (miRNAs) play key regulatory roles in a number of biological processes, which act as critical biomarkers for clinical diagnosis. There are urgent needs to develop advanced tools for accurate and convenient analysis of miRNA in biological circumstances. In this study, an ultrasensitive electrochemical biosensor for miRNA assay is fabricated. Tetrahedral DNA modified gold nanoparticles tags are applied with optimized orientation, which are able to recruit a large number of electrochemical species for remarkable signal responses. Benefiting from the excellent amplification efficiency of the association of strand displacement amplification and catalyzed hairpin assembly, the established method shows ultrahigh sensitivity with the limit of detection as low as 10 aM. A wide linear range from 10-17 to 10-7 M is achieved. In addition, this method is capable to specifically discriminate interfering miRNAs with slightly different sequences. The successful assessment of miRNA levels in human serum samples also demonstrates good practical utility. Therefore, the proposed method has great potential to the applications of miRNA expression profiling and biological studies.
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Affiliation(s)
- Hua Chai
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, People's Republic of China
| | - Mingyuan Wang
- Suzhou Blood Center, Suzhou, 215006, People's Republic of China
| | - Longhai Tang
- Suzhou Blood Center, Suzhou, 215006, People's Republic of China
| | - Peng Miao
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, People's Republic of China; Ji Hua Laboratory, Foshan, 528200, People's Republic of China.
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8
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Chen F, Bai M, Cao X, Xue J, Zhao Y, Wu N, Wang L, Zhang D, Zhao Y. Cellular macromolecules-tethered DNA walking indexing to explore nanoenvironments of chromatin modifications. Nat Commun 2021; 12:1965. [PMID: 33785750 PMCID: PMC8009891 DOI: 10.1038/s41467-021-22284-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 03/02/2021] [Indexed: 02/01/2023] Open
Abstract
Exploring spatial organization and relationship of diverse biomolecules within cellular nanoenvironments is important to elucidate the fundamental processes of life. However, it remains methodologically challenging. Herein, we report a molecular recognition mechanism cellular macromolecules-tethered DNA walking indexing (Cell-TALKING) to probe the nanoenvironments containing diverse chromatin modifications. As an example, we characterize the nanoenvironments of three DNA modifications around one histone posttranslational modification (PTM). These DNA modifications in fixed cells are labeled with respective DNA barcoding probes, and then the PTM site is tethered with a DNA walking probe. Cell-TALKING can continuously produce cleavage records of any barcoding probes nearby the walking probe. New 3'-OH ends are generated on the cleaved barcoding probes to induce DNA amplification for downstream detections. Combining fluorescence imaging, we identify various combinatorial chromatin modifications and investigate their dynamic changes during cell cycles. We also explore the nanoenvironments in different cancer cell lines and clinical specimens. In principle, using high-throughput sequencing instead of fluorescence imaging may allow the detection of complex cellular nanoenvironments containing tens of biomolecules such as transcription factors.
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Affiliation(s)
- Feng Chen
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Min Bai
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Xiaowen Cao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Jing Xue
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Yue Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Na Wu
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Lei Wang
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Medical University, Xi'an, Shaanxi, PR China
| | - Dexin Zhang
- Department of Respiratory Medicine, The Second Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, PR China.
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9
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Wang G, Fan W, Ren W, Liu X, Liu C. High-sensitive sensing of plant microRNA by integrating click chemistry with an unusual on-bead poly(T)-promoted transcription amplification. Anal Chim Acta 2020; 1111:16-22. [PMID: 32312392 DOI: 10.1016/j.aca.2020.03.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 02/12/2020] [Accepted: 03/16/2020] [Indexed: 11/17/2022]
Abstract
MicroRNAs (miRNAs) act as pivotal regulators in plants. Therefore, sensing strategies with high specificity and high sensitivity are desired for plant miRNA analysis in order to unveil the exact biofunctions of miRNAs. Toward this goal, a fluorescent assay is developed based on a two-step signal amplification strategy. In the first step, target miRNA-templated cycling click nucleic acid ligation is employed for target recognition and amplification, the product of which can bind to magnetic microbeads (MBs) and introduce the T7 promoter sequence to the surface. In the second step, the poly(T) containing transcription template partially hybridizes with the T7 promoter sequence on the ligated strand and then regulates the on-bead transcription in a cycling manner with the participation of T7 RNA polymerase. Surprisingly, different from other reported templates, the poly(T) template improves the transcription efficiency to an unexpectedly high level by releasing ultra-long RNA chains in the reaction system. Finally, the RNA intercalating dye, RiboGreen, is utilized to specifically light up the as-produced RNA chains for low-background signal readout. Benefiting from the elaborate design, the detection limit of plant miRNA is down to ∼0.1 amol. This strategy provides a highly specific and highly sensitive platform for plant miRNA detection, which promises potential in the practical applications of miRNA-related biofunctions.
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Affiliation(s)
- Gaoting Wang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, Shaanxi Province, PR China
| | - Wenjiao Fan
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, Shaanxi Province, PR China
| | - Wei Ren
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, Shaanxi Province, PR China
| | - Xiaoling Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, Shaanxi Province, PR China.
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, Shaanxi Province, PR China.
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10
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Zhu D, Lu B, Zhu Y, Ma Z, Wei Y, Su S, Wang L, Song S, Zhu Y, Wang L, Chao J. Cancer-Specific MicroRNA Analysis with a Nonenzymatic Nucleic Acid Circuit. ACS APPLIED MATERIALS & INTERFACES 2019; 11:11220-11226. [PMID: 30816697 DOI: 10.1021/acsami.9b01653] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Sensitive detection of gastric cancer-related biomarkers in human serum provides a promising means for early cancer diagnosis. Herein, we report the design of a nucleic acid circuit for gastric cancer-related microRNA-27a (miRNA-27a) detection based on dual toehold-mediated circular strand displacement amplification (CSDA). In the presence of miRNA-27a, the hybridization between miRNA-27a and probe DNA on magnetic beads through toehold 1 leads to the release of fluorescent DNA and the exposure of a new toehold 2 on linker DNA. After hybridization with catalytic DNA, CSDA is initiated and target miRNA-27a is released to participate in the next cyclic reaction; therefore, a greatly enhanced fluorescence signal is produced. The efficient magnetic separation makes the sensitive detection of miRNA-27a be accomplished within 45 min. With the efficient CSDA, the detection limit of the system (0.8 pM) is ∼100 folds lower than that of the system based on strand displacement without CSDA (79.3 pM). Furthermore, the system also showed good stability and sensitivity to discriminate single-base mismatch, which allows the detection of miRNA-27a in human serum samples. This study provides a novel platform and approach for the rapid quantitative determination of miRNA, which has great potential in clinical diagnosis and disease treatment.
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Affiliation(s)
- Dan Zhu
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM) , Nanjing University of Posts and Telecommunications , Nanjing 210023 , China
| | - Bang Lu
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM) , Nanjing University of Posts and Telecommunications , Nanjing 210023 , China
| | - Yu Zhu
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM) , Nanjing University of Posts and Telecommunications , Nanjing 210023 , China
| | - Zihao Ma
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM) , Nanjing University of Posts and Telecommunications , Nanjing 210023 , China
| | - Yaqi Wei
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM) , Nanjing University of Posts and Telecommunications , Nanjing 210023 , China
| | - Shao Su
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM) , Nanjing University of Posts and Telecommunications , Nanjing 210023 , China
| | - Lihua Wang
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
| | - Shiping Song
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
| | - Ying Zhu
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800 , China
| | - Lianhui Wang
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM) , Nanjing University of Posts and Telecommunications , Nanjing 210023 , China
| | - Jie Chao
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM) , Nanjing University of Posts and Telecommunications , Nanjing 210023 , China
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11
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Qi Y, Lu X, Feng Q, Fan W, Liu C, Li Z. An Enzyme-Free MicroRNA Assay Based On Fluorescence Counting of Click Chemical Ligation-Illuminated Magnetic Nanoparticles with Total Internal Reflection Fluorescence Microscopy. ACS Sens 2018; 3:2667-2674. [PMID: 30456947 DOI: 10.1021/acssensors.8b01169] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
MicroRNAs (miRNAs) have been considered as promising cancer biomarkers. However, the simple but sensitive detection of low levels of miRNAs in biological samples still remains challenging. Herein, we wish to report an entirely enzyme-free, simple, and highly sensitive miRNA assay based on the counting of cycling click chemical ligation (3CL)-illuminated fluorescent magnetic nanoparticles (MNPs) with a total internal reflection fluorescence microscopy (TIRFM). In this strategy, each miRNA molecule can trigger many cycles of click chemical ligation reactions to produce plentiful ligated oligonucleotides (ODNs) with both 5'-biotin and 3'-fluorophore, resulting in efficient signal amplification. It is worth noting that only the ligated ODNs can bring fluorophores onto streptavidin-functionalized MNPs (STV-MNPs). Notably, merely 10 fluorescent molecules on each 50 nm MNP can make it bright enough to be clearly visualized by the TIRFM, which can significantly improve the detection sensitivity for miRNA. Through fluorescence counting of individual MNPs and integrating their fluorescence intensities, the amount of target miRNA can be quantitatively determined. This miRNA assay can be accomplished in a mix-and-read manner just by simply mixing the enzyme-free 3CL reaction system with the MNPs before TIRFM imaging, which avoids tedious immobilization, washing, and purification steps. Despite the extremely simple operation, this strategy exhibits high sensitivity with a quite low detection limit of 50 fM target miRNA as well as high specificity to well discriminate miRNA sequences with a single-base variation. Furthermore, the applicability of this method in real biological samples is also verified through the accurate detection of the miRNA target in cancer cells.
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Affiliation(s)
- Yan Qi
- Key laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an, Shaanxi Province 710119, P. R. China
| | - Xiaohui Lu
- Key laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an, Shaanxi Province 710119, P. R. China
| | - Qinya Feng
- Key laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an, Shaanxi Province 710119, P. R. China
| | - Wenjiao Fan
- Key laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an, Shaanxi Province 710119, P. R. China
| | - Chenghui Liu
- Key laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an, Shaanxi Province 710119, P. R. China
| | - Zhengping Li
- Key laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an, Shaanxi Province 710119, P. R. China
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12
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Mao D, Chen H, Tang Y, Li J, Cao Y, Zhao J. Application of Isothermal Nucleic Acid Signal Amplification in the Detection of Hepatocellular Carcinoma-Associated MicroRNA. Chempluschem 2018; 84:8-17. [DOI: 10.1002/cplu.201800382] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Dongsheng Mao
- Center for Molecular Recognition and Biosensing; School of Life Sciences; Shanghai University; Shanghai 200444 P. R. China
| | - Hong Chen
- Center for Molecular Recognition and Biosensing; School of Life Sciences; Shanghai University; Shanghai 200444 P. R. China
| | - Yingying Tang
- Center for Molecular Recognition and Biosensing; School of Life Sciences; Shanghai University; Shanghai 200444 P. R. China
| | - Jingwen Li
- Center for Molecular Recognition and Biosensing; School of Life Sciences; Shanghai University; Shanghai 200444 P. R. China
- CAS Key Lab of Bio-Medical Diagnostics Institution; Suzhou Institute of Biomedical Engineering and Technology; Chinese Academy of Sciences; Suzhou 215163 P. R. China
| | - Ya Cao
- Center for Molecular Recognition and Biosensing; School of Life Sciences; Shanghai University; Shanghai 200444 P. R. China
| | - Jing Zhao
- Center for Molecular Recognition and Biosensing; School of Life Sciences; Shanghai University; Shanghai 200444 P. R. China
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13
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Fan W, Qi Y, Qiu L, He P, Liu C, Li Z. Click Chemical Ligation-Initiated On-Bead DNA Polymerization for the Sensitive Flow Cytometric Detection of 3'-Terminal 2'-O-Methylated Plant MicroRNA. Anal Chem 2018; 90:5390-5397. [PMID: 29600844 DOI: 10.1021/acs.analchem.8b00589] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A versatile flow cytometric strategy is developed for the sensitive detection of plant microRNA (miRNA) by coupling the target-templated click nucleic acid ligation (CNAL) with on-bead terminal enzymatic DNA polymerization (TEP). Unlike ligase-catalyzed ligation reaction, the plant miRNA-templated enzyme-free CNAL between two single-stranded DNA (ssDNA) probes, respectively modified with Aza-dibenzocyclooctyne (Aza-DBCO) and N3, can not only simplify the operation, but also achieve a much higher ligation efficiency. More importantly, the undesirable nonspecific ligation between the Aza-DBCO- and N3-modified ssDNA, can be effectively eliminated by adding Tween-20, which allows the use of cycling CNAL (CCNAL) in a background-free manner. So each plant miRNA can template many rounds of CNAL reaction to produce numerous ligation products, forming efficient signal amplification. The ligated ssDNA can be anchored on the magnetic beads (MBs) with the 3'-OH termini exposed outside. Then terminal deoxynucleotidyl transferase (TdT), a sequence-independent and template-free polymerase, would specifically catalyze the DNA polymerization along these 3'-OH termini on the MBs, forming poly(T) tails up to thousands of nucleotides long. Each poly(T) tail allows specific binding of numerous 6-carboxyfluorescein (FAM)-labeled poly(A)25 oligonucleotides to accumulate a lot of fluorophores on the MBs, leading to the second step of signal amplification. By integrating the advantages of CCNAL-TEP for highly efficient signal amplification and robust MBs signal readout with powerful flow cytometer, high sensitivity is achieved and the detection limit of plant miRNA has been pushed down to a low level of 5 fM with high specificity to well discriminate even single-base difference between miRNA targets.
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Affiliation(s)
- Wenjiao Fan
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , Shaanxi Province , People's Republic of China
| | - Yan Qi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , Shaanxi Province , People's Republic of China
| | - Liying Qiu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , Shaanxi Province , People's Republic of China
| | - Pan He
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , Shaanxi Province , People's Republic of China
| | - Chenghui Liu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , Shaanxi Province , People's Republic of China
| | - Zhengping Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710119 , Shaanxi Province , People's Republic of China
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14
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Zhao Y, Chen F, Qin J, Wei J, Wu W, Zhao Y. Engineered Janus probes modulate nucleic acid amplification to expand the dynamic range for direct detection of viral genomes in one microliter crude serum samples. Chem Sci 2018; 9:392-397. [PMID: 29629109 PMCID: PMC5868314 DOI: 10.1039/c7sc03994h] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 10/27/2017] [Indexed: 11/21/2022] Open
Abstract
The viral genome load in diverse clinical samples varies over several orders of magnitude (e.g. 1-104 copies per μL), thus a dynamic range-extended and sensitive analysis method is highly desired. However, existing well-developed nucleic acid amplification systems always suffer from either a limited dynamic range or modest sensitivity for analysis of these samples. Herein, we propose a general engineered Janus probe to modulate the thermodynamics and kinetic properties of the amplification reaction. Through rational regulation, the Janus system improves the performance by both reducing the background and enhancing the signal, expanding the operative dynamic range by 2 orders of magnitude. This proposed approach achieves a detection limit for hepatitis B virus (HBV) DNA of down to 3 copies and can be successfully applied for direct quantification of the HBV genome in one microliter crude serum samples without any pretreatment. The results are consistent with clinical diagnosis and hold considerable potential to discriminate healthy volunteers and patients at different disease stages. Whereas, following the same operation, the representative well-developed system provided serious false-negative results using such trace amounts of samples from clinically confirmed positive patients.
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Affiliation(s)
- Yue Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
| | - Feng Chen
- Key Laboratory of Biomedical Information Engineering of Education Ministry , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
| | - Jing Qin
- Key Laboratory of Biomedical Information Engineering of Education Ministry , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
| | - Jing Wei
- Key Laboratory of Biomedical Information Engineering of Education Ministry , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
| | - Wenhua Wu
- Department of Infectious Disease , The Second Affiliated Hospital of Medical College , Xi'an Jiaotong University , Xiwu Road , Xi'an , Shaanxi 710049 , P. R. China
| | - Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China .
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15
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Chen F, Bai M, Zhao Y, Cao K, Cao X, Zhao Y. MnO 2-Nanosheet-Powered Protective Janus DNA Nanomachines Supporting Robust RNA Imaging. Anal Chem 2018; 90:2271-2276. [PMID: 29295617 DOI: 10.1021/acs.analchem.7b04634] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Both biomarker and probe degradations cause serious false assay results. However, protecting a target or a target and a probe simultaneously has rarely been explored. Herein, MnO2-nanosheet-powered target- and probe-protective Janus DNA nanomachines are reported. It is formed in living cells by an RNA-responsive assembly of two chemically modified DNA partzymes and one substrate probe. MnO2 nanosheets are used to facilitate the cellular uptake of DNA reagents and generate Mn2+, which are indispensable DNAzyme cofactors for efficient catalytic cleavage. We find that DNA partzymes with modified sugar moieties (e.g., LNA or ones with 2'-O-methylation) protect the RNA of RNA-DNA hybrids from RNase H degradation. LNA blocks RNase H recruitment on the hybrid best because of its 2'-O, 4'-C methylene bridge structure. In contrast, modifications at DNA phosphate moieties fail to protect the RNA. RNA protection can exclude target-degradation-induced false negative results. In addition, the phosphorothioate-modified substrate probe is known to resist nuclease degradation, which minimizes false positive interference. Compared to canonical DNA systems without chemical modifications, the protective Janus nanomachine avoids false results and supports robust RNA imaging.
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Affiliation(s)
- Feng Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University , Xi'an 710049, P. R. China
| | - Min Bai
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University , Xi'an 710049, P. R. China
| | - Yue Zhao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University , Xi'an 710049, P. R. China
| | - Ke Cao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University , Xi'an 710049, P. R. China
| | - Xiaowen Cao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University , Xi'an 710049, P. R. China
| | - Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University , Xi'an 710049, P. R. China
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16
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A Förster Resonance Energy Transfer Ratiometric Probe Based on Quantum Dot-Cresyl Violet for Imaging Hydrogen Sulfide in Living Cells. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2018. [DOI: 10.1016/s1872-2040(17)61062-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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17
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Miao P, Jiang Y, Zhang T, Huang Y, Tang Y. Electrochemical sensing of attomolar miRNA combining cascade strand displacement polymerization and reductant-mediated amplification. Chem Commun (Camb) 2018; 54:7366-7369. [DOI: 10.1039/c8cc03698e] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
An electrochemical biosensor for miRNA assay with attomolar sensitivity was developed based on cascade strand displacement polymerization and reductant-mediated amplification.
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Affiliation(s)
- Peng Miao
- Suzhou Institute of Biomedical Engineering and Technology
- Chinese Academy of Sciences
- Suzhou 215163
- P. R. China
- University of Science and Technology of China
| | - Yiting Jiang
- Suzhou Institute of Biomedical Engineering and Technology
- Chinese Academy of Sciences
- Suzhou 215163
- P. R. China
- University of Science and Technology of China
| | - Tian Zhang
- Suzhou Institute of Biomedical Engineering and Technology
- Chinese Academy of Sciences
- Suzhou 215163
- P. R. China
- University of Science and Technology of China
| | - Yue Huang
- College of Light Industry and Food Engineering
- Nanjing Forest University
- Nanjing 210037
- P. R. China
| | - Yuguo Tang
- Suzhou Institute of Biomedical Engineering and Technology
- Chinese Academy of Sciences
- Suzhou 215163
- P. R. China
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18
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Chen F, Bai M, Cao K, Zhao Y, Cao X, Wei J, Wu N, Li J, Wang L, Fan C, Zhao Y. Programming Enzyme-Initiated Autonomous DNAzyme Nanodevices in Living Cells. ACS NANO 2017; 11:11908-11914. [PMID: 29045785 DOI: 10.1021/acsnano.7b06728] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Molecular nanodevices are computational assemblers that switch defined states upon external stimulation. However, interfacing artificial nanodevices with natural molecular machineries in living cells remains a great challenge. Here, we delineate a generic method for programming assembly of enzyme-initiated DNAzyme nanodevices (DzNanos). Two programs including split assembly of two partzymes and toehold exchange displacement assembly of one intact DNAzyme initiated by telomerase are computed. The intact one obtains higher assembly yield and catalytic performance ascribed to proper conformation folding and active misplaced assembly. By employing MnO2 nanosheets as both DNA carriers and source of Mn2+ as DNAzyme cofactor, we find that this DzNano is well assembled via a series of conformational states in living cells and operates autonomously with sustained cleavage activity. Other enzymes can also induce corresponding DzNano assembly with defined programming modules. These DzNanos not only can monitor enzyme catalysis in situ but also will enable the implementation of cellular stages, behaviors, and pathways for basic science, diagnostic, and therapeutic applications as genetic circuits.
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Affiliation(s)
- Feng Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, P.R. China
| | - Min Bai
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, P.R. China
| | - Ke Cao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, P.R. China
| | - Yue Zhao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, P.R. China
| | - Xiaowen Cao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, P.R. China
| | - Jing Wei
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, P.R. China
| | - Na Wu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, P.R. China
| | - Jiang Li
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, P.R. China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, P.R. China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, P.R. China
| | - Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, P.R. China
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19
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Wang X, Wang H, Liu C, Wang H, Li Z. A three-way junction structure-based isothermal exponential amplification strategy for sensitive detection of 3′-terminal 2′-O-methylated plant microRNA. Chem Commun (Camb) 2017; 53:1124-1127. [DOI: 10.1039/c6cc08726d] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A versatile and general 3WJ-EXPAR strategy is developed for the sensitive detection of 3′-terminal 2′-O-methylated plant microRNAs.
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Affiliation(s)
- Xiangdong Wang
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
| | - Hui Wang
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
| | - Honghong Wang
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
| | - Zhengping Li
- Key Laboratory of Applied Surface and Colloid Chemistry
- Ministry of Education
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
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20
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Trifunctional molecular beacon-mediated quadratic amplification for highly sensitive and rapid detection of mercury(II) ion with tunable dynamic range. Biosens Bioelectron 2016; 86:892-898. [DOI: 10.1016/j.bios.2016.07.099] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 07/18/2016] [Accepted: 07/27/2016] [Indexed: 11/20/2022]
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21
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Chen F, Zhang D, Zhang Q, Zuo X, Fan C, Zhao Y. Zero-Background Helicase-Dependent Amplification and Its Application to Reliable Assay of Telomerase Activity in Cancer Cell by Eliminating Primer-Dimer Artifacts. Chembiochem 2016; 17:1171-6. [PMID: 26690725 DOI: 10.1002/cbic.201500605] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Indexed: 11/09/2022]
Abstract
Primer-dimer artifacts resulting from unintended template-independent primer-primer interactions often hinder the specific amplification of nucleic acids. We demonstrate, for the first time, zero-background helicase-dependent amplification (HDA), with low concentrations of both ATP and dNTPs. This strategy achieved the reliable evaluation of telomerase activity in cancer cells by eliminating primer-dimer artifacts, which have plagued many previous methods with reduced specificity. We found that the performance of the telomerase assay by zero-background HDA was negatively affected by highly concentrated cellular proteins. This inhibitory effect is attributed to the binding of DNA templates to proteins, thus making them unavailable for polymerases. However, gold nanoparticles were demonstrated to highly attenuate such inhibition by abundant proteins, and to enhance the assay sensitivity and reliability when the reaction was performed with concentrated cell extracts.
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Affiliation(s)
- Feng Chen
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University, Xianning West Road, Xi'an, Shaanxi, 710049, P. R. China
| | - Dexin Zhang
- Department of Respiratory Medicine, The Second Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xiwu Road, Xi'an, Shaanxi, 710049, P. R. China
| | - Qing Zhang
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University, Xianning West Road, Xi'an, Shaanxi, 710049, P. R. China
| | - Xiaolei Zuo
- Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Yuquan Road, Shanghai, 201800, P. R. China
| | - Chunhai Fan
- Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Yuquan Road, Shanghai, 201800, P. R. China
| | - Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University, Xianning West Road, Xi'an, Shaanxi, 710049, P. R. China.
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22
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Chen F, Lin M, Zhao Y, Zhao Y. Catalase-functionalized SiO2 nanoparticles mediate growth of gold nanoparticles for plasmonic biosensing of attomolar microRNA with the naked eye. RSC Adv 2016. [DOI: 10.1039/c5ra27574a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
A plasmonic biosensor for specific detection of attomolar microRNA with the naked eye was developed based on catalase/streptavidin-functionalized SiO2 nanoparticles and hairpin capture probe-coated magnetic beads.
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Affiliation(s)
- Feng Chen
- Key Laboratory of Biomedical Information Engineering of Education Ministry
- School of Life Science and Technology
- Xi'an Jiaotong University
- Xi'an
- P. R. China
| | - Manli Lin
- Key Laboratory of Biomedical Information Engineering of Education Ministry
- School of Life Science and Technology
- Xi'an Jiaotong University
- Xi'an
- P. R. China
| | - Yue Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry
- School of Life Science and Technology
- Xi'an Jiaotong University
- Xi'an
- P. R. China
| | - Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry
- School of Life Science and Technology
- Xi'an Jiaotong University
- Xi'an
- P. R. China
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23
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Wang X, Lu Z, Tan L, Jie G. Highly intense fluorescence of novel carbon nanocrystals combined with a DNAzyme-assisted autocatalytic multiple amplification strategy for sensitive detection of thrombin. Analyst 2016; 141:2865-9. [DOI: 10.1039/c6an00279j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Novel water-soluble CNCs with excellent fluorescence were prepared, and successfully applied to sensitive fluorescence detection of thrombin by using an enzyme-assisted autocatalytic DNA recycling amplification strategy.
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Affiliation(s)
- Xiaochun Wang
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Zhengkun Lu
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Lu Tan
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Guifen Jie
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
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24
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Zhao Y, Liu H, Chen F, Bai M, Zhao Y. Fidelity quantification of mercury( ii) ion via circumventing biothiols-induced sequestration in enzymatic amplification system. RSC Adv 2016. [DOI: 10.1039/c6ra16960k] [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] Open
Abstract
A fidelity quantification of mercury(ii) ion based on nucleic acids amplification is developedviacircumventing biothiols-induced sequestration.
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Affiliation(s)
- Yue Zhao
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education
- School of Life Science and Technology
- Xi'an Jiaotong University
- Xi'an
- P. R. China
| | - Huaqing Liu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education
- School of Life Science and Technology
- Xi'an Jiaotong University
- Xi'an
- P. R. China
| | - Feng Chen
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education
- School of Life Science and Technology
- Xi'an Jiaotong University
- Xi'an
- P. R. China
| | - Min Bai
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education
- School of Life Science and Technology
- Xi'an Jiaotong University
- Xi'an
- P. R. China
| | - Yongxi Zhao
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education
- School of Life Science and Technology
- Xi'an Jiaotong University
- Xi'an
- P. R. China
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25
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Abstract
Isothermal amplification of nucleic acids is a simple process that rapidly and efficiently accumulates nucleic acid sequences at constant temperature. Since the early 1990s, various isothermal amplification techniques have been developed as alternatives to polymerase chain reaction (PCR). These isothermal amplification methods have been used for biosensing targets such as DNA, RNA, cells, proteins, small molecules, and ions. The applications of these techniques for in situ or intracellular bioimaging and sequencing have been amply demonstrated. Amplicons produced by isothermal amplification methods have also been utilized to construct versatile nucleic acid nanomaterials for promising applications in biomedicine, bioimaging, and biosensing. The integration of isothermal amplification into microsystems or portable devices improves nucleic acid-based on-site assays and confers high sensitivity. Single-cell and single-molecule analyses have also been implemented based on integrated microfluidic systems. In this review, we provide a comprehensive overview of the isothermal amplification of nucleic acids encompassing work published in the past two decades. First, different isothermal amplification techniques are classified into three types based on reaction kinetics. Then, we summarize the applications of isothermal amplification in bioanalysis, diagnostics, nanotechnology, materials science, and device integration. Finally, several challenges and perspectives in the field are discussed.
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Affiliation(s)
- Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Feng Chen
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Qian Li
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China.,School of Life Science & Technology, ShanghaiTech University , Shanghai 200031, China
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