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Chen LG, Li J, Sun L, Wang HB. Ratiometric fluorometric assay triggered by alkaline phosphatase: Proof-of-concept toward a split-type biosensing strategy for DNA detection. Talanta 2024; 271:125703. [PMID: 38271841 DOI: 10.1016/j.talanta.2024.125703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024]
Abstract
Herein, a sensitive ratiometric and split-type fluorescent sensing platform has been constructed for DNA detection based on one signal precursor and two fluorescent signal indicators. In this assay, o-phenylenediamine (OPD) was selected as the signal precursor. On one hand, Cu2+ can oxidize OPD to produce 2, 3-diaminophenazine (DAP), which with an emission peak at 555 nm. On the other hand, ascorbic acid (AA) could react with Cu2+ to generate dehydroascorbic acid (DHAA), which could further react with OPD to form 3-(1, 2-dihydroxy ethyl)furo[3, 4-b]quinoxalin-1 (3H)-on (DFQ) with a strong emission peak at 420 nm. As a result, the formation of DAP was inhibited, and leading to the decrease of fluorescence intensity at 555 nm. Alkaline phosphatase (ALP) could catalyze the substrate l-ascorbic acid-2-phosphate (AA2P) to produce AA in situ. Inspired by the successful use of ALP as a biocatalytic marker in bioassay, a split-type ratiometric fluorescent assay has been designed for DNA detection by using H1N1 DNA as the target model. It was realized for ratiometric fluorescent determination of H1N1 in a linear ranging from 50 pM to 1.5 nM with a limit of detection of 10 pM. The novel strategy could reduce the mutual interferences between the biomolecular recognition system and the fluorescence signal conversion system, which improving the accuracy of detection and effectively reducing the background signal. Furthermore, the strategy provided a promising platform for biomarkers detection in the fields of ratiometric fluorescent biosensors and bioanalysis.
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Affiliation(s)
- Lin-Ge Chen
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, PR China
| | - Jiajun Li
- CNOOC Tianjin Research and Design Institute of Chemical Industry, Tianjin, 300131, PR China
| | - Lu Sun
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, PR China
| | - Hai-Bo Wang
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, 464000, PR China.
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方 楚, 唐 田, 周 琛, 张 婧, 林 华, 朱 娅, 杨 加, 汪 川. [Development of a Catalytic Hairpin Assembly-Based Fluorescent Assay for the Rapid Detection of SARS-CoV-2 Target RNA]. SICHUAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF SICHUAN UNIVERSITY. MEDICAL SCIENCE EDITION 2024; 55:183-189. [PMID: 38322527 PMCID: PMC10839497 DOI: 10.12182/20240160601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Indexed: 02/08/2024]
Abstract
Objective To develop a catalytic hairpin assembly (CHA)-based fluorescent assay for the detection of the target RNA of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), so as to realize the rapid nucleic acid testing of SARS-CoV-2. Methods A 24-nt segment of the SARS-CoV-2 nucleocapsid protein gene (N gene, NC_045512.2) was chosen as the target RNA and the hairpin motif 1 (H1) and hairpin motif 2 (H2) were designed based on the principle of CHA reaction. The H1 motif was labelled with a fluorophore group as well as a quencher group. When the target RNA was added to the hairpin motifs, CHA reaction was triggered at room temperature (25 ℃), which led to the amplification of fluorescence signal, thereby enabling the rapid detection of the target RNA. After the optimization of the hairpin motifs and the experimental conditions, the sensitivity and the specificity of the testing method were measured to evaluate its performance. Results We successfully constructed a CHA-based fluorescent assay specifically for the target RNA of SARS-CoV-2. With this method, testing could be completed at room temperature within 30 min. This testing method exhibited excellent specificity and could be used to accurately distinguish the perfectly-matched target RNA from the target RNA with single-base mutations. In addition, the testing method demonstrated good sensitivity, with a detection limit of 50 pmol/L. Conclusion The proposed assay enables the simple and rapid detection of the SARS-CoV-2 target RNA with excellent sensitivity and specificity, showing great promise for further optimization and subsequent clinical application for the rapid detection of SARS-CoV-2 nucleic acid.
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Affiliation(s)
- 楚斌 方
- 四川大学华西公共卫生学院/四川大学华西第四医院 (成都 610041)West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - 田 唐
- 四川大学华西公共卫生学院/四川大学华西第四医院 (成都 610041)West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - 琛 周
- 四川大学华西公共卫生学院/四川大学华西第四医院 (成都 610041)West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - 婧 张
- 四川大学华西公共卫生学院/四川大学华西第四医院 (成都 610041)West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - 华 林
- 四川大学华西公共卫生学院/四川大学华西第四医院 (成都 610041)West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - 娅岚 朱
- 四川大学华西公共卫生学院/四川大学华西第四医院 (成都 610041)West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - 加雪 杨
- 四川大学华西公共卫生学院/四川大学华西第四医院 (成都 610041)West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - 川 汪
- 四川大学华西公共卫生学院/四川大学华西第四医院 (成都 610041)West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
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3
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Hernández Bustos A, Martiny E, Bom Pedersen N, Parvathaneni RP, Hansen J, Ji HP, Astakhova K. Short Tandem Repeat DNA Profiling Using Perylene-Oligonucleotide Fluorescence Assay. Anal Chem 2023; 95:7872-7879. [PMID: 37183373 DOI: 10.1021/acs.analchem.3c00063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
We report an amplification-free genotyping method to determine the number of human short tandem repeats (STRs). DNA-based STR profiling is a robust method for genetic identification purposes such as forensics and biobanking and for identifying specific molecular subtypes of cancer. STR detection requires polymerase amplification, which introduces errors that obscure the correct genotype. We developed a new method that requires no polymerase. First, we synthesized perylene-nucleoside reagents and incorporated them into oligonucleotide probes that recognize five common human STRs. Using these probes and a bead-based hybridization approach, accurate STR detection was achieved in only 1.5 h, including DNA preparation steps, with up to a 1000-fold target DNA enrichment. This method was comparable to PCR-based assays. Using standard fluorometry, the limit of detection was 2.00 ± 0.07 pM for a given target. We used this assay to accurately identify STRs from 50 human subjects, achieving >98% consensus with sequencing data for STR genotyping.
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Affiliation(s)
- Adrián Hernández Bustos
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Region Hovedstaden 2800, Denmark
| | - Elisa Martiny
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Region Hovedstaden 2800, Denmark
| | - Nadia Bom Pedersen
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Region Hovedstaden 2800, Denmark
| | - Rohith Pavan Parvathaneni
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Region Hovedstaden 2800, Denmark
| | - Jonas Hansen
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Region Hovedstaden 2800, Denmark
- School of Medicine, Stanford University, 94305 Stanford, California, United States
| | - Hanlee P Ji
- School of Medicine, Stanford University, 94305 Stanford, California, United States
| | - Kira Astakhova
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Region Hovedstaden 2800, Denmark
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Wang X, Mu X, Li J, Liu G, Zhao S, Tian J. A novel nanoparticle surface-constrained CRISPR-Cas12a 3D DNA walker-like nanomachines for sensitive and stable miRNAs detection. Anal Chim Acta 2023; 1251:340950. [PMID: 36925314 DOI: 10.1016/j.aca.2023.340950] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 02/01/2023] [Accepted: 02/05/2023] [Indexed: 02/10/2023]
Abstract
The CRISPR-Cas system has broad prospects as a new type of nucleic acid signal amplification technology based on the trans-cleavage activity of Cas12a to single-stranded DNA, but the trans-cleavage reaction efficiency is relatively low in solution. In order to overcome this negative factor, a new 3D DNA nanomachine whose CRISPR-Cas12a is limited to the surface of nanoparticles is used for sensitive and stable detection of miRNA. By loading Cas12a activator onto spherical nucleic acid (SNA), the CRISPR-Cas12a activator system on the surface of Au nanoparticles (AuNPs) acts as a walker to carry out continuous recognition-walking-cutting reaction on the surface of AuNPs, which enhances the trans-cleavage activity of Cas12a to SNAs. Benefiting from the confinement effect of spherical nucleic acids surface, a 3D DNA nanomachine has been developed for the detection of miRNA-21, which has achieved high sensitivity and accuracy, and the detection limit is able to reach 8.0 pM. This new 3D DNA walker-like nanomachine provided another insight for future bioanalysis and early clinical diagnoses of disease and liquid biopsy.
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Affiliation(s)
- Xin Wang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China
| | - Xiaomei Mu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China
| | - Jinshen Li
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China
| | - Guang Liu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China
| | - Shulin Zhao
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China
| | - Jianniao Tian
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China.
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Li XL, Jiang H, Zhao L, Song TS, Xie JJ. Self-powered DNA nanomachines for fluorescence detection of lead. Mikrochim Acta 2023; 190:99. [PMID: 36809414 DOI: 10.1007/s00604-023-05673-7] [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: 08/18/2022] [Accepted: 01/24/2023] [Indexed: 02/23/2023]
Abstract
A versatile DNA nanomachine detection system has been developed via the combination of DNAzyme with catalytic hairpin assembly (CHA) technology for achieving accurate and sensitive detection of lead ions (Pb2+). In the presence of target Pb2+, capture DNA nanomachine formed by AuNP and DNAzyme recognized and reacted with Pb2+, which yielded an "active" DNAzyme, that induced the cleavage of substrate strand, and then released the initiator DNA (TT) for CHA. With the help of the initiator DNA TT, self-powered CHA was activated to achieve the signal amplification reaction in the detection of DNA nanomachine. Meanwhile, the initiator DNA TT was released and hybridized with the other H1 strand to initiate another CHA, replacement, and turnovers, producing enhanced fluorescence signal of fluorophore FAM (excitation 490 nm/emission 520 nm) for sensitive determination of Pb2+. Under the optimized conditions, the DNA nanomachine detection system revealed high selectivity toward Pb2+ in the concentration range 50-600 pM, with the limit of detection (LOD) of 31 pM. Recovery tests demonstrated that the DNA nanomachine detection system has excellent detection capability in real samples. Therefore, the proposed strategy can be extended and act as a basic platform for highly accurate and sensitive detection of various heavy metal ions.
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Affiliation(s)
- Xiang-Ling Li
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, People's Republic of China
| | - Han Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, People's Republic of China
| | - Lei Zhao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, People's Republic of China
| | - Tian Shun Song
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, People's Republic of China
| | - Jing Jing Xie
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, People's Republic of China.
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DNA walking system integrated with enzymatic cleavage reaction for sensitive surface plasmon resonance detection of miRNA. Sci Rep 2022; 12:16093. [PMID: 36167754 PMCID: PMC9515148 DOI: 10.1038/s41598-022-20453-8] [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: 06/05/2022] [Accepted: 09/13/2022] [Indexed: 11/20/2022] Open
Abstract
Abnormal expression levels of miRNA are associated with various tumor diseases, for example, glioma tumors are characterized by the up-regulation of miRNA-182. Surface plasmon resonance (SPR) assay for miRNA-182 from glioma patients was performed via DNA walking amplification strategy. The duplex between aminated swing arm DNA (swDNA) and block DNA (blDNA), and aminated track DNA (trDNA) with a biotin tag were tethered on the poly(ethylene glycol) (PEG)-modified chips. Upon formation of miRNA/blDNA duplex, the SPR signal decreased with the walking process of swDNA, as the biotinylated fragment of trDNA (biotin-TTGGAGT) was detached from the sensor surface caused by the nicking endonuclease Nb.BbvCI. Such a repeated hybridization and cleavage cycle occurred continuously and the detachment of more biotinylated fragments of trDNA from the chips led to the attachment of fewer streptavidin (SA) molecules and then smaller SPR signals. MiRNA-182 with concentrations ranging from 5.0 fM to 1.0 pM could be readily determined and a detection limit of 0.62 fM was achieved. The proposed method was highly selective and possessed remarkable capability for evaluating the expression levels of miRNA-182 in serum samples from healthy donors and glioma patients. The sensing protocol holds great promise for early diagnosis of cancer patients.
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7
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Ratiometric fluorescent detection of miRNA-21 via pH-regulated adsorption of DNA on polymer dots and exonuclease III-assisted amplification. Anal Chim Acta 2022; 1232:340450. [DOI: 10.1016/j.aca.2022.340450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/12/2022] [Accepted: 09/25/2022] [Indexed: 11/01/2022]
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8
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Phooplub K, Ouiganon S, Thavarungkul P, Kanatharana P, Buranachai C. Portable device for dual detection of fluorescence and absorbance for biosensing or chemical sensing applications. HARDWAREX 2022; 11:e00268. [PMID: 35509944 PMCID: PMC9058716 DOI: 10.1016/j.ohx.2022.e00268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/18/2021] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
Early detection is key to prevent health problems and could be performed by biosensors and chemical sensors. However, a lot of them still need bulky benchtop equipment. This work presents a portable device for measuring fluorescence and light absorption that can be used with optical biosensors or chemical sensors. It uses a small laser diode as a light source and three filter-mounted photodiodes as detectors, all of which are inexpensive, customizable and widely available commercially. The results from our device show good correlation with that from commercial instruments. Therefore, it could be beneficial for early or on-site detection.
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Affiliation(s)
- Kittirat Phooplub
- Division of Physical Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
- Thailand Center of Excellence in Physics, Commission on Higher Education, 328 Si Ayutthaya Road, Bangkok, Thailand
- Center of Excellence for Trace Analysis and Biosensor, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Sirirat Ouiganon
- Division of Physical Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
- Thailand Center of Excellence in Physics, Commission on Higher Education, 328 Si Ayutthaya Road, Bangkok, Thailand
- Center of Excellence for Trace Analysis and Biosensor, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Panote Thavarungkul
- Division of Physical Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
- Thailand Center of Excellence in Physics, Commission on Higher Education, 328 Si Ayutthaya Road, Bangkok, Thailand
- Center of Excellence for Trace Analysis and Biosensor, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
- Center of Excellence for Innovation in Chemistry, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Proespichaya Kanatharana
- Division of Physical Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
- Center of Excellence for Trace Analysis and Biosensor, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
- Center of Excellence for Innovation in Chemistry, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Chittanon Buranachai
- Division of Physical Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
- Thailand Center of Excellence in Physics, Commission on Higher Education, 328 Si Ayutthaya Road, Bangkok, Thailand
- Center of Excellence for Trace Analysis and Biosensor, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
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9
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Catalytic hairpin assembly as cascade nucleic acid circuits for fluorescent biosensor: design, evolution and application. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116582] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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10
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Wu Y, Fu C, Shi W, Chen J. Recent advances in catalytic hairpin assembly signal amplification-based sensing strategies for microRNA detection. Talanta 2021; 235:122735. [PMID: 34517602 DOI: 10.1016/j.talanta.2021.122735] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/20/2021] [Accepted: 07/23/2021] [Indexed: 12/13/2022]
Abstract
Accumulative evidences have indicated that abnormal expression of microRNAs (miRNAs) is closely associated with many health disorders, making them be regarded as potentialbiomarkers for early clinical diagnosis. Therefore, it is extremely necessary to develop a highly sensitive, specific and reliable approach for miRNA analysis. Catalytic hairpin assembly (CHA) signal amplification is an enzyme-free toehold-mediated strand displacement method, exhibiting significant potential in improving the sensitivity of miRNA detection strategies. In this review, we first describe the potential of miRNAs as disease biomarkers and therapeutics, and summarize the latest advances in CHA signal amplification-based sensing strategies for miRNA monitoring. We describe the characteristics and mechanism of CHA signal amplification and classify the CHA-based miRNA sensing strategies into several categories based on the "signal conversion substance", including fluorophores, enzymes, nanomaterials, and nucleotide sequences. Sensing performance, limit of detection, merits and disadvantages of these miRNA sensing strategies are discussed. Moreover, the current challenges and prospects are also presented.
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Affiliation(s)
- Yan Wu
- Chongqing Key Laboratory of Inorganic Special Functional Materials, College of Chemistry and Chemical Engineering, Yangtze Normal University, Fuling, Chongqing, 408100, China.
| | - Cuicui Fu
- Chongqing Key Laboratory of Inorganic Special Functional Materials, College of Chemistry and Chemical Engineering, Yangtze Normal University, Fuling, Chongqing, 408100, China
| | - Wenbing Shi
- Chongqing Key Laboratory of Inorganic Special Functional Materials, College of Chemistry and Chemical Engineering, Yangtze Normal University, Fuling, Chongqing, 408100, China
| | - Jinyang Chen
- Chongqing Key Laboratory of Inorganic Special Functional Materials, College of Chemistry and Chemical Engineering, Yangtze Normal University, Fuling, Chongqing, 408100, China.
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Deng X, Liu X, Wu S, Zang S, Lin X, Zhao Y, Duan C. Ratiometric Fluorescence Imaging of Intracellular MicroRNA with NIR-Assisted Signal Amplification by a Ru-SiO 2@Polydopamine Nanoplatform. ACS APPLIED MATERIALS & INTERFACES 2021; 13:45214-45223. [PMID: 34524789 DOI: 10.1021/acsami.1c11324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Accurate and sensitive fluorescence imaging of intracellular miRNA is essential for understanding the mechanism underlying some physiological and pathological events, as well as the prevention and diagnosis of diseases. Herein, a highly sensitive ratiometric fluorescent nanoprobe for intracellular miRNA imaging was fabricated by integrating a Ru-SiO2@polydopamine (Ru-SiO2@PDA) nanoplatform with a near-infrared light (NIR)-assisted DNA strand displacement signal amplification strategy. The Ru-SiO2@PDA spheres have excellent biosafety, high photothermal effect, and unique photophysical properties that can both emit a stable red fluorescence and well quench the fluorophores getting closer to them. So, when the fuel DNA and carboxyfluorescein (FAM)-labeled signal DNA are co-assembled on their outer surfaces, the FAM's green fluorescence is quenched, and a low ratiometric signal is obtained. However, in the presence of miRNA, the target displaces the signal DNA from the capture DNA, releasing the signal DNA far away from the Ru-SiO2@PDA. Then, the green fluorescence recovers and leads to an enhanced Igreen/Ired value. Under NIR light irradiation, the Ru-SiO2@PDA increases the local temperature around the probe and triggers the release of fuel DNA, which thus recycles the target miRNA and effectively amplifies the ratiometric signal. Using A549 cells as a model, the nanoprobe realizes the highly sensitive ratiometric fluorescence imaging of miRNA let-7a, as well as its in vivo up- and down-regulation expressions. It provides a facile tool for highly sensitive and accurate intracellular miRNA detection through one-step incubation and may pave a new avenue for single-cell analysis.
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Affiliation(s)
- Xunxun Deng
- School of Chemical Engineering, Dalian University of Technology, Dalian 116023, P. R. China
- Zhangdayu School of Chemistry, Dalian University of Technology, Dalian 116023, P. R. China
| | - Xiaobo Liu
- School of Chemical Engineering, Dalian University of Technology, Dalian 116023, P. R. China
| | - Shuo Wu
- School of Chemical Engineering, Dalian University of Technology, Dalian 116023, P. R. China
| | - Shiyu Zang
- School of Chemical Engineering, Dalian University of Technology, Dalian 116023, P. R. China
| | - Xiaotong Lin
- School of Chemical Engineering, Dalian University of Technology, Dalian 116023, P. R. China
| | - Yanqiu Zhao
- School of Chemical Engineering, Dalian University of Technology, Dalian 116023, P. R. China
| | - Chunying Duan
- Zhangdayu School of Chemistry, Dalian University of Technology, Dalian 116023, P. R. China
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An "off-on" electrochemiluminescence biosensor coupled with strand displacement-powered 3D micromolecule walking nanomachine for ultrasensitive detection of adenosine triphosphate. Mikrochim Acta 2021; 188:237. [PMID: 34184148 DOI: 10.1007/s00604-021-04895-x] [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: 03/25/2021] [Accepted: 06/12/2021] [Indexed: 10/21/2022]
Abstract
A three-dimensional (3D) micromolecule walking nanomachine propelled by strand displacement was developed to establish a novel switching electrochemiluminescence (ECL) biosensor for ultrasensitive detection of adenosine triphosphate (ATP). Generally, walking nanomachines reported previously were limited to DNA walkers, while the proposed 3D walking nanomachine focused on the micromolecule walker. Firstly, TiO2 and silver nanoparticles (Ag NPs) functionalized N-(4-aminobutyl)-N-(ethylisoluminol) (Ag-ABEI) were deposited onto the electrode surface to offer an enhanced ECL signal, resulting from the double catalytic effect of TiO2 and Ag NPs for H2O2. Following, dopamine (DA)-labeled DNA duplex probes (S1/S2-DA) immobilized onto the modified electrode cut down the original ECL signal due to the quenching of DA toward ABEI (signal-off). Target ATP walker moved along the 3D DNA track, simultaneously releasing numerous DNA3, which was applied to displace S2-DA, resulting in the quenched ECL intensity recovery (signal-on). As a result, the biosensor showed a low limit of detection down to 0.5 nM (S/N = 3) and was successfully employed to determine ATP in human serum samples. Thus, the established biosensing strategy holds great potential for biochemical studies and clinical diagnosis.
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Feng C, Zhang C, Guo J, Li G, Ye B, Zou L. Novel preparation method of bipedal DNA walker based on hybridization chain reaction for ultrasensitive DNA biosensing. Anal Chim Acta 2021; 1176:338781. [PMID: 34399897 DOI: 10.1016/j.aca.2021.338781] [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: 04/16/2021] [Revised: 06/05/2021] [Accepted: 06/15/2021] [Indexed: 11/27/2022]
Abstract
In this work, a novel strategy for preparation of bipedal DNA walker (BDW) based on hybridization chain reaction (HCR) with the assistance of Exonuclease III (Exo III) was proposed. Based on this strategy, an electrochemical biosensor was constructed to achieve sensitive detection of CYFRA 21-1 DNA. Firstly, target recognition and circulation were achieved through a one-step catalytic hairpin assembly (CHA) reaction. For further amplification, hybridization chain reaction (HCR) was employed to form duplex-stranded DNA (dsDNA) nanostructure in homogeneous solution. In particular, the elongated single strand of the hairpin DNA for HCR was designed as the Mg2+ DNAzyme sequence. With the assistance of Exo III, dsDNA nanostructure can be digested and transformed into large amounts of BDW. These BDW can cleave the signal probe driven by Mg2+, which was modified on the electrode surface and thus achieved "signal-off" detection of target. This BDW preparation method based on HCR with the digestion of Exo III converted one target input into large amount of BDW. Coupled with the walking cleavage of BDW, a series of cascade amplification endowed high sensitivity with this biosensor and realized ultrasensitive detection of target DNA with the detection limit as low as 3.01 aM.
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Affiliation(s)
- Changrui Feng
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Chi Zhang
- Department of Orthopedics, First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001, PR China
| | - Jiaxin Guo
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Gaiping Li
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Baoxian Ye
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Lina Zou
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou, 450001, PR China.
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14
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Multifunctional nano-biosensor based on metal-organic framework for enhanced fluorescence imaging of intracellular miRNA-122 and synergistic chemo-photothermal therapy of tumor cells. Anal Chim Acta 2021; 1176:338779. [PMID: 34399895 DOI: 10.1016/j.aca.2021.338779] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/31/2021] [Accepted: 06/15/2021] [Indexed: 01/07/2023]
Abstract
A rationally designed multifunctional polydopamine (PDA)-coated metal-organic frameworks (MOFs) biosensors for detection of miRNA-122 with Zn2+-triggered aggregation-induced enhancement (AIE) and synergistic chem-photothermal therapy in vitro was developed for the first time. Further, it was successfully used for enhanced fluorescence imaging of miRNA-122 in living cells. The pH-responsive MOFs structure was decomposed under the influence of acidic environment, and a large amount of free Zn2+ was released as the trigger agent for AIE signal amplification, realizing the ultra-sensitive detection of miRNA-122 and the accurate discrimination of the cells with different expression levels of miRNA-122, with the detection limit as low as 12.5 pM. Meanwhile, ZIF-8 nanoparticles with high loading rate can effectively deliver therapeutic drugs to achieve responsive release. In addition, the modification of versatile PDA-coating provides the biosensor with a faster drug release capability and photothermal conversion performance, demonstrating its superior synergistic chem-photothermal therapy performance. It is expected to play an important role in the integration of cancer diagnosis and synergistic therapy.
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15
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Silver nanocluster-lightened catalytic hairpin assembly for enzyme-free and label-free mRNA detection. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106184] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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16
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Wang L, Zeng H, Yang X, Chen C, Ou S. Integrated nicking enzyme-powered numerous-legged DNA walker prepared by rolling circle amplification for fluorescence detection of microRNA. Mikrochim Acta 2021; 188:214. [PMID: 34052953 DOI: 10.1007/s00604-021-04875-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 05/20/2021] [Indexed: 01/09/2023]
Abstract
MicroRNAs (miRNAs) have been accepted as promising non-invasive biomarkers for cancer early diagnosis. Developing amplified sensing strategies for detecting ultralow concentration of miRNAs in clinical samples still requires much effort. Herein, an integrated fluorescence biosensor using nicking enzyme-powered numerous-feet DNA walking machine was developed for ultrasensitive detection of miRNA. A long numerous-feet walker produced by target-triggered rolling circle amplification autonomously moves along the defined DNA tracks on gold nanorods (AuNRs) with the help of nicking enzyme, leading to the recovery of fluorescence. This results in an amplified fluorescence signal, typically measured at 518 nm emission wavelength. Benefiting from the long walker that dramatically improves movement range, the homogenous and one-step strategy realizes ultrahigh sensitivity with a limit of detection of 0.8 fM. Furthermore, this walking machine has been successfully used to quantification of miRNA in clinical serum samples. The consistency of the gained results between of the developed strategy and reverse transcription quantitative polymerase chain reaction (RT-qPCR) shows that the sensing method has great promise for tumor diagnostics based on nucleic acid. Schematic representation of the fluorescent biosensing strategy, numerous-legged DNA walker prepared by rolling circle amplification on gold nanorods (AuNRs) for microRNA analysis, which can be applied in real samples with good results.
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Affiliation(s)
- Lihua Wang
- Health Management Medical Examination Center, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, 404600, China
| | - Hanqing Zeng
- Department of Hematology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, 404600, China
| | - Xiaolan Yang
- Department of Neurology, the Fengjie People's Hospital, Fengjie Branch of the Second Affiliated Hospital of Chongqing Medical University, Fengjie County, Chongqing, 404600, China
| | - Chaoming Chen
- Department of Neurology, the Fengjie People's Hospital, Fengjie Branch of the Second Affiliated Hospital of Chongqing Medical University, Fengjie County, Chongqing, 404600, China
| | - Shu Ou
- Department of Neurology, the Fengjie People's Hospital, Fengjie Branch of the Second Affiliated Hospital of Chongqing Medical University, Fengjie County, Chongqing, 404600, China.
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Yao Y, Xie G, Zhang X, Yuan J, Hou Y, Chen H. Fast detection of E. coli with a novel fluorescent biosensor based on a FRET system between UCNPs and GO@Fe 3O 4 in urine specimens. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:2209-2214. [PMID: 33908469 DOI: 10.1039/d1ay00320h] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Biosensors based on nanomaterials are becoming a research hotspot for the rapid detection of pathogenic bacteria. Herein, a "turn-on" fluorescent biosensor based on a FRET system was constructed for the fast detection of a representative pathogenic microorganism, namely, E. coli, which causes most urinary tract infections. This biosensor was constructed by utilizing synthesized UCNPs as fluorescent donors with stable luminescence performance in complex biological samples and GO@Fe3O4 as a receptor with both excellent adsorption ability and fluorescence quenching ability. A specific ssDNA selected as an aptamer which could recognize E. coli was immobilized on the UCNPs to form UCNP-Apt nanoprobes. The nanoprobes were adsorbed on the surface of GO@Fe3O4 through the π-stacking interactions between aptamers and GO. In the presence of E. coli, UCNP-Apt nanoprobes detached from GO@Fe3O4 due to the specific recognition of aptamers and bacteria, resulting in obvious fluorescence recovery, and the concentration of bacteria was positively correlated with the intensity of the fluorescence signal; such a "turn-on" signal output mode ensures excellent precision. In addition, the easy magnetic separation of GO@Fe3O4 simplifies the operation process, helping the sensor detect bacteria in 30 minutes with a linear range from 103 to 107 CFU mL-1 and a limit of detection of 467 CFU mL-1. Moreover, recovery test results also showed that the sensor has clinical application potential for the rapid detection of pathogenic microorganisms in complex biological samples.
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Affiliation(s)
- Yuan Yao
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China.
| | - Guoming Xie
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, P. R. China.
| | - Xin Zhang
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China.
| | - Jinshan Yuan
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China.
| | - Yulei Hou
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China.
| | - Hui Chen
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China.
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