1
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Sasa GBK, He B, Chen C, Chen Z, Li S, Tan CS. A dual-targeted electrochemical aptasensor for neuroblastoma-related microRNAs detection. Talanta 2024; 280:126772. [PMID: 39197310 DOI: 10.1016/j.talanta.2024.126772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/23/2024] [Accepted: 08/24/2024] [Indexed: 09/01/2024]
Abstract
Neuroblastoma (NB) is a significant pediatric cancer associated with high mortality rates, demanding innovative and appropriate approaches for its accurate detection. This paper described the design of a dual-target electrochemical aptasensor capable of simultaneously detecting neuroblastoma-associated microRNAs (miRNA-181 and miRNA-184) with exceptional sensitivity. Screen-printed carbon electrodes (SPCEs) were utilized with gold nanorods (AuNRs), and aptamers functionalized gold nanoparticles (AuNPs) to improve sensitivity, specificity, and portable detection ability. The detection method employed in this study includes differential pulse voltammetry (DPV) and cyclic voltammetry (CV). Our aptasensor exhibited remarkable limits of detections (LODs) of 5.10 aM for miRNA-181 and 9.39 aM for miRNA-184, respectively, along with a broad linear range spanning from 0.1 fM to 100 pM for both miRNAs. The practical significance of neuroblastoma diagnosis was shown through the validation of serum samples and comparison with quantitative polymerase chain reaction (qPCR). Our electrochemical aptasensor is user-friendly, easy to engineer, and offers a promising approach for accurately and selectively detecting important miRNA biomarkers in cancer screening and diagnosis, showing potential application in various clinical scenarios.
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Affiliation(s)
| | - Biaxun He
- Medical College, Tianjin University, Tianjin 300072, China
| | - Chong Chen
- Medical College, Tianjin University, Tianjin 300072, China; Department of Clinical Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Zetao Chen
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin 300072, China
| | - Shuang Li
- Medical College, Tianjin University, Tianjin 300072, China
| | - Cherie S Tan
- Medical College, Tianjin University, Tianjin 300072, China.
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2
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Liu X, Wang Q, Diao Z, Huo D, Hou C. Label-free fluorescent biosensor based on AuNPs etching releasing signal for miRNA-155 detection. Talanta 2024; 278:126481. [PMID: 38968655 DOI: 10.1016/j.talanta.2024.126481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/14/2024] [Accepted: 06/25/2024] [Indexed: 07/07/2024]
Abstract
Quantitative microRNA (miRNA) detection is crucial for early breast cancer diagnosis and prognosis. However, quick and stable fluorescence sensing for miRNA identification is still challenging. This work developed a novel label-free detection method based on AuNPs etching for quantitatively detecting miRNA-155. A layer of AuNPs was grown on the surface of mesoporous silica nanoparticles (MSN) loaded with Rhodamine 6G (R6G) using seed-mediated growth, followed by probe attachment. In the presence of miRNA-155, the MSN@R6G@AuNP surface loses the protection of the attached probe, rendering AuNPs susceptible to etching by hydrochloric acid. This results in a significant fluorescent signal being released in the free space. The encapsulation with AuNPs effectively reduces signal leakage, while the rapid etching process shortens detection time. This strategy enables sensitive and fast detection with a detection range of 100 fM to 100 nM, a detection limit of 2.18 fM, and a detection time of 30 min. The recovery rate in normal human serum ranges from 99.02 % to 106.34 %. This work presents a simple biosensing strategy with significant potential for application in tumor diagnosis.
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Affiliation(s)
- Xiaofang Liu
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, College of Chongqing University, Chongqing, 400044, PR China
| | - Qun Wang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, College of Chongqing University, Chongqing, 400044, PR China
| | - Zhan Diao
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, College of Chongqing University, Chongqing, 400044, PR China
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, College of Chongqing University, Chongqing, 400044, PR China.
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, College of Chongqing University, Chongqing, 400044, PR China; Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing, 400044, PR China.
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3
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Tam DY, Li P, Liu LS, Wang F, Leung HM, Lo PK. Versatility of threose nucleic acids: synthesis, properties, and applications in chemical biology and biomedical advancements. Chem Commun (Camb) 2024. [PMID: 39318271 DOI: 10.1039/d4cc04443f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2024]
Abstract
This feature article delves into the realm of α-L-threose nucleic acid (TNA), an artificial nucleic acid analog characterized by a backbone comprising an unconventional four-carbon sugar, α-L-threose, with phosphodiester linkages connecting at the 2' and 3' vicinal positions of the sugar ring. Within this article, we encapsulate the potential, progress, current state of the art, and persisting challenges within TNA research. Kicking off with a historical overview of xeno nucleic acids (XNAs), the discussion transitions to the compelling attributes and structure-property relationships of TNAs as advanced tools when contrasted with natural nucleic acids. Noteworthy aspects such as their advantageous spatial arrangements of functional groups around the sugar ring, stable Watson-Crick base pairing, high binding affinity, biostability, biocompatibility, and in vivo bio-safety are highlighted. Moreover, the narrative unfolds the latest advancements in chemical and biological methodologies for TNA synthesis, spanning from monomer and oligomer synthesis to polymerization, alongside cutting-edge developments in enzyme engineering aimed at bolstering large-scale TNA synthesis for in vitro selection initiatives. The article sheds light on the evolution of TNA aptamers over time, expounding on the tools and selection techniques engineered to unearth superior binding aptamers and TNA catalysts. Furthermore, the article accentuates the recent applications of TNAs across diverse domains such as molecular detection, immunotherapy, gene therapy, synthetic biology, and molecular computing. In conclusion, we summarize the key aspects of recent TNA research, address persisting gaps and challenges, and provide crucial insights and future perspectives in the dynamic domain of TNA research.
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Affiliation(s)
- Dick Yan Tam
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, P. R. China.
- Key Laboratory of Biochip Technology, Biotech and Health Care, Shenzhen Research Institute of City University of Hong Kong, 518057, Shenzhen, P. R. China
| | - Pan Li
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, P. R. China.
- Key Laboratory of Biochip Technology, Biotech and Health Care, Shenzhen Research Institute of City University of Hong Kong, 518057, Shenzhen, P. R. China
| | - Ling Sum Liu
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, 82 Wood Lane, London, W12 0BZ, UK
| | - Fei Wang
- The Tenth Affiliated Hospital, Southern Medical University (Dongguan People's Hospital), 523059 Dongguan, P. R. China
| | - Hoi Man Leung
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, P. R. China.
- Key Laboratory of Biochip Technology, Biotech and Health Care, Shenzhen Research Institute of City University of Hong Kong, 518057, Shenzhen, P. R. China
| | - Pik Kwan Lo
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, P. R. China.
- Key Laboratory of Biochip Technology, Biotech and Health Care, Shenzhen Research Institute of City University of Hong Kong, 518057, Shenzhen, P. R. China
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4
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Dong W, Yan W, Xu Y, Shang X, Wang W, Qiu J, Wang B, Wang H, Zhang Z, Zhao T. Multiplex Profiling of miR-122 for Preclinical and Clinical Evaluation of Drug-Induced Liver Injury by a Full-Scale Platform. ACS NANO 2024; 18:24860-24871. [PMID: 39195723 DOI: 10.1021/acsnano.4c05081] [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: 08/29/2024]
Abstract
Diagnostic and monitoring for drug-induced liver injury (DILI) predominantly rely on serum aminotransferases. However, owing to their widespread expression across multiple organs, a significant challenge emerges from the absence of reliable biomarkers for DILI diagnosis. Herein, we introduce a concept for DILI detection, circumventing the nonspecific elevation and delayed release of aminotransferases and then straightforwardly focusing on the core feature of DILI, abnormal gene expression caused by drug overdose. The developed full-scale platform integrates the properties of spherical nucleic acids with elaborately designed fluorescence in situ hybridization sequences, enabling the sensitive and specific profiling of drug-overdosed miR-122 expression alterations across molecular, cellular, organismal, and clinical scales and effectively bypassing the phenotypic features of disease. Furthermore, the diagnostic efficacies of serum and total RNA extracted from both mouse and human blood samples for DILI diagnosis were analyzed using the receiver operating characteristic curve and principal component analysis. We anticipate that this universal platform holds potential in facilitating DILI diagnosis, therapeutic evaluation, and prognosis.
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Affiliation(s)
- Wuqi Dong
- School of Basic Medical Sciences, Biopharmaceutical Research Institute, Anhui Provincial Institute of Translational Medicine, Anhui Medical University, Hefei, Anhui 230032, China
| | - Weizhen Yan
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yuechen Xu
- The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230032, China
| | - Xiaofei Shang
- School of Basic Medical Sciences, Biopharmaceutical Research Institute, Anhui Provincial Institute of Translational Medicine, Anhui Medical University, Hefei, Anhui 230032, China
| | - Wanrong Wang
- The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230032, China
| | - Jie Qiu
- School of Basic Medical Sciences, Biopharmaceutical Research Institute, Anhui Provincial Institute of Translational Medicine, Anhui Medical University, Hefei, Anhui 230032, China
| | - Baoxin Wang
- School of Basic Medical Sciences, Biopharmaceutical Research Institute, Anhui Provincial Institute of Translational Medicine, Anhui Medical University, Hefei, Anhui 230032, China
| | - Hua Wang
- The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230032, China
| | - Zhongping Zhang
- School of Chemistry and Chemical Engineering, Anhui University, Hefei, Anhui 230601, China
| | - Tingting Zhao
- School of Basic Medical Sciences, Biopharmaceutical Research Institute, Anhui Provincial Institute of Translational Medicine, Anhui Medical University, Hefei, Anhui 230032, China
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5
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Yu L, Peng Y, Sheng M, Wang Q, Jin Z, Huang J, Yang X. Electrochemical Biosensing Platform Based on Toehold-Mediated Strand Displacement Reaction and DSN Enzyme-Assisted Amplification for Two-Target Detection. ACS APPLIED MATERIALS & INTERFACES 2024; 16:45695-45703. [PMID: 39157906 DOI: 10.1021/acsami.4c08515] [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: 08/20/2024]
Abstract
Simultaneous detection of multiple targets is of great significance for accurate disease diagnosis. Herein, based on duplex-specific nuclease (DSN) assisted signal amplification and the toehold-mediated strand displacement reaction (TSDR), we constructed an electrochemical biosensor with high sensitivity and high specificity for dual-target detection. MiRNA-141 and miRNA-133a were used as the targets, and ferrocene (Fc) and methylene blue (MB) with significant peak potential differentiation were used as the electrochemical signal probes. The elaborately designed hairpin probe H1, which was fixed on the electrode surface, could be hybridized with the target miRNA-141 to perform signal amplification by the DSN-assisted enzyme cleavage cycle; thus, miRNA-141 could be detected by Fc signal changes at 0.41 V. The hairpin H1 can also combine with the MB-labeled signal probe (SP) output from miRNA-133a-induced TSDR, and the detection of miRNA-133a can be realized according to the response signal generated by MB at -0.26 V. The two sensing lines are independent of each other, and there is no mutual interference in the detection process. Therefore, two independent detection lines could be connected in series, and the simultaneous detection of two targets can be achieved on a single electrode. This novel detection strategy provides a new way to simultaneously detect different biomarkers.
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Affiliation(s)
- Linying Yu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yao Peng
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Mengting Sheng
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Qian Wang
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Zhiying Jin
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jianshe Huang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
| | - Xiurong Yang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
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6
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Xie Q, Chen J, Zhang J, Chu Z, Zhang F, Wang Q. Quantification of multiple microRNAs by microchip electrophoresis assisted by strand displacement amplification. J Chromatogr A 2024; 1730:465087. [PMID: 38889586 DOI: 10.1016/j.chroma.2024.465087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/01/2024] [Accepted: 06/11/2024] [Indexed: 06/20/2024]
Abstract
MicroRNAs (miRNAs) are increasingly recognized as potential biomarkers for the early diagnosis of cancer. However, the concurrent detection of multiple miRNAs in biological samples presents a significant challenge due to their high homogeneity and low abundance. This study introduced a novel approach combining strand displacement amplification (SDA) with microchip electrophoresis (MCE) for the simultaneous quantitation of trace levels of three miRNAs associated with cancer: miRNA-21, miRNA-145, and miRNA-221. Specifically designed probes were utilized to selectively capture the target miRNAs, thereby initiating the SDA process in a single solution without cross-interference. Under optimized conditions, the SDA-MCE method achieved the limit of detection (LOD) as low as 0.02 fM (S/N = 3) and the limit of quantitation (LOQ) as low as 0.1 fM across a broad linear range spanning from 0.1 fM to 1 pM. The SDA reaction was completed in approximately 1.5 h, and all target products were separated within 135 s through MCE. Application of this method for the simultaneous detection of these three miRNAs in human lung cancer cell samples yielded satisfactory results. Featuring high sensitivity, rapid analysis, minimal reagent consumption, and straightforward operation, the proposed MCE-SDA strategy holds considerable promise for multi-miRNAs detection applications.
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Affiliation(s)
- Qihui Xie
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Jingyi Chen
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Jingzi Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Zhaohui Chu
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Fan Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China.
| | - Qingjiang Wang
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China.
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7
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Zhou S, Shan F, Cao Y, Huang P, Yang H, Liu S. In Situ Intracellular Autocatalytic Hairpin Assembly of the Y-Shaped DNA Nanostructure for miR-155 Sensing and Gene Silencing. Anal Chem 2024. [PMID: 39150789 DOI: 10.1021/acs.analchem.4c02490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2024]
Abstract
miR-155 is a class of cancer markers closely related to cancer metastasis and invasion. Combining in situ detection with gene silencing not only helps to analyze the information on the abundance and spatial location of microRNA expression in the cell but also synergizes the therapy. In this work, we prepared HD@CM vesicles with three hairpin DNAs by using MCF-7 cell membranes. The hairpin DNAs can be triggered by endogenous miR-155, which opens the autocatalytic molecular circuit (ACHA) and obtains Y-shaped DNA nanostructures. This nanostructure not only detects endogenous miR-155 with high sensitivity for in situ imaging but also enables gene regulation of intracellular survivin mRNA. The levels of miR-155 in MDA-MB-231, MCF-7, Hela, and HEK-293T cells are found to be 7703, 3978, 1696, and 1229 copies/cell, respectively, as detected by HD@CMs. The fluorescence produced by HD@CM after coincubation with different cells is found to be proportional to the intracellular miR-155 content by confocal imaging. In addition, the gene regulatory function of the Y-shaped DNA structure resulted in significant inhibition of survivin protein expression and apoptosis rates of up to 83%. We look forward to the future application of our HD@CM platform for the precise diagnosis and programmable treatment of clinical cancers.
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Affiliation(s)
- Sisi Zhou
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Fanshu Shan
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Yu Cao
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Puzhen Huang
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Haitang Yang
- Food and Pharmacy College, Xuchang University, Xuchang 461000, China
| | - Songqin Liu
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
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8
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Wang H. A Review of Nanotechnology in microRNA Detection and Drug Delivery. Cells 2024; 13:1277. [PMID: 39120308 PMCID: PMC11311607 DOI: 10.3390/cells13151277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/27/2024] [Accepted: 07/28/2024] [Indexed: 08/10/2024] Open
Abstract
MicroRNAs (miRNAs) are small, non-coding RNAs that play a crucial role in regulating gene expression. Dysfunction in miRNAs can lead to various diseases, including cancers, neurological disorders, and cardiovascular conditions. To date, approximately 2000 miRNAs have been identified in humans. These small molecules have shown promise as disease biomarkers and potential therapeutic targets. Therefore, identifying miRNA biomarkers for diseases and developing effective miRNA drug delivery systems are essential. Nanotechnology offers promising new approaches to addressing scientific and medical challenges. Traditional miRNA detection methods include next-generation sequencing, microarrays, Northern blotting, and reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Nanotechnology can serve as an effective alternative to Northern blotting and RT-qPCR for miRNA detection. Moreover, nanomaterials exhibit unique properties that differ from larger counterparts, enabling miRNA therapeutics to more effectively enter target cells, reduce degradation in the bloodstream, and be released in specific tissues or cells. This paper reviews the application of nanotechnology in miRNA detection and drug delivery systems. Given that miRNA therapeutics are still in the developing stages, nanotechnology holds great promise for accelerating miRNA therapeutics development.
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Affiliation(s)
- Hsiuying Wang
- Institute of Statistics, National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
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9
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Fan Q, Sun XH, Wu N, Wang YH, Wang JH, Yang T. An extracellular vesicle microRNA-initiated 3D DNAzyme motor for colorectal cancer diagnosis. Analyst 2024; 149:3910-3919. [PMID: 38910520 DOI: 10.1039/d4an00635f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
MicroRNA is regarded as a significant biomarker for cancer diagnosis, disease process evaluation and therapeutic guidance, and dual-parameter measurement may contribute to a more accurate and realistic assessment. To meet the urgent need for simultaneous detection of multiple biomarkers, we combined three-dimensional DNAzyme motors with single molecule imaging technique to construct a convenient, intuitive, and sensitive approach for the simultaneous detection of dual miRNAs in the free state or in extracellular vesicles. Quantification of target miRNAs can be realized through the detection of amplified fluorescence signals generated by the target miRNA-initiated cleavage of fluorescent substrate strands by the DNAzyme motors. The practicability was systematically validated with microRNA-21-5p and microRNA-10b-5p as targets, acquiring a satisfactory sensitivity sufficient to detect low abundance targets at 0.5 or 1 pM to 100 pM. Besides, the extracellular vesicular miRNAs can be conveniently detected without extraction. The clinical applicability was verified with a series of extracellular vesicles from clinical samples, which exhibited good distinguishability between colorectal cancer patients and healthy donors. In addition to the advantages of good specificity and high sensitivity, the system has potential to be easily adapted by minor alteration of the DNA sequences and fluorophore sets for detection of multiple miRNAs and even other types of biomarkers such as proteins. Therefore, it shows promise to be widely applied in various fields such as early diagnosis of cancer and its prognostic assessment.
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Affiliation(s)
- Qian Fan
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China.
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xu-Hong Sun
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China.
| | - Na Wu
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China.
- Institute of Precision Medicine, Fujian Medical University, Fujian 350004, China
| | - Yuan-He Wang
- Department of Gastrointestinal Cancer, Liaoning Cancer Hospital & Institute, Cancer Hospital of China Medical University, Shenyang 110042, China.
| | - Jian-Hua Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China.
| | - Ting Yang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China.
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10
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Li S, Pei XY, Liu XY, Wang SL, Xu W, Wang JJ, Feng Z, Ding H, Zhang YF, Zhang R. Sensitive fluorescence detection of miRNA-124 in cardiomyocytes under oxidative stress using a nucleic acid probe. Heliyon 2024; 10:e33588. [PMID: 39040278 PMCID: PMC11260977 DOI: 10.1016/j.heliyon.2024.e33588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 05/26/2024] [Accepted: 06/24/2024] [Indexed: 07/24/2024] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs of 18-25 bases. miRNAs are also important new biomarkers that can be used for disease diagnosis in the future. Studies have shown that miR-124 levels are significantly elevated during acute myocardial infarction (AMI) and play a key role in the cardiovascular system. A variety of methods have been established to detect myocardial infarction-related miRNAs. However, most require complex miRNA extraction and isolation, and these methods are virtually undetectable when RNA levels are low in the sample. It may lead to biased results. Thus, it is necessary to develop a technique that can detect miRNA without extracting it, which means that intracellular detection is of great significance. Here, we improved the traditional silicon spheres and obtained a biosensor that could effectively capture and detect specific noncoding nucleic acids through the layer-by-layer assembly method. The sensor is protected by hyaluronic acid so it can successfully escape the lysosome into the cell and achieve detection. With the help of a full-featured microplate reader, we determined that the detection limit of the biosensor could reach 1 fM, meeting the needs of intracellular detection. At the same time, we prepared an oxidative stress cardiomyocyte infarction model and successfully captured the overexpressed miR-124 in the infarcted cells to achieve in situ detection. This study could provide a new potential tool to develop miRNAs for sensitive diagnosis in AMI, and the proposed strategy implies its potential for biomedical research.
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Affiliation(s)
- Shuo Li
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shandong, China
- Institute for Translational Medicine, Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, 266021, China
| | - Xiang-Yu Pei
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shandong, China
- Institute for Translational Medicine, Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, 266021, China
| | - Xin-Yi Liu
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shandong, China
- Institute for Translational Medicine, Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, 266021, China
| | - Shu-Liang Wang
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shandong, China
- Institute for Translational Medicine, Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, 266021, China
| | - Wen Xu
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shandong, China
- Institute for Translational Medicine, Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, 266021, China
| | - Jing-Jing Wang
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shandong, China
- Institute for Translational Medicine, Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, 266021, China
| | - Zhen Feng
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shandong, China
- Institute for Translational Medicine, Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, 266021, China
| | - Han Ding
- Institute for Translational Medicine, Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, 266021, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Yin-Feng Zhang
- Institute for Translational Medicine, Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao, 266021, China
| | - Rui Zhang
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, Shandong, China
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11
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Wang S, Guang J, Gao Y, Fan B, Liang Y, Pan J, Li L, Meng W, Hu F. Fluorescent DNA tetrahedral probe with catalytic hairpin self-assembly reaction for imaging of miR-21 and miR-155 in living cells. Mikrochim Acta 2024; 191:462. [PMID: 38990374 DOI: 10.1007/s00604-024-06529-4] [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: 03/29/2024] [Accepted: 06/26/2024] [Indexed: 07/12/2024]
Abstract
A CHA-based fluorescent DNA tetrahedral probe (FDTp) has been designed to detect the microRNAs miR-21 and miR-155 sensitively and specifically in living cells. The design consisted of functional elements (H1, H2, and Protector) connected to a DNA tetrahedron modified with two pairs of fluorophores and quenching groups. In the presence of miR-21, the chain displacement effect was triggered and Cy3 fluorescence was emitted. In the presence of miR-155, the signal of the catalytic hairpin assembly (CHA) between H1 and H2 on FDTp was amplified, making the fluorescence of FAM sensitive to miR-155. Using this method, the detection limit for miR-155 was 5 pM. The FDTp successfully imaged miR-21 and miR-155 in living cells and distinguished a variety of cell lines based on their expression levels of miR-21 and miR-155. The detection and imaging of dual targets in this design ensured the accuracy of tumor diagnosis and provided a new method for early tumor diagnosis.
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Affiliation(s)
- Shan Wang
- Key Laboratory of Biomedical Functional Materials, School of Sciences, China Pharmaceutical University, Nanjing, 211198, China
| | - Jiejie Guang
- Key Laboratory of Biomedical Functional Materials, School of Sciences, China Pharmaceutical University, Nanjing, 211198, China
- Pharmacy Department, Huangshan City People's Hospital, Liyuan Road, Tunxi District, Huangshan, 245000, China
| | - Yahui Gao
- Key Laboratory of Biomedical Functional Materials, School of Sciences, China Pharmaceutical University, Nanjing, 211198, China
| | - Bingyuan Fan
- Key Laboratory of Biomedical Functional Materials, School of Sciences, China Pharmaceutical University, Nanjing, 211198, China
| | - Yan Liang
- Key Laboratory of Biomedical Functional Materials, School of Sciences, China Pharmaceutical University, Nanjing, 211198, China
| | - Jinru Pan
- Key Laboratory of Biomedical Functional Materials, School of Sciences, China Pharmaceutical University, Nanjing, 211198, China
| | - Li Li
- Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China.
| | - Wei Meng
- Key Laboratory of Biomedical Functional Materials, School of Sciences, China Pharmaceutical University, Nanjing, 211198, China.
| | - Fang Hu
- Key Laboratory of Biomedical Functional Materials, School of Sciences, China Pharmaceutical University, Nanjing, 211198, China.
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12
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Liu X, Jia Y, Zheng C. Recent progress in Surface-Enhanced Raman Spectroscopy detection of biomarkers in liquid biopsy for breast cancer. Front Oncol 2024; 14:1400498. [PMID: 39040452 PMCID: PMC11260621 DOI: 10.3389/fonc.2024.1400498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/24/2024] [Indexed: 07/24/2024] Open
Abstract
Breast cancer is the most commonly diagnosed cancer in women globally and a leading cause of cancer-related mortality. However, current detection methods, such as X-rays, ultrasound, CT scans, MRI, and mammography, have their limitations. Recently, with the advancements in precision medicine and technologies like artificial intelligence, liquid biopsy, specifically utilizing Surface-Enhanced Raman Spectroscopy (SERS), has emerged as a promising approach to detect breast cancer. Liquid biopsy, as a minimally invasive technique, can provide a temporal reflection of breast cancer occurrence and progression, along with a spatial representation of overall tumor information. SERS has been extensively employed for biomarker detection, owing to its numerous advantages such as high sensitivity, minimal sample requirements, strong multi-detection ability, and controllable background interference. This paper presents a comprehensive review of the latest research on the application of SERS in the detection of breast cancer biomarkers, including exosomes, circulating tumor cells (CTCs), miRNA, proteins and others. The aim of this review is to provide valuable insights into the potential of SERS technology for early breast cancer diagnosis.
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Affiliation(s)
- Xiaobei Liu
- Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yining Jia
- Department of Breast Surgery, The Second Hospital of Shandong University, Jinan, China
- Institute of Translational Medicine of Breast Disease Prevention and Treatment, Shandong University, Jinan, China
| | - Chao Zheng
- Department of Breast Surgery, The Second Hospital of Shandong University, Jinan, China
- Institute of Translational Medicine of Breast Disease Prevention and Treatment, Shandong University, Jinan, China
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13
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Jeung JH, Han H, Jang SH, Lee CY, Ahn JK. One-pot, one-step, label-free miRNA detection method based on the structural transition of dumbbell probe. Talanta 2024; 274:125944. [PMID: 38537347 DOI: 10.1016/j.talanta.2024.125944] [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: 12/19/2023] [Revised: 02/15/2024] [Accepted: 03/16/2024] [Indexed: 05/04/2024]
Abstract
In this study, we present a one-pot, one-step, label-free miRNA detection method through a structural transition of a specially designed dumbbell-shape probe, initiating a rolling circle transition (RCT). In principle, target miRNA binds to right loop of the dumbbell probe (DP), which allows structural change of the DP to circular form, exposing a sequence complementary to the T7 promoter (T7p) previously hidden within the stem. This exposure allows T7 RNA polymerase to initiate RCT, producing a repetitive Mango aptamer sequence. TO1-biotin, fluorescent dye, binds to the aptamer, inducing a detectable enhancement of fluorescence intensity. Without miR-141, the DP stays closed, RCT is prevented, and the fluorescence intensity remains low. By employing this novel strategy, target miRNA was successfully identified with a detection of 73 pM and a dynamic linear range of 0-10 nM. Additionally, the method developed enables one-pot, one-step, and label-free detection of miRNA, demonstrating potential for point-of-care testing (POCT) applications. Furthermore, the practical application of the designed technique was demonstrated by reliably detecting the target miRNA in the human serum sample. We also believe that the conceived approach could be widely used to detect not only miRNAs but also diverse biomolecules by simply replacing the detection probe.
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Affiliation(s)
- Jae Hoon Jeung
- Material & Component Convergence R&D Department, Korea Institute of Industrial Technology (KITECH), Ansan, Republic of Korea; Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Hyogu Han
- Material & Component Convergence R&D Department, Korea Institute of Industrial Technology (KITECH), Ansan, Republic of Korea; Department of Chemistry, Gangneung-Wonju National University, Gangneung, 25457, Republic of Korea
| | - Se Hee Jang
- Material & Component Convergence R&D Department, Korea Institute of Industrial Technology (KITECH), Ansan, Republic of Korea; Department of Medical Device Engineering and Management, College of Medicine, Yonsei University, Seoul, 03722, Republic of Korea
| | - Chang Yeol Lee
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
| | - Jun Ki Ahn
- Material & Component Convergence R&D Department, Korea Institute of Industrial Technology (KITECH), Ansan, Republic of Korea.
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14
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Wang S, Wei Z, Li L, Luo Y, Huang Z, Yang X, Tang Y. A label-free and rapid fluorometric strategy for microRNA detection using CRISPR-Cas12a coupled with copper nanoparticles. Mikrochim Acta 2024; 191:405. [PMID: 38896292 DOI: 10.1007/s00604-024-06496-w] [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: 05/02/2024] [Accepted: 06/07/2024] [Indexed: 06/21/2024]
Abstract
CRISPR-Cas12a with robust trans-cleavage activity were employed to mitigate background fluorescence signal, achieving sensitive detection of miRNA-21. The activation of trans-cleavage activity of Cas12a was achieved by utilizing cDNA as a trigger. Upon the presence of target miRNA-21, cDNA hybridizes with it forming a DNA/RNA double-stranded structure. Exonuclease III (ExoIII) facilitates the degradation of cDNA, releasing the target for subsequent cycles. Due to cDNA degradation, the trans-cleavage activity of Cas12a remains unactivated and does not disrupt the synthesis template of copper nanoparticles. Addition of Cu2+ and AA leads to the formation of highly fluorescent copper nanoparticles. Conversely, in absence of miRNA-21, intact cDNA activates trans-cleavage activity of Cas12a, resulting in degradation of the synthesis template and failure in synthesizing fluorescent copper nanoparticles. This method exhibits excellent selectivity with a low limit of detection (LOD) at 5 pM. Furthermore, we successfully applied this approach to determine miRNA-21 in cell lysates and human serum samples, providing a new approach for sensitive determination of biomarkers in biochemical research and disease diagnosis.
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Affiliation(s)
- Shirong Wang
- Clinical Research Center for Neurological Diseases of Guangxi Province, Affiliated Hospital of Guilin Medical University, Guilin, China
- Department of Cardiology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Zaiwa Wei
- The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Liangxian Li
- Key Laboratory of Brain and Cognitive Neuroscience, Guilin Medical University, Guilin, Guangxi, China
| | - Yu Luo
- Clinical Research Center for Neurological Diseases of Guangxi Province, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Zhimei Huang
- Clinical Research Center for Neurological Diseases of Guangxi Province, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Xing Yang
- Clinical Research Center for Neurological Diseases of Guangxi Province, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Yafang Tang
- Clinical Research Center for Neurological Diseases of Guangxi Province, Affiliated Hospital of Guilin Medical University, Guilin, China.
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15
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Yan Y, Liao L. MicroRNA Expression Profile in Patients Admitted to ICU as Novel and Reliable Approach for Diagnostic and Therapeutic Purposes. Mol Biotechnol 2024; 66:1357-1375. [PMID: 37314613 DOI: 10.1007/s12033-023-00767-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 05/06/2023] [Indexed: 06/15/2023]
Abstract
The ability to detect early metabolic changes in patients who have an increased mortality risk in the intensive care units (ICUs) could increase the likelihood of predicting recovery patterns and assist in disease management. Markers that can predict the disease progression of patients in the ICU might also be beneficial for improving their medical profile. Although biomarkers have been used in the ICU more frequently in recent years, the clinical use of most of them is limited. A wide range of biological processes are influenced by microRNAs (miRNAs) that modulate the translation and stability of specific mRNAs. Studies suggest that miRNAs may serve as a diagnostic and therapeutic biomarker in ICUs by profiling miRNA dysregulation in patient samples. To improve the predictive value of biomarkers for ICU patients, researchers have proposed both investigating miRNAs as novel biomarkers and combining them with other clinical biomarkers. Herein, we discuss recent approaches to the diagnosis and prognosis of patients admitted to an ICU, highlighting the use of miRNAs as novel and robust biomarkers for this purpose. In addition, we discuss emerging approaches to biomarker development and ways to improve the quality of biomarkers so that patients in ICU get the best outcomes possible.
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Affiliation(s)
- Youqin Yan
- ICU Department, People's Hospital of Changshan, Changshan, China
| | - Linjun Liao
- ICU Department, People's Hospital of Changshan, Changshan, China.
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16
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Ouyang R, Huang Y, Ma Y, Feng M, Liu X, Geng C, Zhao Y, Zhou S, Liu B, Miao Y. Nanomaterials promote the fast development of electrochemical MiRNA biosensors. RSC Adv 2024; 14:17929-17944. [PMID: 38836170 PMCID: PMC11149695 DOI: 10.1039/d3ra08258j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 05/18/2024] [Indexed: 06/06/2024] Open
Abstract
Cancer has become the leading cause of death worldwide. In recent years, molecular diagnosis has demonstrated great potential in the prediction and diagnosis of cancer. MicroRNAs (miRNAs) are short oligonucleotides that regulate gene expression and cell function and are considered ideal biomarkers for cancer detection, diagnosis, and patient prognosis. Therefore, the specific and sensitive detection of ultra-low quantities of miRNA is of great significance. MiRNA biosensors based on electrochemical technology have advantages of high sensitivity, low cost and fast response. Nanomaterials show great potential in miRNA electrochemical detection and promote the rapid development of electrochemical miRNA biosensors. Some methods and signal amplification strategies for miRNA detection in recent years are reviewed herein, followed by a discussion of the latest progress in electrochemical miRNA detection based on different types of nanomaterial. Future perspectives and challenges are also proposed for further exploration of nanomaterials to bring breakthroughs in electrochemical miRNA detection.
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Affiliation(s)
- Ruizhuo Ouyang
- Institute of Bismuth and Rhenium Science, University of Shanghai for Science and Technology Shanghai 200093 China
| | - Ying Huang
- Institute of Bismuth and Rhenium Science, University of Shanghai for Science and Technology Shanghai 200093 China
| | - Yuanhui Ma
- Institute of Bismuth and Rhenium Science, University of Shanghai for Science and Technology Shanghai 200093 China
| | - Meina Feng
- Institute of Bismuth and Rhenium Science, University of Shanghai for Science and Technology Shanghai 200093 China
| | - Xi Liu
- Institute of Bismuth and Rhenium Science, University of Shanghai for Science and Technology Shanghai 200093 China
| | - Chongrui Geng
- Institute of Bismuth and Rhenium Science, University of Shanghai for Science and Technology Shanghai 200093 China
| | - Yuefeng Zhao
- Institute of Bismuth and Rhenium Science, University of Shanghai for Science and Technology Shanghai 200093 China
| | - Shuang Zhou
- Cancer Institute, Tongji University School of Medicine Shanghai 200093 China
| | - Baolin Liu
- School of Health Science and Engineering, University of Shanghai for Science and Technology Shanghai 200093 China
| | - Yuqing Miao
- Institute of Bismuth and Rhenium Science, University of Shanghai for Science and Technology Shanghai 200093 China
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17
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Wang H, Liu J, Fang Y, Shen X, Liu H, Yu L, Zeng S, Cai S, Zhou J, Li Z. Design and analysis of self-priming extension DNA hairpin probe for miRNA detection based on a unified dynamic programming framework. Anal Chim Acta 2024; 1303:342530. [PMID: 38609269 DOI: 10.1016/j.aca.2024.342530] [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: 12/19/2023] [Revised: 02/03/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024]
Abstract
MicroRNAs (miRNAs) are potential biomarkers for cancer diagnosis and prognosis, methods for detecting miRNAs with high sensitivity, selectivity, and stability are urgently needed. Various nucleic acid probes that have traditionally been for this purpose suffer several drawbacks, including inefficient signal-to-noise ratios and intensities, high cost, and time-consuming method establishment. Computing tools used for investigating the thermodynamics of DNA hybridization reactions can accurately predict the secondary structure of DNA and the interactions between DNA molecules. Herein, NUPACK was used to design a series of nucleic acid probes and develop a phosphorothioated-terminal hairpin formation and self-priming extension (PS-THSP) signal amplification strategy, which enabled the ultrasensitive detection of miR-200a in serum samples. The free and binding energies of the DNA detection probes calculated using NUPACK, as well as the biological experimental results, were considered synthetically to select the best sequence and experimental conditions. A unified dynamic programming framework, NUPACK analysis and the experimental data, were complementary and improved the designed model in all respects. Our study demonstrates the feasibility of using computer technology such as NUPACK to simplify the experimental process and provide intuitive results.
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Affiliation(s)
- Hecheng Wang
- Institute of Drug Metabolism and Pharmaceutical Analysis, National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jiatong Liu
- Institute of Drug Metabolism and Pharmaceutical Analysis, National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Yanyan Fang
- Institute of Drug Metabolism and Pharmaceutical Analysis, National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xudan Shen
- Institute of Drug Metabolism and Pharmaceutical Analysis, National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Hui Liu
- Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310020, China
| | - Lushan Yu
- Institute of Drug Metabolism and Pharmaceutical Analysis, National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Sheng Cai
- Institute of Drug Metabolism and Pharmaceutical Analysis, National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Jingjing Zhou
- Beijing Lab for Cardiovascular Precision Medicine, Echocardiography Medical Center, Maternal-Fetal Medicine Center in Fetal Heart Disease, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China.
| | - Zheyong Li
- Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310020, China; Zhejiang University Sir Run Run Shaw Alaer Hospital, Alaer, Xinjiang, 843300, China.
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18
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Meng X, Pang X, Yang J, Zhang X, Dong H. Recent Advances in Electrochemiluminescence Biosensors for MicroRNA Detection. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307701. [PMID: 38152970 DOI: 10.1002/smll.202307701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 12/06/2023] [Indexed: 12/29/2023]
Abstract
Electrochemiluminescence (ECL) as an analytical technology with a perfect combination of electrochemistry and spectroscopy has received considerable attention in bioanalysis due to its high sensitivity and broad dynamic range. Given the selectivity of bio-recognition elements and the high sensitivity of the ECL analysis technique, ECL biosensors are powerful platforms for the sensitive detection of biomarkers, achieving the accurate prognosis and diagnosis of diseases. MicroRNAs (miRNAs) are crucial biomarkers involved in a variety of physiological and pathological processes, whose aberrant expression is often related to serious diseases, especially cancers. ECL biosensors can fulfill the highly sensitive and selective requirements for accurate miRNA detection, prompting this review. The ECL mechanisms are initially introduced and subsequently categorize the ECL biosensors for miRNA detection in terms of the quenching agents. Furthermore, the work highlights the signal amplification strategies for enhancing ECL signal to improve the sensitivity of miRNA detection and finally concludes by looking at the challenges and opportunities in ECL biosensors for miRNA detection.
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Affiliation(s)
- Xiangdan Meng
- Beijing Key Laboratory for Bioengineering and Sensing Technology Research Centre for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 10083, P. R. China
| | - Xuejiao Pang
- Beijing Key Laboratory for Bioengineering and Sensing Technology Research Centre for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 10083, P. R. China
| | - Junyan Yang
- School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing, 100083, P. R. China
| | - Xueji Zhang
- Beijing Key Laboratory for Bioengineering and Sensing Technology Research Centre for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 10083, P. R. China
- Marshall Laboratory of Biomedical Engineering, Precision Medicine and Health Research Institute, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Guangdong, 518060, P. R. China
| | - Haifeng Dong
- Beijing Key Laboratory for Bioengineering and Sensing Technology Research Centre for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 10083, P. R. China
- Marshall Laboratory of Biomedical Engineering, Precision Medicine and Health Research Institute, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Guangdong, 518060, P. R. China
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19
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Yin M, Jiao J, Lu L, Hu B, Xue L, Dai F, Wang X, Wang Z, Wang T, Chen Q. A simultaneous strategy with multiple-signal amplification and self-calibration for ultrasensitive assay of miRNA-21 based on 3D MNPs-IL-rGO-AuNPs. Biosens Bioelectron 2024; 249:116009. [PMID: 38199082 DOI: 10.1016/j.bios.2024.116009] [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: 10/26/2023] [Revised: 12/17/2023] [Accepted: 01/04/2024] [Indexed: 01/12/2024]
Abstract
MicroRNA-21 (miRNA-21) is a significant biomarker for the development and progression of diverse cancers but is present in relatively low concentrations. Detecting such low-abundance molecules accurately can be challenging, especially in early-stage cancers where the concentration may be even lower. Herein, a self-calibration biosensing platform based on 3D novel MNPs-IL-rGO-AuNPs nanocomposites was successfully established for the ultrasensitive detection of miRNA-21. Duplex-specific nuclease (DSN) was introduced to recognize perfectly matched duplexes and trigger target recycling, enhancing the specificity and sensitivity of the biosensor. DSN-assisted target recycling, in conjunction with magnetic separation enrichment and high-performance MNPs-IL-rGO-AuNPs, collectively formed a multiple-signal amplification strategy. The obtained biosensor could output dual signals in both electrochemical and fluorescent modes, enabling self-correcting detection to enhance the accuracy. The obtained dual-mode biosensor prepared exhibited a wide detection range from 5 fM to 100 nM with a remarkably low LOD of 1.601 fM. It accomplished the sensitive evaluation of miRNA-21 in total RNA extracted from various human cancer cell lines and normal cell lines. Additionally, the greatly satisfactory outcomes in the analysis of human serum samples suggested that the proposed biosensor was a powerful screening candidate in early clinical diagnosis of cancer.
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Affiliation(s)
- Mengai Yin
- The Key Laboratory of Bioactive Materials Ministry of Education, College of Life Science, Nankai University, Weijin Road No.94, Tianjin, 300071, PR China
| | - Jun Jiao
- The Key Laboratory of Bioactive Materials Ministry of Education, College of Life Science, Nankai University, Weijin Road No.94, Tianjin, 300071, PR China.
| | - Lina Lu
- The Key Laboratory of Bioactive Materials Ministry of Education, College of Life Science, Nankai University, Weijin Road No.94, Tianjin, 300071, PR China
| | - Bingxin Hu
- The Key Laboratory of Bioactive Materials Ministry of Education, College of Life Science, Nankai University, Weijin Road No.94, Tianjin, 300071, PR China
| | - Lan Xue
- The Key Laboratory of Bioactive Materials Ministry of Education, College of Life Science, Nankai University, Weijin Road No.94, Tianjin, 300071, PR China
| | - Fuju Dai
- The Key Laboratory of Bioactive Materials Ministry of Education, College of Life Science, Nankai University, Weijin Road No.94, Tianjin, 300071, PR China
| | - Xiangrui Wang
- The Key Laboratory of Bioactive Materials Ministry of Education, College of Life Science, Nankai University, Weijin Road No.94, Tianjin, 300071, PR China
| | - Zhijie Wang
- The Key Laboratory of Bioactive Materials Ministry of Education, College of Life Science, Nankai University, Weijin Road No.94, Tianjin, 300071, PR China
| | - Tong Wang
- The Key Laboratory of Bioactive Materials Ministry of Education, College of Life Science, Nankai University, Weijin Road No.94, Tianjin, 300071, PR China
| | - Qiang Chen
- The Key Laboratory of Bioactive Materials Ministry of Education, College of Life Science, Nankai University, Weijin Road No.94, Tianjin, 300071, PR China.
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20
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Wang H, Yu R, Zhu Q, Tian Z, Li F. A highly sensitive biotin-based probe for small RNA northern blot and its application in dissecting miRNA function in pepper. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:263-276. [PMID: 38078656 DOI: 10.1111/tpj.16585] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/26/2023] [Accepted: 12/01/2023] [Indexed: 04/02/2024]
Abstract
Small RNAs play important roles in regulation of plant development and response to various stresses. Northern blot is an important technique in small RNA research. Isotope- and biotin- (or digoxigenin) labeled probes are frequently used in small RNA northern blot. However, isotope-based probe is limited by strict environmental regulation and availability in many places in the world while biotin-based probe is usually suffered from low sensitivity. In this study, we developed a T4 DNA polymerase-based method for incorporation of a cluster of 33 biotin-labeled C in small RNA probe (T4BC33 probe). T4BC33 probe reaches similar sensitivity as 32P-labeled probe in dot blot and small RNA northern blot experiments. Addition of locked nucleic acids in T4BC33 probe further enhanced its sensitivity in detecting low-abundance miRNAs. With newly developed northern blot method, expression of miR6027 and miR6149 family members was validated. Northern blot analysis also confirmed the successful application of virus-based miRNA silencing in pepper, knocking down accumulation of Can-miR6027a and Can-miR6149L. Importantly, further analysis showed that knocking-down Can-miR6027a led to upregulation of a nucleotide binding-leucine rich repeat domain protein coding gene (CaRLb1) and increased immunity against Phytophthora capsici in pepper leaves. Our study provided a highly sensitive and convenient method for sRNA research and identified new targets for genetic improvement of pepper immunity against P. capsici.
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Affiliation(s)
- Hongzheng Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ruimin Yu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiangqiang Zhu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhendong Tian
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Feng Li
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, 430070, China
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21
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Yu S, Lei X, Qu C. MicroRNA Sensors Based on CRISPR/Cas12a Technologies: Evolution From Indirect to Direct Detection. Crit Rev Anal Chem 2024:1-17. [PMID: 38489095 DOI: 10.1080/10408347.2024.2329229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
MicroRNA (miRNA) has emerged as a promising biomarker for disease diagnosis and a potential therapeutic targets for drug development. The detection of miRNA can serve as a noninvasive tool in diseases diagnosis and predicting diseases prognosis. CRISPR/Cas12a system has great potential in nucleic acid detection due to its high sensitivity and specificity, which has been developed to be a versatile tool for nucleic acid-based detection of targets in various fields. However, conversion from RNA to DNA with or without amplification operation is necessary for miRNA detection based on CRISPR/Cas12a system, because dsDNA containing PAM sequence or ssDNA is traditionally considered as the activator of Cas12a. Until recently, direct detection of miRNA by CRISPR/Cas12a system has been reported. In this review, we provide an overview of the evolution of biosensors based on CRISPR/Cas12a for miRNA detection from indirect to direct, which would be beneficial to the development of CRISPR/Cas12a-based sensors with better performance for direct detection of miRNA.
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Affiliation(s)
- Songcheng Yu
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Xueying Lei
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Chenling Qu
- School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou, China
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22
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Chen T, Yang J, Tang Y, Fan X, Zhou W, Jiang B, Wang D. Label-free and highly sensitive detection of microRNA from cancer cells via target-induced cascade amplification generation of lighting-up RNA aptamers. Anal Chim Acta 2024; 1289:342187. [PMID: 38245202 DOI: 10.1016/j.aca.2023.342187] [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: 10/23/2023] [Revised: 12/24/2023] [Accepted: 12/29/2023] [Indexed: 01/22/2024]
Abstract
The abnormal expression levels of miRNAs have been proven to be highly related to the generation of various diseases and are also closely associated with the stages and types of disease development. The novel RNA aptamers-based homogenous fluorescent methods were simple, with low background signal and high signal-to-noise ratio, but lacked effective signal amplification technology to achieve sensitive detection of trace miRNA markers. There is an urgent need for combining effective nucleic acid amplification technology with RNA aptamer to achieve highly sensitive and accurate detection of miRNA. For this purpose, a new DNA multi-arm nanostructure-based dual rolling circle transcription machinery for the generation of lighting-up MG RNA aptamers is constructed for label-free and highly sensitive sensing of miRNA-21. In this system, the target miRNA-21 induces a structural transformation of the DNA multi-arm nanostructure probe to recycle miRNA-21 and trigger two independent rolling circle transcription reactions to generate two long RNAs, which can partially hybridize with each other to generate large amounts of complete MG RNA aptamers. These RNA aptamers can associate with organic MG dye to produce significantly enhanced fluorescence signals to accomplish ultrasensitive miRNA-21 detection down to 0.9 fM. In addition, this method exhibits high selectivity to distinguish miRNA-21 even with single nucleotide mismatch, and also has potential application capability to monitor different expression levels of miRNA-21 from different cancer cells. The effective collaboration between MG RNA aptamer and rolling circle transcription reaction makes this fluorescent method show the significant advantages of low background signal, high signal-to-noise ratio and high detection sensitivity. It has great potential to be a promising means to achieve label-free and highly sensitive monitoring of other trace biological markers via a simple change of target sequence.
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Affiliation(s)
- Tiantian Chen
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, PR China
| | - Jirong Yang
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, PR China
| | - Yaqin Tang
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, PR China
| | - Xiaocheng Fan
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, PR China
| | - Wenjiao Zhou
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, PR China.
| | - Bingying Jiang
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, PR China
| | - Ding Wang
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, PR China
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23
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Lavecchia di Tocco F, Botti V, Cannistraro S, Bizzarri AR. Detection of miR-155 Using Peptide Nucleic Acid at Physiological-like Conditions by Surface Plasmon Resonance and Bio-Field Effect Transistor. BIOSENSORS 2024; 14:79. [PMID: 38391998 PMCID: PMC10887097 DOI: 10.3390/bios14020079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/21/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024]
Abstract
MicroRNAs are small ribonucleotides that act as key gene regulators. Their altered expression is often associated with the onset and progression of several human diseases, including cancer. Given their potential use as biomarkers, there is a need to find detection methods for microRNAs suitable for use in clinical setting. Field-effect-transistor-based biosensors (bioFETs) appear to be valid tools to detect microRNAs, since they may reliably quantitate the specific binding between the immobilized probe and free target in solution through an easily detectable electrical signal. We have investigated the detection of human microRNA 155 (miR-155) using an innovative capturing probe constituted by a synthetic peptide nucleic acid (PNA), which has the advantage to form a duplex even at ionic strengths approaching the physiological conditions. With the aim to develop an optimized BioFET setup, the interaction kinetics between miR-155 and the chosen PNA was preliminarily investigated by using surface plasmon resonance (SPR). By exploiting both these results and our custom-made bioFET system, we were able to attain a low-cost, real-time, label-free and highly specific detection of miR-155 in the nano-molar range.
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Affiliation(s)
| | | | | | - Anna Rita Bizzarri
- Biophysics and Nanoscience Centre, DEB, Università della Tuscia, Largo dell’Università, 01100 Viterbo, Italy; (F.L.d.T.); (V.B.); (S.C.)
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24
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Zhang Y, Sun M, Xie J, Chen J, Huang T, Duan WJ, Chen JX, Chen J, Dai Z, Li M. Dual-Signal Amplification Strategy Based on Catalytic Hairpin Assembly and APE1-Assisted Amplification for High-Contrast miRNA Imaging in Living Cells. Anal Chem 2024; 96:910-916. [PMID: 38171356 DOI: 10.1021/acs.analchem.3c05013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Early tumor diagnosis is crucial to successful treatment. Earlier studies have shown that microRNA is a biomarker for early tumor diagnosis. The development of highly sensitive miRNA detection methods, especially in living cells, plays an indispensable role for early diagnosis and treatment of tumor. Although the catalytic hairpin assembly (CHA)-based miRNA analysis strategy is commonly used for disease diagnosis, further application of CHA is hindered due to its low amplification efficiency and low tumor recognition contrast. To address these limitations, we propose a dual-signal amplification strategy based on CHA and APE1-assisted amplification, enabling highly sensitive and high-contrast miRNA imaging. The miR-221 was selected as a target model. This dual-signal amplification strategy has exhibited high amplification efficiency, which could analyze miRNA as low as 21 fM. This strategy also exhibited high specificity, which could distinguish target miRNA and nontarget with single-base differences. Moreover, this method showed significant potential for practical application, as it could successfully distinguish the expression difference of miR-221 in the plasma samples of normal people and patients. Most importantly, the expression level of the APE1 enzyme in tumor cells is higher than that in normal cells, allowing this strategy to sensitively and specifically image miRNA within tumor cells. This proposed method has also been successfully used to indicate fluctuations of intracellular miRNA and to distinguish miRNA expression between normal cells and cancer cells with high contrast. We anticipate that this method will provide fresh insights and can be a powerful tool for tumor diagnosis and treatment based on miRNA analysis.
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Affiliation(s)
- Ya Zhang
- Center of Clinical Laboratory, The First Affiliated Hospital of Jinan University, Guangzhou 510632, P.R. China
| | - Mengxu Sun
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, P.R. China
| | - Juan Xie
- Center of Clinical Laboratory, The First Affiliated Hospital of Jinan University, Guangzhou 510632, P.R. China
| | - Jing Chen
- Center of Clinical Laboratory, The First Affiliated Hospital of Jinan University, Guangzhou 510632, P.R. China
| | - Ting Huang
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, P.R. China
| | - Wen-Jun Duan
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, P.R. China
| | - Jin-Xiang Chen
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, P.R. China
| | - Jun Chen
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, P.R. China
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Qingdao University of Science and Technology, Qingdao 266042, P.R. China
| | - Zong Dai
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, P.R. China
| | - Minmin Li
- Center of Clinical Laboratory, The First Affiliated Hospital of Jinan University, Guangzhou 510632, P.R. China
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25
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Liao L, Gong T, Jiang B, Yuan R, Xiang Y. Target-initiated triplex signal amplification cascades for non-label and sensitive fluorescence sensing of microRNA. Analyst 2024; 149:451-456. [PMID: 38099654 DOI: 10.1039/d3an01928d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The aberrant expression of microRNAs (miRs) in cells is closely linked to the initiation and progression of various diseases. Sensitive monitoring of their level is hence vital for biomedical research and disease diagnosis. Herein, a highly sensitive and non-label fluorescence sensor based on multiple recycling signal amplification cascades is constructed for the detection of miR-21 in human sera. The presence of miR-21 initiates the primer-fueled target recycling process for the generation of many primer/hairpin templates for the subsequent auto-cycling primer extension (APE) amplification cycles, which result in the formation of lots of long-stem hairpins. The enzyme-based cleavage of such hairpins via polymerization/excision cycles further leads to the generation of abundant G-quadruplex strands, which associate with the thioflavin T (ThT) dye to emit remarkably magnified fluorescence for detecting miR-21 in the range of 1 pM-100 nM with a 0.32 pM detection limit without labeling the probes. Besides, the proposed assay can selectively discriminate miR-21 against other control molecules and realize the sensing of low levels of miR-21 in diluted sera. With features of high sensitivity via the triplex signal amplification cycles and simplicity in a non-label homogeneous manner, our miR sensing protocol can be a robust means for detecting various nucleic acids for the early diagnosis of diseases.
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Affiliation(s)
- Lei Liao
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, PR China.
| | - Tingting Gong
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, PR China.
| | - Bingying Jiang
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, PR China.
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
| | - Yun Xiang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
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26
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Yu X, Ding S, Zhao Y, Xu M, Wu Z, Zhao C. A highly sensitive and robust electrochemical biosensor for microRNA detection based on PNA-DNA hetero-three-way junction formation and target-recycling catalytic hairpin assembly amplification. Talanta 2024; 266:125020. [PMID: 37541007 DOI: 10.1016/j.talanta.2023.125020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/06/2023]
Abstract
Robust and sensitive methods for the detection of microRNAs (miRNAs) are crucial in the clinical diagnosis of cancers. In this study, a novel electrochemical biosensor with high sensitivity for miRNA-21 detection is developed, which relies on the formation of a peptide nucleic acid (PNA)-DNA hetero-three-way junction (H3WJ) and target-recycling catalytic hairpin assembly (CHA) amplification. The electroneutral PNA probes are initially immobilized onto a gold electrode to construct the sensor. Upon introduction of miRNA-21, target-recycling CHA is initiated, resulting in abundant double-stranded CHA products. Subsequently, association between the PNA probes and these products leads to the formation of PNA-DNA H3WJs. Consequently, the electrode surface is densely populated with numerous electroactive Ferrocene (Fc) groups, resulting in a significantly amplified current response for highly sensitive detection of miRNA-21 at concentrations as low as 0.15 fM. This approach demonstrates remarkable specificity towards target miRNAs and can be utilized for quantitative monitoring of miRNA-21 expression in human cancer cells. More importantly, the sensor exhibits exceptional stability and shows a significant reduction in background noise during miRNA detection, making this method a highly promising sensing platform for monitoring various miRNA biomarkers to facilitate the diagnosis of diverse cancers.
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Affiliation(s)
- Xiaomeng Yu
- School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Shuyu Ding
- School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China
| | - Yang Zhao
- College of Science and Technology, Ningbo University, Ningbo, 315300, PR China
| | - Mengjia Xu
- Affiliated Cixi Hospital, Wenzhou Medical University, Cixi, 315300, Zhejiang, PR China
| | - Zimiao Wu
- Affiliated Cixi Hospital, Wenzhou Medical University, Cixi, 315300, Zhejiang, PR China
| | - Chao Zhao
- School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China.
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27
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Liao Q, Fu X, Zhuo L, Chen H. An efficient model for predicting human diseases through miRNA based on multiple-types of contrastive learning. Front Microbiol 2023; 14:1325001. [PMID: 38163075 PMCID: PMC10755968 DOI: 10.3389/fmicb.2023.1325001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 11/16/2023] [Indexed: 01/03/2024] Open
Abstract
Multiple studies have demonstrated that microRNA (miRNA) can be deeply involved in the regulatory mechanism of human microbiota, thereby inducing disease. Developing effective methods to infer potential associations between microRNAs (miRNAs) and diseases can aid early diagnosis and treatment. Recent methods utilize machine learning or deep learning to predict miRNA-disease associations (MDAs), achieving state-of-the-art performance. However, the problem of sparse neighborhoods of nodes due to lack of data has not been well solved. To this end, we propose a new model named MTCL-MDA, which integrates multiple-types of contrastive learning strategies into a graph collaborative filtering model to predict potential MDAs. The model adopts a contrastive learning strategy based on topology, which alleviates the damage to model performance caused by sparse neighborhoods. In addition, the model also adopts a semantic-based contrastive learning strategy, which not only reduces the impact of noise introduced by topology-based contrastive learning, but also enhances the semantic information of nodes. Experimental results show that our model outperforms existing models on all evaluation metrics. Case analysis shows that our model can more accurately identify potential MDA, which is of great significance for the screening and diagnosis of real-life diseases. Our data and code are publicly available at: https://github.com/Lqingquan/MTCL-MDA.
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Affiliation(s)
- Qingquan Liao
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
| | - Xiangzheng Fu
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
| | - Linlin Zhuo
- School of Data Science and Artificial Intelligence, Wenzhou University of Technology, Wenzhou, China
| | - Hao Chen
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
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28
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Meng F, Wang Y, Lv X, Feng F, Yang G. Electrochemiluminescent bioassay based on Ru@Zr-BTC-MOFs nanoparticles for determination of let-7a miRNA using the hybridization chain reaction. Mikrochim Acta 2023; 191:23. [PMID: 38091146 DOI: 10.1007/s00604-023-06107-0] [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: 07/10/2023] [Accepted: 11/19/2023] [Indexed: 12/18/2023]
Abstract
Carboxyl-rich tris(4,4'-dicarboxylic acid-2,2'-bipyridyl) ruthenium(II) ([Ru(dcbpy)3]2+) and 1,3,5-phenyl tricarboxylic acid (H3BTC) were used as the organic ligand to synthesize the metal-organic frameworks by a simple one-pot hydrothermal method with ZrCl4 as metal ion source. Subsequently, the excellent electrochemiluminescence (ECL) luminophore (denoted as Ru@Zr-BTC-MOFs) was obtained. The Ru@Zr-BTC-MOFs displayed outstanding ECL properties, and a sensitive ECL bioassay based on Ru@Zr-BTC-MOFs was designed for the detection of let-7a microRNA (miRNA) using hybrid chain reaction (HCR). Under the optimal experimental conditions, the proposed bioassay exhibited a good linear relationship in the range from 50.0 fM to 5.00 × 102 pM with a detection limit of 3.71 fM. Besides, the proposed sensor exhibited satisfactory performance in real samples. The recovery was 91 ~ 108%, and the relative standard deviation was less than 5.6%. It might have potential clinical applications for detecting miRNA in biomedical research and clinical diagnosis. The schematic diagram of the preparation of Ru@Zr-BTC-MOFs (a) and ECL sensor for detecting let -7a (b).
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Affiliation(s)
- Fei Meng
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China
| | - Yisi Wang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China
| | - Xinxin Lv
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China
| | - Fang Feng
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China.
| | - Gongjun Yang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China.
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29
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Cheng X, Li X, Kang Y, Zhang D, Yu Q, Chen J, Li X, Du L, Yang T, Gong Y, Yi M, Zhang S, Zhu S, Ding S, Cheng W. Rapid in situ RNA imaging based on Cas12a thrusting strand displacement reaction. Nucleic Acids Res 2023; 51:e111. [PMID: 37941139 PMCID: PMC10711451 DOI: 10.1093/nar/gkad953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/09/2023] [Accepted: 10/12/2023] [Indexed: 11/10/2023] Open
Abstract
RNA In situ imaging through DNA self-assembly is advantaged in illustrating its structures and functions with high-resolution, while the limited reaction efficiency and time-consuming operation hinder its clinical application. Here, we first proposed a new strand displacement reaction (SDR) model (Cas12a thrusting SDR, CtSDR), in which Cas12a could overcome the inherent reaction limitation and dramatically enhance efficiency through energy replenishment and by-product consumption. The target-initiated CtSDR amplification was established for RNA analysis, with order of magnitude lower limit of detection (LOD) than the Cas13a system. The CtSDR-based RNA in situ imaging strategy was developed to monitor intra-cellular microRNA expression change and delineate the landscape of oncogenic RNA in 66 clinic tissue samples, possessing a clear advantage over classic in situ hybridization (ISH) in terms of operation time (1 h versus 14 h) while showing comparable sensitivity and specificity. This work presents a promising approach to developing advanced molecular diagnostic tools.
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Affiliation(s)
- Xiaoxue Cheng
- The Center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
- Biobank Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Xiaosong Li
- The Center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Yuexi Kang
- The Center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Decai Zhang
- Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510000, PR China
| | - Qiubo Yu
- Molecular Medicine Diagnostic and Testing Center, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Junman Chen
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Xinyu Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Li Du
- The Center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Tiantian Yang
- The Center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Yao Gong
- The Center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Ming Yi
- The Center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Songzhi Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Shasha Zhu
- The Center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Wei Cheng
- The Center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
- Biobank Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
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30
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Chen J, Yu S, Qian Z, He K, Li B, Cao Y, Tang K, Yu S, Wu YX. Target-triggered enzyme-free amplification for highly efficient AND-gated bioimaging in living cells. Analyst 2023; 148:5963-5971. [PMID: 37867382 DOI: 10.1039/d3an01157g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
Rapid, simultaneous, and sensitive detection of biomolecules has important application prospects in disease diagnosis and biomedical research. However, because the content of intracellular endogenous target biomolecules is usually very low, traditional detection methods can't be used for effective detection and imaging, and to enhance the detection sensitivity, signal amplification strategies are frequently required. The hybridization chain reaction (HCR) has been used to detect many disease biomarkers because of its simple operation, good reproducibility, and no enzyme involvement. Although HCR signal amplification methods have been employed to detect and image intracellular biomolecules, there are still false positive signals. Therefore, a target-triggered enzyme-free amplification system (GHCR system) was developed, as a fluorescent AND-gated sensing platform for intracellular target probing. The false positive signals can be well avoided and the accuracy of detection and imaging can be improved by using the design of the AND gate. Two cancer markers, GSH and miR-1246, were used as two orthogonal inputs for the AND gated probe. The AND-gated probe only works when GSH and miR-1246 are the inputs at the same time, and FRET signals can be the output. In addition to the use of AND-gated imaging, FRET-based high-precision ratiometric fluorescence imaging was employed. FRET-based ratiometric fluorescent probes have a higher ability to resist interference from the intracellular environment, they can avoid false positive signals well, and they are expected to have good specificity. Due to the advantages of HCR, AND-gated, and FRET fluorescent probes, the GHCR system exhibited highly efficient AND-gated FRET bioimaging for intracellular endogenous miRNAs with a lower detection limit of 18 pM, which benefits the applications of ratiometric intracellular biosensing and bioimaging and offers a novel concept for advancing the diagnosis and therapeutic strategies in the field of cancer.
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Affiliation(s)
- Jia Chen
- State Key Laboratory Base of Novel Functional Materials and Preparation Science, Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Shengrong Yu
- State Key Laboratory Base of Novel Functional Materials and Preparation Science, Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China.
- Ningbo Zhenhai Institute of Mass Spectrometry, Ningbo, Zhejiang 315211, China
| | - Zhiling Qian
- State Key Laboratory Base of Novel Functional Materials and Preparation Science, Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Kangdi He
- State Key Laboratory Base of Novel Functional Materials and Preparation Science, Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Bingqian Li
- State Key Laboratory Base of Novel Functional Materials and Preparation Science, Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Yuting Cao
- State Key Laboratory Base of Novel Functional Materials and Preparation Science, Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Keqi Tang
- State Key Laboratory Base of Novel Functional Materials and Preparation Science, Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China.
- Ningbo Zhenhai Institute of Mass Spectrometry, Ningbo, Zhejiang 315211, China
| | - Shengjia Yu
- Department of Thoracic Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Yong-Xiang Wu
- State Key Laboratory Base of Novel Functional Materials and Preparation Science, Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Institute of Mass Spectrometry, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, China.
- Ningbo Zhenhai Institute of Mass Spectrometry, Ningbo, Zhejiang 315211, China
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31
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Pagoni M, Cava C, Sideris DC, Avgeris M, Zoumpourlis V, Michalopoulos I, Drakoulis N. miRNA-Based Technologies in Cancer Therapy. J Pers Med 2023; 13:1586. [PMID: 38003902 PMCID: PMC10672431 DOI: 10.3390/jpm13111586] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/02/2023] [Accepted: 11/04/2023] [Indexed: 11/26/2023] Open
Abstract
The discovery of therapeutic miRNAs is one of the most exciting challenges for pharmaceutical companies. Since the first miRNA was discovered in 1993, our knowledge of miRNA biology has grown considerably. Many studies have demonstrated that miRNA expression is dysregulated in many diseases, making them appealing tools for novel therapeutic approaches. This review aims to discuss miRNA biogenesis and function, as well as highlight strategies for delivering miRNA agents, presenting viral, non-viral, and exosomic delivery as therapeutic approaches for different cancer types. We also consider the therapeutic role of microRNA-mediated drug repurposing in cancer therapy.
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Affiliation(s)
- Maria Pagoni
- Research Group of Clinical Pharmacology and Pharmacogenomics, Faculty of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Claudia Cava
- Department of Science, Technology and Society, University School for Advanced Studies IUSS Pavia, 27100 Pavia, Italy;
| | - Diamantis C. Sideris
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece;
| | - Margaritis Avgeris
- Laboratory of Clinical Biochemistry—Molecular Diagnostics, Second Department of Pediatrics, School of Medicine, “P. & A. Kyriakou” Children’s Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Vassilios Zoumpourlis
- Biomedical Applications Unit, Institute of Chemical Biology, National Hellenic Research Foundation (NHRF), 11635 Athens, Greece;
| | - Ioannis Michalopoulos
- Centre of Systems Biology, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece;
| | - Nikolaos Drakoulis
- Research Group of Clinical Pharmacology and Pharmacogenomics, Faculty of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15701 Athens, Greece
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Jing W, Gong F, Liu G, Deng Y, Liu J, Yang W, Sun X, Li Y, Gao J, Zhou X, Ma N. Petal size is controlled by the MYB73/TPL/HDA19-miR159-CKX6 module regulating cytokinin catabolism in Rosa hybrida. Nat Commun 2023; 14:7106. [PMID: 37925502 PMCID: PMC10625627 DOI: 10.1038/s41467-023-42914-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/25/2023] [Indexed: 11/06/2023] Open
Abstract
The size of plant lateral organs is determined by well-coordinated cell proliferation and cell expansion. Here, we report that miR159, an evolutionarily conserved microRNA, plays an essential role in regulating cell division in rose (Rosa hybrida) petals by modulating cytokinin catabolism. We uncover that Cytokinin Oxidase/Dehydrogenase6 (CKX6) is a target of miR159 in petals. Knocking down miR159 levels results in the accumulation of CKX6 transcripts and earlier cytokinin clearance, leading to a shortened cell division period and smaller petals. Conversely, knocking down CKX6 causes cytokinin accumulation and a prolonged developmental cell division period, mimicking the effects of exogenous cytokinin application. MYB73, a R2R3-type MYB transcription repressor, recruits a co-repressor (TOPLESS) and a histone deacetylase (HDA19) to form a suppression complex, which regulates MIR159 expression by modulating histone H3 lysine 9 acetylation levels at the MIR159 promoter. Our work sheds light on mechanisms for ensuring the correct timing of the exit from the cell division phase and thus organ size regulation by controlling cytokinin catabolism.
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Affiliation(s)
- Weikun Jing
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
- School of Food and Medicine, Shenzhen Polytechnic, Shenzhen, Guangdong, 518055, China
| | - Feifei Gong
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Guoqin Liu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yinglong Deng
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Jiaqi Liu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Wenjing Yang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xiaoming Sun
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yonghong Li
- School of Food and Medicine, Shenzhen Polytechnic, Shenzhen, Guangdong, 518055, China
| | - Junping Gao
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xiaofeng Zhou
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China.
| | - Nan Ma
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China.
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Botti V, Lavecchia di Tocco F, Cannistraro S, Bizzarri AR. Hybridization Kinetics of miR-155 on Gold Surfaces as Investigated by Surface Plasmon Resonance and Atomic Force Spectroscopy. ACS OMEGA 2023; 8:38941-38949. [PMID: 37901511 PMCID: PMC10601050 DOI: 10.1021/acsomega.3c03318] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/15/2023] [Indexed: 10/31/2023]
Abstract
miRNAs are short noncoding RNA single strands, with a crucial role in several biological processes. miRNAs are dysregulated in several human diseases, and their detection is an important goal for diagnosis and screening. Innovative biosensors for miRNAs are commonly based on the hybridization process between a miRNA and its corresponding complementary strand (or suitable aptamers) immobilized onto an electrode surface forming a duplex. A detailed description of the hybridization kinetics in working conditions deserves a great deal of interest for the optimization of the biosensing process. Surface plasmon resonance (SPR) and atomic force spectroscopy (AFS) were applied to investigate the hybridization process between miR-155, a multifunctional miRNA that constitutes an important marker overexpressed in several diseases, and its complementary strand (antimiR-155), immobilized on the gold-coated surface of a commercial electrode. Under well-adjusted pH, ionic strength, surface coverage, and concentration, we found that miR-155 has a high affinity for antimiR-155 with kinetics well described by the 1:1 Langmuir model. Both techniques provided an association rate of about 104 M-1 s-1, while a dissociation rate of 10-5 and 10-4 s-1 was assessed by SPR and AFS, respectively. These results allowed us to establish optimized measurement running times for applications in biosensing. An analysis of AFS data also led us to evaluate the binding free energy for the duplex, which was found to be close to that of free molecules in solution. These results could guide in the implementation of fine-tuned working conditions of a biosensor for detecting miRNAs based on correspondent complementary strands.
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Affiliation(s)
- Valentina Botti
- Biophysics and Nanoscience Centre,
DEB, Università della Tuscia, Largo dell’Università, 01100 Viterbo, Italy
| | | | - Salvatore Cannistraro
- Biophysics and Nanoscience Centre,
DEB, Università della Tuscia, Largo dell’Università, 01100 Viterbo, Italy
| | - Anna Rita Bizzarri
- Biophysics and Nanoscience Centre,
DEB, Università della Tuscia, Largo dell’Università, 01100 Viterbo, Italy
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Du Y, Qi Y, Kang Q, Yang X, Xiang H. A fluorescent sensor based on strand displacement amplification and primer exchange reaction coupling for label-free detection of miRNA. Anal Chim Acta 2023; 1279:341780. [PMID: 37827678 DOI: 10.1016/j.aca.2023.341780] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/30/2023] [Accepted: 09/02/2023] [Indexed: 10/14/2023]
Abstract
MicroRNAs (miRNAs) are closely associated with human disease occurrence, including cancers, diabetes, inflammation, heart diseases, and viral infections, and their rapid and accurate detection is vital for the diagnosis and treatment of these diseases. Based on one-step reaction of strand displacement amplification (SDA) and primer exchange reaction (PER), a label-free and highly sensitive miRNA-21 detection strategy was developed. In this strategy, the target miRNA-21 binds directly to the hairpin template, triggering the SDA reaction and generating a large number of single strand DNAs as primers for PER amplification. With the help of polymerase, plenty of G-quadruplex fragments of different lengths were accumulated, and the organic dye thioflavin T selectively binds to these G-quadruplex fragments to produce a strong fluorescent signal. There is a wide detection range in this method, miRNA-21 can be detected in the range of 10 fM - 1 nM, the detection limit is low (1.25 fM). This method has good specificity and can effectively distinguish single-base mismatches of miRNA. In addition, the versatility of the method was validated by changing the target recognition site of SDA template.
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Affiliation(s)
- Yumin Du
- Key Laboratory of Medical Diagnostics, Ministry of Education, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yinxiao Qi
- Key Laboratory of Medical Diagnostics, Ministry of Education, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Qi Kang
- Department of Nuclear Medicine, Huaihe Hospital, Henan University, PR China
| | - Xiaoyan Yang
- Qilu Hospital of Shandong University Dezhou Hospital, Shandong, PR China
| | - Hua Xiang
- Key Laboratory of Medical Diagnostics, Ministry of Education, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
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35
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Liu WJ, Wang LJ, Zhang CY. Progress in quantum dot-based biosensors for microRNA assay: A review. Anal Chim Acta 2023; 1278:341615. [PMID: 37709484 DOI: 10.1016/j.aca.2023.341615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/15/2023] [Accepted: 07/11/2023] [Indexed: 09/16/2023]
Abstract
MicroRNAs (miRNAs) are responsible for post-transcriptional gene regulation, and may function as valuable biomarkers for diseases diagnosis. Accurate and sensitive analysis of miRNAs is in great demand. Quantum dots (QDs) are semiconductor nanomaterials with superior optoelectronic features, such as high quantum yield and brightness, broad absorption and narrow emission, long fluorescence lifetime, and good photostability. Herein, we give a comprehensive review about QD-based biosensors for miRNA assay. Different QD-based biosensors for miRNA assay are classified by the signal types including fluorescent, electrochemical, electrochemiluminescent, and photoelectrochemical outputs. We highlight the features, principles, and performances of the emerging miRNA biosensors, and emphasize the challenges and perspectives in this field.
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Affiliation(s)
- Wen-Jing Liu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Li-Juan Wang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China.
| | - Chun-Yang Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China.
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36
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Nie L, Zeng X, Hongbo L, Wang S, Lu Z, Yu R. Entropy-driven DNA circuit with two-stage strand displacement for elegant and robust detection of miRNA let-7a. Anal Chim Acta 2023; 1269:341392. [PMID: 37290851 DOI: 10.1016/j.aca.2023.341392] [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: 12/27/2022] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 06/10/2023]
Abstract
MicroRNAs (miRNAs) research in cancer diagnosis is expanding, on account of miRNAs were demonstrated to be key indicator of gene expression and hopeful candidates for biomarkers. In this study, a stable miRNA-let-7a fluorescent biosensor was successfully designed based on an exonuclease Ⅲ-assisted two-stage strand displacement reaction (SDR). First, an entropy-driven SDR containing a three-chain structure of the substrate is used in our designed biosensor, leading to reduce the reversibility of the target recycling process in each step. The target acts on the first stage to start the entropy-driven SDR, which generates the trigger used to stimulate the exonuclease Ⅲ-assisted SDR in the second stage. At the same time, we design a SDR one-step amplification strategy as a comparison. Expectly, this developed two-stage strand displacement system has a low detection limit of 25.0 pM as well as a broad detection range of 4 orders of magnitude, making it more sensitive than the SDR one-step sensor, whose detection limit is 0.8 nM. In addition, this sensor has high specificity across members of the miRNA family. Therefore, we can take advantage of this biosensor to promote miRNA research in cancer diagnosis sensing systems.
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Affiliation(s)
- Lanxin Nie
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China
| | - Xiaogang Zeng
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China
| | - Li Hongbo
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China; Key Laboratory of Energy Catalysis and Conversion of Nanchang, Nanchang, 330022, PR China; State Key Laboratory for Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, PR China.
| | - Suqin Wang
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China
| | - Zhanghui Lu
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China; Key Laboratory of Energy Catalysis and Conversion of Nanchang, Nanchang, 330022, PR China.
| | - Ruqin Yu
- State Key Laboratory for Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, PR China
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37
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Song Z, Zhang QY, Li JJ, Su JL, Liu YH, Yang GJ, Wang HS. Visual and Electrochemical Detection of let-7a: A Tumor Suppressor and Biomarker. J Med Chem 2023. [PMID: 37248170 DOI: 10.1021/acs.jmedchem.3c00499] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Let-7a, a type of low-expressed microRNAs in cancer cells, has been investigated as a promising biomarker and therapeutic target for tumor suppression. Developing simple and sensitive detection methods for let-7a is important for cancer diagnosis and treatment. In this work, the hybridization chain reaction (HCR) was initiated by let-7a via two hairpin primers (H1 and H2). After the HCR, the remaining hairpin H1 was further detected by lateral flow assay (LFA) and electrochemical impedance spectroscopy. For LFA, biotin-modified H1(bio-H1) and free H2 were used for HCR. With the decrease of let-7a concentration, the color of T line gradually increased. As for electrochemical methods, the H1'-AuNP-modified electrode was used for detection of bio-H1 based on the difference of impedance (ΔRct) detected without and with different concentrations of let-7a participating in the HCR. This method could detect let-7a in the range of 10.0 fM and 1.0 nM with detection limits of 4.2 fM.
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Affiliation(s)
- Zhen Song
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Qiang-Yan Zhang
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Jia-Jing Li
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Jing-Lian Su
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Yuan-Hua Liu
- Department of Chemotherapy, Nanjing Medical University Affiliated Cancer Hospital, Cancer Institute of Jiangsu Province, Nanjing 210009, P. R. China
| | - Gong-Jun Yang
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, P. R. China
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), China Pharmaceutical University, Nanjing 210009, P. R. China
| | - Huai-Song Wang
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, P. R. China
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), China Pharmaceutical University, Nanjing 210009, P. R. China
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38
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Ho V, Baker JR, Willison KR, Barnes PJ, Donnelly LE, Klug DR. Single cell quantification of microRNA from small numbers of non-invasively sampled primary human cells. Commun Biol 2023; 6:458. [PMID: 37100999 PMCID: PMC10133449 DOI: 10.1038/s42003-023-04845-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 04/17/2023] [Indexed: 04/28/2023] Open
Abstract
Expression levels of microRNAs (miRNAs) in single cells are low and conventional miRNA detection methods require amplification that can be complex, time-consuming, costly and may bias results. Single cell microfluidic platforms have been developed; however, current approaches are unable to absolutely quantify single miRNA molecules expressed in single cells. Herein, we present an amplification-free sandwich hybridisation assay to detect single miRNA molecules in single cells using a microfluidic platform that optically traps and lyses individual cells. Absolute quantification of miR-21 and miR-34a molecules was achieved at a single cell level in human cell lines and validated using real-time qPCR. The sensitivity of the assay was demonstrated by quantifying single miRNA molecules in nasal epithelial cells and CD3+ T-cells, as well as nasal fluid collected non-invasively from healthy individuals. This platform requires ~50 cells or ~30 µL biofluid and can be extended for other miRNA targets therefore it could monitor miRNA levels in disease progression or clinical studies.
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Affiliation(s)
- Vanessa Ho
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse Street, London, SW3 6LY, UK
| | - Jonathan R Baker
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse Street, London, SW3 6LY, UK
| | - Keith R Willison
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
| | - Peter J Barnes
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse Street, London, SW3 6LY, UK
| | - Louise E Donnelly
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse Street, London, SW3 6LY, UK.
| | - David R Klug
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
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39
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Roychoudhury A, Dear JW, Kersaudy-Kerhoas M, Bachmann TT. Amplification-free electrochemical biosensor detection of circulating microRNA to identify drug-induced liver injury. Biosens Bioelectron 2023; 231:115298. [PMID: 37054598 DOI: 10.1016/j.bios.2023.115298] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/23/2023] [Accepted: 04/04/2023] [Indexed: 04/15/2023]
Abstract
Drug-induced liver injury (DILI) is a major challenge in clinical medicine and drug development. There is a need for rapid diagnostic tests, ideally at point-of-care. MicroRNA 122 (miR-122) is an early biomarker for DILI which is reported to increase in the blood before standard-of-care markers such as alanine aminotransferase activity. We developed an electrochemical biosensor for diagnosis of DILI by detecting miR-122 from clinical samples. We used electrochemical impedance spectroscopy (EIS) for direct, amplification free detection of miR-122 with screen-printed electrodes functionalised with sequence specific peptide nucleic acid (PNA) probes. We studied the probe functionalisation using atomic force microscopy and performed elemental and electrochemical characterisations. To enhance the assay performance and minimise sample volume requirements, we designed and characterised a closed-loop microfluidic system. We presented the EIS assay's specificity for wild-type miR-122 over non-complementary and single nucleotide mismatch targets. We successfully demonstrated a detection limit of 50 pM for miR-122. Assay performance could be extended to real samples; it displayed high selectivity for liver (miR-122 high) comparing to kidney (miR-122 low) derived samples extracted from murine tissue. Finally, we successfully performed an evaluation with 26 clinical samples. Using EIS, DILI patients were distinguished from healthy controls with a ROC-AUC of 0.77, a comparable performance to qPCR detection of miR-122 (ROC-AUC: 0.83). In conclusion, direct, amplification free detection of miR-122 using EIS was achievable at clinically relevant concentrations and in clinical samples. Future work will focus on realising a full sample-to-answer system which can be deployed for point-of-care testing.
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Affiliation(s)
- Appan Roychoudhury
- Infection Medicine, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
| | - James W Dear
- Centre for Cardiovascular Science, University of Edinburgh, The Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Maïwenn Kersaudy-Kerhoas
- Infection Medicine, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK; Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, EH14 4AS, UK
| | - Till T Bachmann
- Infection Medicine, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK.
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40
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Studies on the application of single-stranded DNA and PNA probes for electrochemical detection of miRNA 141. Bioelectrochemistry 2023; 150:108363. [PMID: 36608369 DOI: 10.1016/j.bioelechem.2022.108363] [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: 04/06/2022] [Revised: 12/09/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022]
Abstract
The abnormal concentration of microRNAs (miRNAs) can be associated with occurrence of various diseases including cancer, cardiovascular and neurodegenerative, hence they can be considered as potential biomarkers. An attractive approach could be the application of electrochemical methods, particularly where hybridization event between single-stranded deoxyribonucleic acid (ssDNA) or peptide-nucleic acid (PNA) with miRNA strand happens. Recently, the use of various nanomaterials such as gold nanoparticles, graphene oxide, quantum dots as well as catalyzed hairpin assembly or hybridization chain reaction were proposed to further enhance the performance of elaborated sensors. Herein, we present the studies on selection of receptor layer composition for detection of miRNA 141. The possibility of formation of receptor layer and further duplex monolayer between ssDNA or PNA with miRNA was analyzed by atomic force microscopy (AFM) technique. The interaction of ssDNA and PNA probes with miRNA was further verified using surface plasmon resonance (SPR) and quartz - crystal microbalance (QCM) techniques. On the basis of impedance spectroscopy it was shown that the use of unlabelled ssDNA as receptor layer provided 0.1 pM detection limit. This shows that proposed biosensor that is simple in preparation and use is an attractive alternative to other recently presented approaches.
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41
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Liu J, Hu X, Hu Y, Chen P, Xu H, Hu W, Zhao Y, Wu P, Liu GL. Dual AuNPs detecting probe enhanced the NanoSPR effect for the high-throughput detection of the cancer microRNA21 biomarker. Biosens Bioelectron 2023; 225:115084. [PMID: 36693286 DOI: 10.1016/j.bios.2023.115084] [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: 07/29/2022] [Revised: 09/18/2022] [Accepted: 01/14/2023] [Indexed: 01/18/2023]
Abstract
The microRNA21 (miR-21), a specific tumor biomarker, is crucial for the diagnosis of several cancer types, and investigation of its overexpression pattern is important for cancer diagnosis. Herein, we report a low-cost, rapid, ultrasensitive, and convenient biosensing strategy for the detection of miR-21 using a nanoplasmonic array chip coupled with gold nanoparticles (AuNPs). This sensing platform combines the surface plasmon resonance effect of nanoplasmonics (NanoSPR) and the localized surface plasmon resonance (LSPR) effect, which allows the real-time monitoring of the subtle optical density (OD) changes caused by the variations in the dielectric constant in the process of the hybridization of the target miRNA. Using this method, the miRNA achieves a broad detection range from 100 aM to 1 μM, and with a limit of detection (LoD) of 1.85 aM. Furthermore, this assay also has a single-base resolution to discriminate the highly homologous miRNAs. More importantly, this platform has high throughput characteristics (96 samples can be detected simultaneously). This strategy exhibits more than 86.5 times enhancement in terms of sensitivity compared to that of traditional biosensors.
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Affiliation(s)
- Juxiang Liu
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luo Yu Road, Wuhan, 430074, China
| | - Xulong Hu
- Institute of Geophysics and Geomatics, China University of Geosciences, Wuhan, 430074, China
| | - Yinxia Hu
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Ping Chen
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luo Yu Road, Wuhan, 430074, China
| | - Hao Xu
- Liangzhun (Shanghai) Industrial Co. Ltd., Shanghai, 200336, China
| | - Wenjun Hu
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luo Yu Road, Wuhan, 430074, China
| | - Yanteng Zhao
- Department of Blood Transfusion, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
| | - Ping Wu
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luo Yu Road, Wuhan, 430074, China; School of Pharmacy, Wenzhou Medical University, Wenzhou, 325035, China; Research Units of Clinical Translation of Cell Growth Factors and Diseases Research, Chinese Academy of Medical Science, Wenzhou, 325035, China.
| | - Gang L Liu
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luo Yu Road, Wuhan, 430074, China.
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42
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Zhang Q, Zhang X, Zou X, Ma F, Zhang CY. CRISPR/Cas-Based MicroRNA Biosensors. Chemistry 2023; 29:e202203412. [PMID: 36477884 DOI: 10.1002/chem.202203412] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/03/2022] [Accepted: 12/07/2022] [Indexed: 12/12/2022]
Abstract
As important post-transcriptional regulators, microRNAs (miRNAs) play irreplaceable roles in diverse cellular functions. Dysregulated miRNA expression is implicated in various diseases including cancers, and thus miRNAs have become the valuable biomarkers for disease monitoring. Recently, clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR/Cas) system has shown great promise for the development of next-generation biosensors because of its precise localization capability, good fidelity, and high cleavage activity. Herein, we review recent advance in development of CRISPR/Cas-based biosensors for miRNA detection. We summarize the principles, features, and performance of these miRNA biosensors, and further highlight the remaining challenges and future directions.
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Affiliation(s)
- Qian Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, P.R. China
| | - Xinyi Zhang
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Zhongshan, 528458, P.R. China
| | - Xiaoran Zou
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, P.R. China
| | - Fei Ma
- School of Chemistry and Chemical Engineering, Southeast University Institution, Nanjing, 211189, P.R. China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, P.R. China
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Song C, Liu C, Chen J, Ma Z, Tang S, Pan R, Suo X, Yan Z, Lee HK, Shen W. Self-Generation of Distinguishable Fluorescent Probes via a One-Pot Process for Multiple MicroRNA Detection by Liquid Chromatography. Anal Chem 2023; 95:4113-4121. [PMID: 36787427 DOI: 10.1021/acs.analchem.2c04941] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
To address the challenge of signal production and separation for multiple microRNA (miRNA) detection, in this work, a "one-pot" process to self-generate distinguishable fluorescent probes was developed. Based on a long and short probe amplification strategy, the generated G-quadruplex fluorescent dye-free probes can be separated and detected by a high-performance liquid chromatography-fluorescence platform. The free hairpin probes enriched in guanine with different lengths and base sequences were designed and could be opened by the target miRNAs (miRNA-10b, miRNA-21, and miRNA-210). Cleaved G-quadruplex probes with fluorescent signal could be generated in a one-pot process after a duplex-specific nuclease-based cleavage, and the detection of multiple miRNAs could be realized in one run. No solid nanomaterials were applied in the assay, which avoided the blocking of the column. Moreover, without modification of expensive fluorescein, the experimental cost was greatly reduced. The one-pot reaction process also eliminated tedious preparation steps and suggested feasibility of automation. The limits of detection of miRNA-10b, miRNA-21, and miRNA-210 were 2.19, 2.20, and 2.75 fM, respectively. Notably, this method was successfully applied to multiplex detection of miRNAs in serum samples from breast cancer patients within 30 min.
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Affiliation(s)
- Chang Song
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu Province, P. R. China
| | - Chang Liu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu Province, P. R. China
| | - Jisen Chen
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu Province, P. R. China
| | - Ziyu Ma
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu Province, P. R. China
| | - Sheng Tang
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu Province, P. R. China
| | - Ruirong Pan
- Affiliated Hospital of Jiangsu University, Zhenjiang 212001, Jiangsu Province, P. R. China
| | - Xiaocen Suo
- Testing Center of Yangzhou University, Yangzhou 225000, Jiangsu Province, P. R. China
| | - Zuowei Yan
- ACD/Labs, (Advanced Chemistry Development, Inc.), Pudong 201210, Shanghai, P. R. China
| | - Hian Kee Lee
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu Province, P. R. China.,Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Wei Shen
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu Province, P. R. China
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44
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Li R, Li F, Zhang Y, He Y, Wang Y, Wang F. Miniature Hierarchical DNA Hybridization Circuit for Amplified Multiplexed MicroRNA Imaging. Anal Chem 2023; 95:3848-3855. [PMID: 36745869 DOI: 10.1021/acs.analchem.2c05373] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Accurate diagnosis requires the development of multiple-guaranteed DNA circuits. Nevertheless, for reliable multiplexed molecular imaging, existing DNA circuits are limited by poor cell-delivering homogeneity due to their cumbersome and dispersive reactants. Herein, we developed a compact-yet-efficient hierarchical DNA hybridization (HDH) circuit for in situ simultaneous analysis of multiple miRNAs, which could be further exploited for specifically discriminating cancer cells from normal ones. By integrating the traditional hybridization chain reaction and catalytic hairpin assembly reactants into two highly organized hairpins, the HDH circuit is fitted with condensed components and multiple response domains, thus permitting the programmable multiple microRNA-guaranteed sequential activations and the localized cascaded signal amplification. The synergistic multi-recognition and amplification features of the HDH circuit facilitate the magnified detection of multiplex endogenous miRNAs in living cells. The in vitro and cellular imaging experimental results revealed that the HDH circuit displayed a reliable sensing performance with high selective cell-identification capacity. We anticipate that this compact design can provide a powerful toolkit for accurate diagnostics and pathological evolution.
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Affiliation(s)
- Ruomeng Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Fengzhe Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Yanping Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Yuqiu He
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Yushi Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P.R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P.R. China.,Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan 430072, P.R. China
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45
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Isothermal exponential amplification reactions triggered by circular templates (cEXPAR) targeting miRNA. Mol Biol Rep 2023; 50:3653-3659. [PMID: 36807240 DOI: 10.1007/s11033-023-08291-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 01/17/2023] [Indexed: 02/21/2023]
Abstract
BACKGROUND Isothermal exponential amplification reaction (EXPAR) is an emerging amplification technique that is most frequently used to amplify microRNA (miRNA). However, EXPAR also exhibits non-specific background amplification in the absence of the targeted sequence, which limits the attainable assay sensitivity of EXPAR. METHODS AND RESULTS A novel modified isothermal EXPAR based on circular amplification templates (cEXPAR) was developed in this study. The circular template consists of two same linear fragments that complement the target sequence, and these two linear fragments are separated by two nicking agent recognition sequences (NARS). Compared with the linear structure template, this circular template allows DNA or RNA fragments to be randomly paired with two repeated sequences and can be successfully amplified. This reaction system developed in this study could rapidly synthesize short oligonucleotide fragments (12-22 bp) through simultaneous nicking and displacement reactions. Highly sensitive chain reactions can be specifically triggered by as low as a single copy of target molecule, and non-specific amplification can be effectively eliminated in this optimized system. Moreover, the proposed approach applied to miRNA test can discriminate single-nucleotide variations between miRNAs. CONCLUSION The newly developed cEXPAR assay provides a useful alternative tool for rapid, sensitive, and highly specific detection of miRNAs.
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Xu L, Hou S, Huang X, Wang M, Li C, Dong N, Lin Z. Highly sensitive homogeneous electrochemiluminescence biosensor for microRNA-155 based on enzyme-free cascade signal amplification and magnetic assisted enrichment. J Electroanal Chem (Lausanne) 2023. [DOI: 10.1016/j.jelechem.2023.117274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
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47
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Han Y, Hu H, Yu L, Zeng S, Min JZ, Cai S. A duplex-specific nuclease (DSN) and catalytic hairpin assembly (CHA)-mediated dual amplification method for miR-146b detection. Analyst 2023; 148:556-561. [PMID: 36562478 DOI: 10.1039/d2an01759h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A novel method for detecting miRNA has been developed using a combination of duplex-specific nuclease signal amplification (DSNSA) and a catalytic hairpin assembly (CHA). In this work, a biotinylated trigger release (BTR) probe with a biotin group at the 3'-end and a CHA reaction sequence trigger as an initiator (catalyst I) at the 5'-end was designed to hybridize target miRNA. The DSN enzyme was introduced to initiate the DSNSA. The miRNA was released to consume more BTR probes and amplify the signals. Subsequently, streptavidin-coated magnetic beads (SA-MBs) were added to the DSNSA reaction solution to remove excess BTR probes that did not hybridize with miRNA, which would then separate BTR probes and catalyst-I, to ensure detection with high selectivity and sensitivity. The catalyst-I remaining in the solution could trigger the CHA reaction to enable signal amplification in the second step. The developed method exhibits a sensitive detection limit and excellent selectivity in identifying a high sequence homology among family members.
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Affiliation(s)
- Yu Han
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, Department of Pharmaceutical Analysis, College of Pharmacy Yanbian University, Yanji 133002, Jilin Province, China. .,Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Haihong Hu
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Lushan Yu
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Jun Zhe Min
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, Department of Pharmaceutical Analysis, College of Pharmacy Yanbian University, Yanji 133002, Jilin Province, China.
| | - Sheng Cai
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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Wang Q, He Y, He S, Yu S, Jiang Y, Wang F. An entropy-driven DNA nanomachine for microRNA detection using a personal glucose meter. Chem Commun (Camb) 2023; 59:1345-1348. [PMID: 36647734 DOI: 10.1039/d2cc06479k] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Herein, we developed a reliable and portable biosensor (TDR-PGM nanomachine) for the sensitive detection of microRNA by integrating an efficient toehold-mediated strand displacement reaction module (TDR) and a personal glucose meter (PGM). The system provides a versatile methodology for microRNA detection in real samples and holds broad prospects in point-of-care diagnosis.
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Affiliation(s)
- Qing Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430072, P. R. China.
| | - Yuqiu He
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430072, P. R. China.
| | - Shizhen He
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430072, P. R. China.
| | - Shanshan Yu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430072, P. R. China.
| | - Yuqian Jiang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430072, P. R. China.
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430072, P. R. China. .,Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, Hubei, 430072, P. R. China
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Liu L, Wang X, Li Y, Liu J. Evaluation of probe-based ultra-sensitive detection of miRNA using a single-molecule fluorescence imaging method: miR-126 used as the model. Front Bioeng Biotechnol 2023; 11:1081488. [PMID: 36761298 PMCID: PMC9902880 DOI: 10.3389/fbioe.2023.1081488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/09/2023] [Indexed: 01/25/2023] Open
Abstract
This study proposed a new detection method of miRNA based on single-molecule fluorescence imaging, a method that has been successfully developed to measure the light signal of individual molecules labeled with proper fluorophores. We designed probes 1 and 2 to be labeled with Cy5 dye and BHQ2 quencher at the 3'terminals, respectively. Probe 1 consisted of two parts, the longer part complementary to miR-126 and the shorter part complementary to probe 2. After hybridization, miR-126 bound to probe 1 by replacing probe 2 and assembled into a double-stranded DNA with probe 1. The abundance of miR-126 was quantified by detecting image spots of Cy5 dye molecules from probe 1/miR-126 complexes. MiR-126 single-molecule imaging method showed high specificity and sensitivity for miR-126 with a detection limit of 50 fM. This method has good selectivity for miR-126 detection with 2.1-fold, 8.8-fold, and 26.9-41.3-fold higher than those of single-base mismatched miR-126, three-base mismatched miR-126 and non-complementary miRNAs (miR-221, miR-16, miR-143 and miR-141). The method to detect miR-126 was validated in breast cancer cell lines. Our single-molecule miRNA imaging showed high specificity and sensitivity for miRNAs. By changing the base pair sequence of the designed probes, our method would be able to detect different miRNAs.
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Affiliation(s)
- Longkai Liu
- School of Pharmacy, Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xiaoning Wang
- Department of Pharmacy, Qingdao Municipal Hospital, Qingdao, China,*Correspondence: Xiaoning Wang, ; Yan Li, ; Jianwei Liu,
| | - Yan Li
- School of Pharmacy, Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai, China,*Correspondence: Xiaoning Wang, ; Yan Li, ; Jianwei Liu,
| | - Jianwei Liu
- School of Pharmacy, Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai, China,*Correspondence: Xiaoning Wang, ; Yan Li, ; Jianwei Liu,
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50
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Ultrasensitive visual detection of miRNA-143 using a CRISPR/Cas12a-based platform coupled with hyperbranched rolling circle amplification. Talanta 2023; 251:123784. [DOI: 10.1016/j.talanta.2022.123784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/21/2022] [Accepted: 07/24/2022] [Indexed: 11/20/2022]
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