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Sun Y, Peng Y, Sun Y, Xu D. An enzyme-free and label-free multiplex detection of miRNAs by entropy-driven circuit coupled with capillary electrophoresis. Talanta 2024; 281:126850. [PMID: 39276573 DOI: 10.1016/j.talanta.2024.126850] [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: 06/04/2024] [Revised: 08/23/2024] [Accepted: 09/07/2024] [Indexed: 09/17/2024]
Abstract
MicroRNAs (miRNAs) are currently recognized as important biomarkers for the early diagnosis and prognostic treatment of cancer. Herein, we developed a simple and label-free method for the multiplex detection of miRNAs, based on entropy-driven circuit (EDC) amplification and non-gel sieving capillary electrophoresis-LED induced fluorescence detection (NGCE-LEDIF) platform. In this system, three different lengths of fuel chains were designed to catalyze three EDC, targeting miRNA-21, miRNA-155, and miRNA-10b, respectively. In the presence of target miRNA, the EDC cycle amplification reaction was triggered, generating numerous stable double-strands products (F-DNA/L-DNA). Since the three miRNAs correspond to three different lengths of F-DNA/L-DNA, they can be easily isolated and detected by NGCE. This strategy has good sensitivity, with detection limits of 68 amol, 292.2 amol, and 394 amol for miRNA-21, miRNA-155, and miRNA-10b, respectively. Additionally, this method has good specificity and can effectively distinguish single-base mismatches of miRNA. The recoveries of the three miRNAs in deproteinized healthy human serum ranged from 91.28 % to 108.4 %, with a relative standard deviation (RSD) of less than 7.9 %. This method was further applied to detect cellular miRNAs in human breast cancer (MCF-7) cell extracts, revealing an up-regulation of miRNA-21, miRNA-155, and miRNA-10b in MCF-7 cells. The successful spiked recovery in human serum and RNA extraction from MCF-7 cells underscores the practicality of this method. Therefore, this strategy has broad application prospects in biomedical research.
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Affiliation(s)
- Yanyan Sun
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, No 163, Xianlin Avenue, Nanjing, 210023, PR China
| | - Yufei Peng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, No 163, Xianlin Avenue, Nanjing, 210023, PR China
| | - Yunlong Sun
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, No 163, Xianlin Avenue, Nanjing, 210023, PR China
| | - Danke Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, No 163, Xianlin Avenue, Nanjing, 210023, PR China.
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2
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Tian Z, Luo J, Zhang C, Li Y, Hu S, Li Y. Photonic crystal-enhanced fluorescence biosensor with logic gate operation based on one-pot cascade amplification DNA circuit for enzyme-free and ultrasensitive analysis of two microRNAs. Talanta 2024; 277:126428. [PMID: 38897009 DOI: 10.1016/j.talanta.2024.126428] [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: 02/20/2024] [Revised: 05/18/2024] [Accepted: 06/13/2024] [Indexed: 06/21/2024]
Abstract
The development of sensitive and efficient analytical methods for multiple biomarkers is crucial for cancer screening at early stage. MicroRNAs (miRNAs) are a kind of biomarkers with diagnostic potential for cancer. However, the ultrasensitive and logical analysis of multiple miRNAs with simple operation still faces some challenges. Herein, a photonic crystal (PC)-enhanced fluorescence biosensor with logic gate operation based on one-pot cascade amplification DNA circuit was developed for enzyme-free and ultrasensitive analysis of two cancer-related miRNAs. The fluorescence biosensor was performed by biochemical recognition amplification module (BCRAM) and physical enhancement module (PEM) to achieve logical and sensitive detection. In the BCRAM, one-pot cascade amplification circuit consisted of the upstream parallel entropy-driven circuit (EDC) and the downstream shared catalytic hairpin assembly (CHA). The input of target miRNA would trigger each corresponding EDC, and the parallel EDCs released the same R strand for triggering subsequent CHA; thus, the OR logic gate was obtained with minimization of design and operation. In the PEM, photonic crystal (PC) array was prepared easily for specifically enhancing the fluorescence output from BCRAM by the optical modulation capabilities; meanwhile, the high-throughput signal readout was achieved by microplate analyzer. Benefiting from the integrated advantages of two modules, the proposed biosensor achieved ultrasensitive detection of two miRNAs with easy logic gate operation, obtaining the LODs of 8.6 fM and 6.7 fM under isothermal and enzyme-free conditions. Hence, the biosensor has the advantages of high sensitivity, easy operation, multiplex and high-throughput analysis, showing great potential for cancer screening at early stage.
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Affiliation(s)
- Ziyi Tian
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jie Luo
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Chuyan Zhang
- Precision Medicine Center, Medical Equipment Innovation Research Center, Med-X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yongru Li
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Shunming Hu
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yongxin Li
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
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3
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Fan Z, Zhou J, Shu Q, Dong Y, Li Y, Zhang T, Bai G, Yu H, Lu F, Li J, Zhao X. Aptamer-bivalent-cholesterol-mediated proximity entropy-driven exosomal protein reporter for tumor diagnosis. Biosens Bioelectron 2024; 251:116104. [PMID: 38368644 DOI: 10.1016/j.bios.2024.116104] [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: 11/19/2023] [Revised: 02/03/2024] [Accepted: 02/05/2024] [Indexed: 02/20/2024]
Abstract
Exosomal proteins from the parental cells are considered to be promising biomarker sets for precise tumor diagnostics and monitoring. However, the accurate quantitative analysis of low-abundance exosomal proteins remains challenging due to the heterogeneity of clinical samples. Here, we standardized the exosomal concentration with a fluorogenic membrane probe and developed an aptamer-bivalent-cholesterol-mediated Proximity Entropy-driven Exosomal Protein Reporter (PEEPR). The proposed PEEPR enables the in-situ analysis of multiple exosomal proteins by integrating bivalent cholesterol anchor (exosomal lipid bilayer) and aptamer (exosomal proteins) with a proximity entropy-driven circuit. Based on this strategy, we successfully achieved detection limits of 3.9 pg/mL exosomal GPC-3 and 3.4 pg/mL exosomal PD-L1. Notably, the standardization of exosome concentrations is designed to avoid errors due to biological heterogeneity. The results showed that evaluating the levels of exosomal GPC-3 and PD-L1 in clinical samples via this strategy could accurately differentiate healthy individuals, hepatitis B patients, and hepatocellular carcinoma patients. In summary, PEEPR is a promising clinical diagnostic strategy for the quantitative analysis of a variety of tumor-associated exosomal proteins for the precise diagnosis and personalized treatment monitoring of tumors.
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Affiliation(s)
- Zhichao Fan
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Jie Zhou
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China; Department of Laboratory Medicine, Xingcheng Special Service Sanatorium of Strategic Support Force, Huludao, 125100, China
| | - Qiuxia Shu
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Yan Dong
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Yingxue Li
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Tingrui Zhang
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Gang Bai
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China; School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Hua Yu
- Department of General Surgery, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China
| | - Fanghao Lu
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Jianjun Li
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China.
| | - Xiang Zhao
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China.
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Yang H, Dong Q, Xu D, Feng X, He P, Song W, Zhou H. An "off-on-off" type electrochemical biosensor for detecting multiple biomarkers with DNAzyme-mediated entropy-driven catalytic and DSN enzyme-assisted recycling amplification. Anal Chim Acta 2023; 1283:341978. [PMID: 37977795 DOI: 10.1016/j.aca.2023.341978] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/06/2023] [Accepted: 10/27/2023] [Indexed: 11/19/2023]
Abstract
In this work, an intelligent and versatile electrochemical biosensor was constructed to detect two types of biomarkers by utilizing "off-on-off" switching. Firstly, human apurinic/apyrimidinic endonuclease1(APE1) mediated specific cleavage of the AP site, initiating activation DNAzyme and entropy-driven catalytic (EDC) reaction. Subsequently, large amounts of ferrocene labeled single-stranded DNA was released and captured with a remarkable electrochemical signal, achieving "off-on" state. In the presence of microRNA 21(miRNA-21), the DNA/RNA heteroduplexes were formed and cleaved by duplex-specific nuclease (DSN) with recovery the target miRNA-21, causing the current suppression in an "on-off" state. This sensor achieved highly sensitive detection of APE1 and miRNA-21 with a detection limit of 2.5 mU·mL-1 and 1.33 × 10-20 M, respectively, and also exhibited good selectivity, reproducibility and stability. Moreover, this proposed biosensor made it possible to realize analysis of multiple types of biomarkers on a single sensor, which improved utilization and analysis efficiency compared to traditional sensors. This study might open a new avenue to design multifunctional sensing platform for biological research and early disease diagnosis.
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Affiliation(s)
- Huan Yang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, PR China; Shandong Key Laboratory of Biochemical Analysis, PR China; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, PR China; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Qi Dong
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, PR China; Shandong Key Laboratory of Biochemical Analysis, PR China; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, PR China; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Dandan Xu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, PR China; Shandong Key Laboratory of Biochemical Analysis, PR China; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, PR China; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Xinmiao Feng
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, PR China; Shandong Key Laboratory of Biochemical Analysis, PR China; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, PR China; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Peng He
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, PR China; Shandong Key Laboratory of Biochemical Analysis, PR China; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, PR China; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Weiling Song
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, PR China; Shandong Key Laboratory of Biochemical Analysis, PR China; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, PR China; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
| | - Hong Zhou
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, PR China; Shandong Key Laboratory of Biochemical Analysis, PR China; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, PR China; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
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5
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Ma H, Chen L, Lv J, Yan X, Li Y, Xu G. The rate-limiting procedure of 3D DNA walkers and their applications in tandem technology. Chem Commun (Camb) 2023; 59:10330-10342. [PMID: 37615403 DOI: 10.1039/d3cc02597g] [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: 08/25/2023]
Abstract
DNA walkers, artificial dynamic DNA nanomachines, can mimic actin to move rapidly along a predefined nucleic acid track. They can generally be classified as one- (1D), two- (2D), and three-dimensional (3D) DNA walkers. In particular, 3D DNA walkers demonstrate amazing sustainable walking ability, strong enrichment ability, and fantastic signal amplification ability. In light of these, 3D DNA walkers have been widely used in fields such as biosensors, bioanalysis and cell imaging. Most notably, the strong compatibility of 3D DNA walkers allows their integration with a range of amplification strategies, effectively enhancing signal transduction and amplifying biosensor sensing signals. Herein, we first systematically expound the walking principle of the 3D walkers in this review. Then, by presenting representative examples, the research direction of 3D walkers in recent years is discussed. Furthermore, we also categorize and evaluate diverse tandem signal amplification strategies in 3D walkers. Finally, the challenges and development trends of 3D DNA walkers in the emerging field of analysis are carefully discussed. It is believed that this work can provide new ideas for researchers to quickly understand 3D DNA walkers and their applications in diverse biosensors.
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Affiliation(s)
- Hongmin Ma
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China.
| | - Long Chen
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China.
| | - Jingnan Lv
- The Second Affiliated People's Hospital of Soochow University, Suzhou 215008, China
| | - Xiaoyu Yan
- Guang'an Vocational & Technical College, Sichuan 638000, China
| | - Yonghao Li
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China.
| | - Guoxin Xu
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China.
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Fan Z, Weng Q, Li Y, Zeng T, Wang J, Zhang H, Yu H, Dong Y, Zhao X, Li J. Accurate and rapid quantification of PD-L1 positive exosomes by a triple-helix molecular probe. Anal Chim Acta 2023; 1251:340984. [PMID: 36925282 DOI: 10.1016/j.aca.2023.340984] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/19/2023]
Abstract
Programmed death ligand-1 (PD-L1) positive exosomes (P-Exo) have been widely used for tumor diagnosis. However, accurate and rapid quantification of P-Exo remains challenging due to the heterogeneity of clinical individuals and isolation techniques. In this study, the triple-helix molecular probe (THMP) coupled with high-affinity silica-based TiO2 magnetic beads was used to isolate exosomes and to analyze the relative abundance of P-Exo in total exosomes (T-Exo). By employing this strategy, the entire analysis was completed within 70 min and the detection limit for P-Exo was 880 particles μL-1. Additionally, the relative abundance of P-Exo in T-Exo (RAP-Exo/T-Exo) was calculated from their fluorescence ratio, which could avoid errors due to differences in samples and separation methods, and identify 1.5 × 103 P-Exo from 5 × 106 T-Exo per microliter. RAP-Exo/T-Exo values were not only effective in distinguishing healthy volunteers from breast cancer patients, but also highly positively correlated with the stage of breast carcinoma. Overall, this strategy opens a new avenue for rapid and quantitative analysis of P-Exo, providing an opportunity for precise diagnosis and prediction of treatment efficacy in cancer.
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Affiliation(s)
- Zhichao Fan
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China; School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Qin Weng
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China; School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Yingxue Li
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Tian Zeng
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Junyi Wang
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Honglan Zhang
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Hua Yu
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China; Department of General Surgery, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China
| | - Yan Dong
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China.
| | - Xiang Zhao
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China.
| | - Jianjun Li
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China.
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7
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Hao J, Wang J, Dong Y, Yang J, Wang Z, Zhao X, Zeng T, Zhao X, Liang H, Li J. Homogeneous, Simple, and Direct Analysis of Exosomal PD-L1 via Aptamer-Bivalent-Cholesterol-Anchor Assembly of DNAzyme (ABCzyme) for Tumor Immunotherapy. Anal Chem 2023; 95:6854-6862. [PMID: 37027485 DOI: 10.1021/acs.analchem.2c05461] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
Abstract
Breakthroughs in immune checkpoint inhibitor (ICI) therapy have revolutionized clinical tumor therapy. Immunohistochemistry (IHC) analysis of PD-L1 in tumor tissue has been used to predict the response to tumor immunotherapy, but the results are not reproducible, and IHC is invasive and cannot be used to monitor the dynamic changes in PD-L1 expression during treatment. Monitoring the expression level of the PD-L1 protein on exosomes (exosomal PD-L1) is promising for both tumor diagnosis and tumor immunotherapy. Here, we established an aptamer-bivalent-cholesterol-anchor assembly of DNAzyme (ABCzyme) analytical strategy that can directly detect exosomal PD-L1 with a minimum lower limit of detection of 5.21 pg/mL. In this way, we found that the levels of exosomal PD-L1 are significantly elevated in the peripheral blood of patients with progressive disease. The precise analysis of exosomal PD-L1 by the proposed ABCzyme strategy provides a potentially convenient method for the dynamic monitoring of tumor progression in patients who receive immunotherapy and proves to be a potential and effective liquid biopsy method for tumor immunotherapy.
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Affiliation(s)
- Jie Hao
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Junyi Wang
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Yan Dong
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Jingyao Yang
- The Department of Hyperbaric Oxygen, Xingcheng Special Service Sanatorium of Strategic Support Force, Liaoning 125105, China
| | - Zhe Wang
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Xiaoxin Zhao
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Tian Zeng
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Xiang Zhao
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Houjie Liang
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Jianjun Li
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
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