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Zhou Q, Li T, Li X, Wei L, Luo J, Bai L, Duan WJ, Xie B, Sun B, Chen JX, Dai Z, Chen J. Dual miRNA-Triggered DNA Walker Assisted by APE1 for Specific Recognition of Tumor Cells. Anal Chem 2024; 96:6774-6783. [PMID: 38634427 DOI: 10.1021/acs.analchem.4c00554] [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: 04/19/2024]
Abstract
The identification of a specific tumor cell is crucial for the early diagnosis and treatment of cancer. However, it remains a challenge due to the limited sensitivity and accuracy, long response time, and low contrast of the recent approaches. In this study, we develop a dual miRNA-triggered DNA walker (DMTDW) assisted by APE1 for the specific recognition of tumor cells. miR-10b and miR-155 were selected as the research models. Without miR-10b and miR-155 presence, the DNA walker remains inactive as its walking strand of W is locked by L1 and L2. After miR-10b and miR-155 are input, the DNA walker is triggered as miR-10b and miR-155 bind to L1 and L2 of W-L1-L2, respectively, unlocking W. The DNA walker is driven by endogenous APE1 that is highly catalytic and is highly expressed in the cytoplasm of tumor cells but barely expressed in normal cells, ensuring high contrast and reaction efficiency for specific recognition of tumor cells. Dual miRNA input is required to trigger the DNA walker, making this strategy with a high accuracy. The DMTDW strategy exhibited high sensitivity for miRNA analysis with a detection limit of 44.05 pM. Living cell-imaging experiments confirmed that the DMTDW could effectively respond to the fluctuation of miRNA and specifically identified MDA-MB-231 cells from different cell lines. The proposed DMTDW is sensitive, rapid, and accurate for specific tumor cell recognition. We believe that the DMTDW strategy can become a powerful diagnostic tool for the specific recognition of tumor cells.
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Affiliation(s)
- Qianying Zhou
- 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, PR China
| | - Tong Li
- 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, PR China
| | - Xidong Li
- 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, PR China
| | - Lintao Wei
- 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, PR China
| | - Jiaxin Luo
- 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, PR China
| | - Lingling Bai
- 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, PR 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, PR China
| | - Baoping Xie
- 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, PR China
| | - Bin 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, PR 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, PR China
| | - Zong Dai
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, PR 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, PR China
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2
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Sun M, Chen X, Chen X, Zhou Q, Huang T, Li T, Xie B, Li C, Chen JX, Dai Z, Chen J. Label-free fluorescence detection of human 8-oxoguanine DNA glycosylase activity amplified by target-induced rolling circle amplification. Anal Chim Acta 2024; 1287:342084. [PMID: 38182379 DOI: 10.1016/j.aca.2023.342084] [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: 10/05/2023] [Revised: 11/21/2023] [Accepted: 11/26/2023] [Indexed: 01/07/2024]
Abstract
BACKGROUND Human 8-oxoG DNA glycosylase 1 (hOGG1) is one of the important members of DNA glycosylase for Base excision repair (BER), the abnormal activity of which can lead to the failure of BER and the appearance of various diseases, such as breast cancer, bladder cancer, Parkinson's disease and lung cancer. Therefore, it is important to detect the activity of hOGG1. However, traditional detection methods suffer from time consuming, complicated operation, high false positive results and low sensitivity. Thus, it remains a challenge to develop simple and sensitive hOGG1 analysis strategies to facilitate early diagnosis and treatment of the relative disease. RESULTS A target-induced rolling circle amplification (TIRCA) strategy for label-free fluorescence detection of hOGG1 activity was proposed with high sensitivity and specificity. The TIRCA strategy was constructed by a hairpin probe (HP) containing 8-oxoG site and a primer probe (PP). In the presence of hOGG1, the HP transformed into dumbbell DNA probe (DDP) after the 8-oxoG site of which was removed. Then the DDP formed closed circular dumbbell probe (CCDP) by ligase. CCDP could be used as amplification template of RCA to trigger RCA. The RCA products containing repeated G4 sequences could combine with ThT to produce enhanced fluorescence, achieving label-free fluorescence sensing of hOGG1. Given the high amplification efficiency of RCA and the high fluorescence quantum yield of the G4/ThT, the proposed TIRCA achieved highly sensitive measurement of hOGG1 activity with a detection limit of 0.00143 U/mL. The TIRCA strategy also exhibited excellent specificity for hOGG1 analysis over other interference enzymes. SIGNIFICANCE This novel TIRCA strategy demonstrates high sensitivity and high specificity for the detection of hOGG1, which has also been successfully used for the screening of inhibitors and the analysis of hOGG1 in real samples. We believe that this TIRCA strategy provides new insight into the use of the isothermal nucleic acid amplification as a useful tool for hOGG1 detection and will play an important role in disease early diagnosis and treatment.
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Affiliation(s)
- 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, China
| | - Xiao Chen
- Neurology Division, Department of Obstetrics and Gynecology, The First People's Hospital of Tianmen in Hubei Province, Tianmen, 431700, China
| | - Xiang Chen
- Neurology Division, Department of Obstetrics and Gynecology, The First People's Hospital of Tianmen in Hubei Province, Tianmen, 431700, China
| | - Qianying Zhou
- 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, 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, China
| | - Tong Li
- 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, China
| | - Baoping Xie
- 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, China
| | - Chunrong Li
- Qiannan Medical College for Nationalities, Duyun, 558000, 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, China
| | - Zong Dai
- Key Laboratory of Sensing Technology and Biomedical Instrument of Guangdong Province, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen, 518107, 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, China; Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Qingdao University of Science and Technology, Qingdao, 266042, China.
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3
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Qiu Y, Liu B, Zhou W, Tao X, Liu Y, Mao L, Wang H, Yuan H, Yang Y, Li B, Wang W, Qiu Y. Repair-driven DNA tetrahedral nanomachine combined with DNAzyme for 8-oxo guanine DNA glycosylase activity assay, drug screening and intracellular imaging. Analyst 2024; 149:537-545. [PMID: 38088097 DOI: 10.1039/d3an01521a] [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: 01/16/2024]
Abstract
8-oxo guanine DNA glycosylase (8-oxoG DNA glycosylase), a crucial DNA repair enzyme, is essential for maintaining genome integrity and preventing diseases caused by DNA oxidative damage. Imaging 8-oxoG DNA glycosylase in living cells requires a dependable technique. In this study, we designed a DNAzyme-modified DNA tetrahedral nanomachine (DTDN) powered by 8-oxoG restoration. Incorporating a molecular beacon probe (MB), the constructed platform was used for amplified in situ monitoring of 8-oxoG DNA glycosylase. Under normal conditions, duplexing with a complementary strand modified with two 8-oxoG sites inhibited the activity of DNAzyme. The restoration of DNAzyme activity by the repair of intracellular 8-oxoG DNA glycosylase on 8-oxoG bases can initiate a signal amplification reaction. This detection system can detect 8-oxoG DNA glycosylase activity linearly between 0 and 20 U mL-1, with a detection limit as low as 0.52 U mL-1. Using this method, we were able to screen 14 natural compounds and identify 6 of them as 8-oxoG DNA glycosylase inhibitors. In addition, a novel approach was utilized to assess the activity of 8-oxoG DNA glycosylase in living cells. In conclusion, this method provides a universal tool for monitoring the activity of 8-oxoG DNA glycosylase in vitro and in living cells, which holds great promise for elucidating the enzyme's functionality and facilitating drug screening endeavors.
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Affiliation(s)
- Yun Qiu
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China.
| | - Bin Liu
- College of Biology, Hunan University, Changsha 410082, China
| | - Wenchao Zhou
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China.
| | - Xueqing Tao
- College of Biology, Hunan University, Changsha 410082, China
| | - Yang Liu
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China.
| | - Linxi Mao
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China.
| | - Huizhen Wang
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China.
| | - Hanwen Yuan
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China.
| | - Yupei Yang
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China.
| | - Bin Li
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China.
| | - Wei Wang
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China.
| | - Yixing Qiu
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China.
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4
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Liu WJ, Song R, Zou XR, Li DL, Xu Q, Zhang CY. Enzymatic DNA repairing amplification-powered construction of an Au nanoparticle-based nanosensor for single-molecule monitoring of cytosine deaminase activity in cancer cells. Anal Chim Acta 2023; 1281:341895. [PMID: 38783732 DOI: 10.1016/j.aca.2023.341895] [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: 09/29/2023] [Accepted: 10/09/2023] [Indexed: 05/25/2024]
Abstract
APOBEC3A (A3A) is a cytidine deaminase with critical roles in molecular diagnostics. Herein, we demonstrate the enzymatic DNA repairing amplification-powered construction of an Au nanoparticle-based nanosensor for single-molecule monitoring of A3A activity in cancer cells. Target A3A can convert cytosine (C) in substrate probe to uracil (U), and then the template binds with substrate probe to form a dsDNA containing U/A base pairs. Uracil DNA glycosylase (UDG) excises the U base to produce an apurinic/apyrimidinic (AP) site that can be cleaved by apurinic/apyrimidic endonuclease 1 (APE1) to obtain the substrate fragment with 3'-OH end. Subsequently, the substrate fragment initiates cyclic enzymatic repairing amplification (ERA), releasing trigger-1 and trigger-2. The resultant trigger-1 can act as the primer to induce multiple cycles of cyclic ERA, producing numerous trigger-1 and trigger-2. The hybridization of trigger-2 with signal probe forms the dsDNA duplexes with an AP site, inducing the cyclic cleavage of signal probes by APE1 to release abundant Cy5 molecules from the AuNPs. Released Cy5 molecules can be easily quantified by single-molecule imaging. This nanosensor allows for specific and sensitive detection of A3A activity with a detection limit of 0.855 aM, and it can further measure kinetic parameters, screen inhibitors, and quantify endogenous A3A activity at the single-cell level, with prospect application in disease diagnostics and therapy.
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Affiliation(s)
- Wen-Jing Liu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China; School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Rui Song
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China
| | - Xiao-Ran Zou
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China
| | - Dong-Ling Li
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Qinfeng Xu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China.
| | - Chun-Yang Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China.
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5
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Cheng X, Song H, Ren D, Gao M, Xia X, Yu P, Bian X. Rolling circle transcription and CRISPR/Cas12a-assisted versatile bicyclic cascade amplification assay for sensitive uracil-DNA glycosylase detection. Talanta 2023; 262:124684. [PMID: 37220689 DOI: 10.1016/j.talanta.2023.124684] [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: 12/08/2022] [Revised: 05/14/2023] [Accepted: 05/17/2023] [Indexed: 05/25/2023]
Abstract
Uracil-DNA glycosylase (UDG) is pivotal in maintaining genome integrity and aberrant expressed UDG is highly relevant to numerous diseases. Sensitive and accurate detecting UDG is critically significant for early clinical diagnosis. In this research, we demonstrated a sensitive UDG fluorescent assay based on rolling circle transcription (RCT)/CRISPR/Cas12a-assisted bicyclic cascade amplification strategy. Target UDG catalyzed to remove uracil base of DNA dumbbell-shape substrate probe (SubUDG) to produce an apurinic/apyrimidinic (AP) site, at which SubUDG was cleaved by apurinic/apyrimidinic endonuclease (APE1) subsequently. The exposed 5'-PO4 was ligated with the free 3'-OH terminus to form an enclosed DNA dumbbell-shape substrate probe (E-SubUDG). E-SubUDG functioned as a template can actuate T7 RNA polymerase-mediated RCT signal amplification, generating multitudes of crRNA repeats. The resultant Cas12a/crRNA/activator ternary complex activated the activity of Cas12a, causing a significantly enhanced fluorescence output. In this bicyclic cascade strategy, target UDG was amplified via RCT and CRISPR/Cas12a, and the whole reaction was completed without complex procedures. This method enabled sensitive and specific monitor UDG down to 0.0005 U/mL, screen corresponding inhibitors, and analyze endogenous UDG in A549 cells at single-cell level. Importantly, this assay can be extended to analyze other DNA glycosylase (hAAG and Fpg) by altering the recognition site in DNA substrates probe rationally, thereby offering a potent tool for DNA glycosylase-associated clinical diagnosis and biomedical research.
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Affiliation(s)
- Xia Cheng
- Department of Pharmacy, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huahua Song
- Experimental Nuclear Medicine Laboratory, Core Facility of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dandan Ren
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China
| | - Mingcong Gao
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China
| | - Xinyi Xia
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, PR China
| | - Ping Yu
- Department of Pharmacy, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Xiaolan Bian
- Department of Pharmacy, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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6
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Zhao NN, Zhang X, Zou X, Zhang Y, Zhang CY. Controllable assembly of dendritic DNA nanostructures for ultrasensitive detection of METTL3-METTL14 m 6A methyltransferase activity in cancer cells and human breast tissues. Biosens Bioelectron 2023; 228:115217. [PMID: 36924687 DOI: 10.1016/j.bios.2023.115217] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/12/2023] [Accepted: 03/07/2023] [Indexed: 03/13/2023]
Abstract
N6-Methyladenosine (m6A) is a reversible chemical modification in eukaryotic messenger RNAs and long noncoding RNAs. The aberrant expression of RNA methyltransferase METTL3-METTL14 complex may change the m6A methylation level and cause multiple diseases including cancers. The conventional METTL3-METTL14 assays commonly suffer from time-consuming procedures and poor sensitivity. Herein, we develop a controllable amplification machinery based on MazF-activated terminal deoxynucleotidyl transferase (TdT)-assisted dendritic DNA structure assembly for ultrasensitive detection of METTL3-METTL14 complex activity in cancer cells and breast tissues. The presence of METTL3-METTL14 complex catalyzes the formation of m6A in detection probe, effectively preventing the cleavage of methylated detection probes by MazF. The methylated detection probes with 3'-OH termini can function as the primers for template-free polymerization catalyzed by TdT on magnetic beads (MBs), producing long chains of poly-thymidine (poly-T) sequences. Then poly-T sequences hybridize with signal probes that contain poly-adenine (poly-A) sequence, inducing TdT-mediated polymerization and the subsequent hybridization with more poly-A signal probes for generating dendritic DNA nanostructures assembled on MBs. After magnetic separation and elevated temperature treatment, the signal probes are disassembled from MBs to generate a high fluorescence signal. This method possesses excellent specificity and high sensitivity with a limit of detection (LOD) of 2.61 × 10-15 M, and it can accurately quantify cellular METTL3-METTL14 complex at single-cell level. Furthermore, it can screen inhibitors, evaluate kinetic parameters, and discriminate breast cancer tissues from normal tissues.
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Affiliation(s)
- Ning-Ning Zhao
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China
| | - Xinyi Zhang
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Zhongshan, 528458, China
| | - Xiaoran Zou
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China
| | - Yan Zhang
- College of Chemistry and Chemical Engineering, Qilu Normal University, Jinan, 250200, China.
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China.
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7
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Tian T, Zhang K, Yang W, Zhong Q, Wang B, Guo W, Liu B. A ratiometric SERS aptasensor array for human DNA glycosylaseat single-cell sensitivity/resolution. Talanta 2023; 259:124544. [PMID: 37086683 DOI: 10.1016/j.talanta.2023.124544] [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: 02/09/2023] [Revised: 04/05/2023] [Accepted: 04/09/2023] [Indexed: 04/24/2023]
Abstract
Human 8-oxoguanine DNA glycosylase (hOGG1) is involved in the cellular genomic 8-oxoguanine (8-oxoG) excision repair to maintain genome stability. Accurate detection of hOGG1 activity is essential for clinical diagnosis and treatment of various human pathology. Yet, the quantitative detection of hOGG1 remains challenging for existing methods due to poor reproducibility and portability. Herein, we propose a ratiometric array-based SERS point-of-care testing method for hOGG1 activity. A kind of reproducible, uniform and stable plasmonic multi-microarray reaction cells was constructed by assembling AuNPs on the substrate modified by aminosilane and segmented by silica gel gasket, which greatly improved the sensitivity, portability and repeatability of SERS measurement. Based on this, the ratiometric method is further used to effectively overcome the instability of single SERS signal intensity, which allows signal rationing and provides built-in correction for environment effects. In specific, we designed two different Raman-labeled probes for the detection of hOGG1, a thiol- and Cy3-labeled aptamer as an internal standard and a Rox-labeled 8-oxoG-modified complementary aptamer as a signal probe. The ratio value between Cy3 and Rox SERS intensity is well linear with the hOGG1 activity on logarithmic scales in the range from 5 × 10-5 to 5 × 10-3 U/mL, and the limit of detection reaches 3.3 × 10-5 U/mL. Moreover, this strategy can be applied for the screening of inhibitors and the monitoring of cellular hOGG1 activity fluctuation at single-cell levels, providing a flexible and adaptive tool for clinical diagnosis, biochemical processes and drug discovery.
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Affiliation(s)
- Tongtong Tian
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, 136 Yi Xue Yuan Road, Shanghai, 200032, PR China; Department of Chemistry, State Key Laboratory of Molecular Engineering of Polymers and Institute of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China
| | - Kun Zhang
- Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Wenjing Yang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, 136 Yi Xue Yuan Road, Shanghai, 200032, PR China
| | - Qingmei Zhong
- Department of Chemistry, State Key Laboratory of Molecular Engineering of Polymers and Institute of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China
| | - Beili Wang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, 136 Yi Xue Yuan Road, Shanghai, 200032, PR China.
| | - Wei Guo
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, 136 Yi Xue Yuan Road, Shanghai, 200032, PR China.
| | - Baohong Liu
- Department of Chemistry, State Key Laboratory of Molecular Engineering of Polymers and Institute of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China.
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8
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Zhao NN, Yu XD, Tian X, Xu Q, Zhang CY. Mix-and-Detection Assay with Multiple Cyclic Enzymatic Repairing Amplification for Rapid and Ultrasensitive Detection of Long Noncoding RNAs in Breast Tissues. Anal Chem 2023; 95:3082-3088. [PMID: 36692970 DOI: 10.1021/acs.analchem.2c05353] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Long noncoding RNAs (lncRNAs) are valuable biomarkers and therapeutic targets, and they play essential roles in various pathological and biological processes. So far, the reported lncRNA assays usually suffer from unsatisfactory sensitivity and time-consuming procedures. Herein, we develop a mix-and-read assay based on multiple cyclic enzymatic repairing amplification (ERA) for sensitive and rapid detection of mammalian metastasis-associated lung adenocarcinoma transcript 1 (lncRNA MALAT1). In this assay, we design two three-way junction (3WJ) probes including a 3WJ template and a 3WJ primer to specifically recognize lncRNA MALAT1, and the formation of a stable 3WJ structure induces cyclic ERA to generate triggers. The resulting triggers subsequently hybridize with a free 3WJ template and act as primers to initiate new rounds of cyclic ERA, generating abundant triggers. The hybridization of triggers with signal probes forms stable double-stranded DNA duplexes that can be specifically cleaved by apurinic/apyrimidinic endonuclease 1 to produce a high fluorescence signal. This assay can be carried out in a mix-and-read manner within 10 min under an isothermal condition (50 °C), which is the rapidest and simplest method reported so far for the lncRNA MALAT1 assay. This method can sensitively detect lncRNA MALAT1 with a limit of detection of 0.87 aM, and it can accurately measure endogenous lncRNA MALAT1 at the single-cell level. Moreover, this method can distinguish lncRNA MALAT1 expression in breast cancer patient tissues and their corresponding healthy adjacent tissues. Importantly, the extension of this assay to different RNAs detection can be achieved by simply replacing the corresponding target recognition sequences.
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Affiliation(s)
- Ning-Ning Zhao
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, Shandong 250014, China
| | - Xiao-Di Yu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, Shandong 250014, China
| | - Xiaorui Tian
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, Shandong 250014, China
| | - Qinfeng Xu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, Shandong 250014, China
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9
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Sun H, Zhou S, Liu Y, Lu P, Qi N, Wang G, Yang M, Huo D, Hou C. A fluorescent biosensor based on exponential amplification reaction-initiated CRISPR/Cas12a (EIC) strategy for ultrasensitive DNA methyltransferase detection. Anal Chim Acta 2023; 1239:340732. [PMID: 36628729 DOI: 10.1016/j.aca.2022.340732] [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: 10/20/2022] [Revised: 12/09/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022]
Abstract
DNA methyltransferase (DNA MTase) catalyzes the process of DNA methylation, and the aberrant DNA MTase activity is closely associated with cancer incidence and progression. Inspired by the exponential amplification reaction (EXPAR) characteristics, we developed an EXPAR-initiated CRISPR/Cas12a (EIC) strategy for sensitively detecting DNA MTase activity. A hairpin probe (HP) was designed with a palindromic sequence in the stem as substrate and NH2-modified 3' end to prevent nonspecific amplification. HP could be methylated by DNA adenine methyltransferase (Dam MTase) and then digested by DpnI to generate an oligonucleotide that can serve as an EXPAR primer. With the assistance of Nt.BstNBI nicking enzyme and Vent(exo-) polymerase, this primer bound to template and induced EXPAR. Interestingly, the product of Cycle 1 in EXPAR can function as primer to initiate Cycle 2. Both EXPAR products can further activate the collateral cleavage of CRISPR/Cas12a-crRNA, resulting in the fragmentation of fluorescence reporters and fluorescence recovery. Due to the highly efficient amplification (about 5 times signal-to-noise of SDA) and the robust trans-cleavage of CRISPR/Cas12a, the EIC system owned an extreme limit of detection (LOD) of 2 × 10-4 U/mL and a broad detection range from 2 × 10-4 to 10 U/mL for Dam MTase. In addition, this method has succeeded in inhibitor screening and evaluation, showing magnificent promise in drug discovery and cancer therapy.
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Affiliation(s)
- Human Sun
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400044, PR China.
| | - Shiying Zhou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400044, PR China
| | - Yin Liu
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400044, PR China
| | - Peng Lu
- Chongqing University Three Gorges Hospital, Chongqing, 404000, PR China
| | - Na Qi
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400044, PR China
| | - Guixue Wang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400044, PR China
| | - Mei Yang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400044, PR China.
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College, 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.
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400044, PR China; National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, PR China.
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10
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Yilmaz E, Baghban N, Soylak M. Solid-Phase Extraction (SPE) of Salmon Sperm DNA Using a Polyaniline@Molybdenum(IV) Sulfide@Multiwalled Carbon Nanotubes (MWCNTs) Nanocomposite with Spectrophotometric Detection. ANAL LETT 2022. [DOI: 10.1080/00032719.2022.2139835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Erkan Yilmaz
- Faculty of Pharmacy, Department of Analytical Chemistry, Erciyes University, Kayseri, Turkey
- Technology Research & Application Center (ERU-TAUM), Erciyes University, Kayseri, Turkey
- ERNAM-Nanotechnology Application and Research Center, Erciyes University, Kayseri, Turkey
| | - Neda Baghban
- Faculty of Sciences, Department of Chemistry, Erciyes University, Kayseri, Turkey
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Mustafa Soylak
- Technology Research & Application Center (ERU-TAUM), Erciyes University, Kayseri, Turkey
- Faculty of Sciences, Department of Chemistry, Erciyes University, Kayseri, Turkey
- Turkish Academy of Sciences (TUBA), Ankara, Turkey
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11
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Luo B, Zhang Y, An P, Lan F, Wu Y. Covalent organic framework nanosheet anchored with highly dispersed Au nanoparticles as a novel nanoprobe for DNA methylation detection. J Colloid Interface Sci 2022; 626:241-250. [DOI: 10.1016/j.jcis.2022.06.162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/08/2022] [Accepted: 06/28/2022] [Indexed: 10/31/2022]
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12
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Li X, Wang Y, Tang H, Yang B, Zhao Y, Wu P. Evaluation of the sequence-dependent relative activity of APE1 for optimal biosensing design. Biosens Bioelectron 2022; 214:114539. [DOI: 10.1016/j.bios.2022.114539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 07/01/2022] [Indexed: 11/02/2022]
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13
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Li J, Zhu Z, Zhang M, Zhang Q, Sun W, Wang Y, Jiang L, Guo Z, Wang Y, Liu S, Huang J, Yu J. Target-manipulated drawstring DNAzyme for ultrasensitive detection of UDG using Au@Ag NRs indicator. Anal Chim Acta 2022; 1218:340010. [PMID: 35701040 DOI: 10.1016/j.aca.2022.340010] [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: 03/06/2022] [Revised: 05/15/2022] [Accepted: 05/26/2022] [Indexed: 11/01/2022]
Abstract
Uracil-DNA glycosylase (UDG) is a common glycosylase that can expressly recognize and remove damaged uracil bases, and the ultrasensitive detection of which is significant to maintain genomic stability and early clinical diagnosis of disease. Herein, we proposed a sensitive colorimetric sensing platform to detect UDG. Combined with target-manipulated drawstring DNAzyme and Au@Ag nanorods (Au@Ag NRs) indicator, we achieved in naked-eyes observation and ultrasensitive detection of UDG. Briefly, when the UDG exists, the dynamic reaction of rope pulling will occur generating the active conformation of DNAzyme. The cutting effect will be further produced when we add Mg2+, thus the generated trigger chain can mediate the occurrence of CHA reaction, followed by generating amount of ·OH which can etch Au@Ag NRs causing the shifted of localized surface plasmon resonance (LSPR) peak. By contrast, there is no obvious shift of LSPR peak. This strategy shows extraordinary specificity and sensitivity toward UDG providing a detection limit of 4.6 × 10-5 U mL-1. By using of this method, we detected UDG specifically in complex samples, proving that it's potential applications in biomedical research and clinical diagnosis are fantastic.
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Affiliation(s)
- Jingjing Li
- College of Biological Sciences and Technology, University of Jinan, Jinan, 250022, PR China
| | - Zhixue Zhu
- College of Biological Sciences and Technology, University of Jinan, Jinan, 250022, PR China
| | - Manru Zhang
- Shandong Institute of Medical Device and Pharmaceutical Packaging Inspection, Jinan, 250101, PR China
| | - Qingxin Zhang
- School of Water Conservancy and Environment, University of Jinan, Jinan, 250022, PR China
| | - Wenyu Sun
- College of Biological Sciences and Technology, University of Jinan, Jinan, 250022, PR China
| | - Yeru Wang
- College of Biological Sciences and Technology, University of Jinan, Jinan, 250022, PR China
| | - Long Jiang
- School of Water Conservancy and Environment, University of Jinan, Jinan, 250022, PR China
| | - Zhiqiang Guo
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, PR China
| | - Yu Wang
- College of Biological Sciences and Technology, University of Jinan, Jinan, 250022, PR China
| | - Su Liu
- School of Water Conservancy and Environment, University of Jinan, Jinan, 250022, PR China
| | - Jiadong Huang
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, PR China.
| | - Jinghua Yu
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, PR China
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14
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Wei SH, Liu M, Hu J, Zhang CY. Target-Initiated Cascade Signal Amplification Lights up a G-Quadruplex for a Label-Free Detection of Circular Ribonucleic Acids. Anal Chem 2022; 94:9193-9200. [PMID: 35703015 DOI: 10.1021/acs.analchem.2c01901] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Circular ribonucleic acids (circRNAs) are a type of RNA that originates through back-splicing events from linear primary transcripts. CircRNAs display high structural resistance and tissue specificity. Accurate quantification of the circRNA expression level is of vital importance to disease diagnosis. Herein, we construct a label-free fluorescent biosensor for ultrasensitive analysis of circRNAs based on the integration of target-initiated cascade signal amplification strategy with a light-up G-quadruplex. This assay involves only one assistant probe that targets the circRNA-specific back-splice junction. When circRNA is present, it hybridizes with the assistant probe to initiate the duplex-specific nuclease (DSN)-catalyzed cyclic cleavage reaction, producing abundant triggers with 3'OH termini. Then, terminal deoxynucleotidyl transferase (TdT) catalyzes the addition of dGTP and dATP at the 3'-OH termini of the resultant triggers to obtain abundant long G-rich DNA sequences that can form efficient G-quadruplex products. The addition of Thioflavin T (ThT) can light up G-quadruplex, generating an enhanced fluorescence. This assay may be performed isothermally without the involvement of any nucleic acid templates, exogenous primers, and specific labeled probes. Importantly, this biosensor can discriminate target circRNA from one-base mismatched circRNA and exhibits good performance in human serum. Moreover, it can accurately detect circRNA in cancer cells at a single-cell level and even differentiate the circRNA levels in the tissues of healthy persons and nonsmall cell lung cancer (NSCLC) patients, with promising applications in circRNA-related cancer diagnosis and therapeutics.
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Affiliation(s)
- Shu-Hua Wei
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Meng Liu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Juan Hu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
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15
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Wei XR, Meng Y, Xu Q, Hu J, Zhang CY. Label-free and homogeneous detection of flap endonuclease 1 by ligation-promoted hyperbranched rolling circle amplification platform. Talanta 2022; 243:123342. [DOI: 10.1016/j.talanta.2022.123342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/14/2022] [Accepted: 02/28/2022] [Indexed: 01/19/2023]
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16
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Sun Y, Zang L, Lu J. Base excision-initiated terminal deoxynucleotide transferase-assisted amplification for simultaneous detection of multiple DNA glycosylases. Anal Bioanal Chem 2022; 414:3319-3327. [DOI: 10.1007/s00216-022-03978-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/08/2022] [Accepted: 02/14/2022] [Indexed: 11/30/2022]
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17
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Closing-upon-repair DNA tetrahedron nanoswitch for FRET imaging the repair activity of 8-oxoguanine DNA glycosylase in living cells. Anal Chim Acta 2022; 1196:339481. [DOI: 10.1016/j.aca.2022.339481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/29/2021] [Accepted: 01/10/2022] [Indexed: 11/19/2022]
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18
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Hua X, Fan J, Yang L, Wang J, Wen Y, Su L, Zhang X. Rapid detection of miRNA via development of consecutive adenines (polyA)-based electrochemical biosensors. Biosens Bioelectron 2022; 198:113830. [PMID: 34861526 DOI: 10.1016/j.bios.2021.113830] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 11/11/2021] [Accepted: 11/19/2021] [Indexed: 12/12/2022]
Abstract
Herein, we report rapid electrochemical detection of miRNA let-7a based on a DNA probe consisting of a polyA and Fc-co-labeled harpin structure (the polyA-H probe). The polyA-H probe could be facilely immobilized on Au surfaces through the interactions between polyA and Au, followed by its pre-hybridization with a single strand (S1). The probe's surface density could be optimized for minimizing steric hindrance via changing the polyA block length. The target let-7a could be rapidly amplified via loop-mediated isothermal amplification (LAMP) with four simplified primers, followed by inducing the formation of dimeric i-motif (DIM) structure via H+-induced rapid folding of two C-rich sequences of motif strand 1 and strand 2. It was found that, after introducing the as-formed DIM to hybridize the S1, the immobilized polyA20-H probe could rapidly revert to its hairpin structure, sending out a turn-on electrochemical signal of the Fc. The total time for detecting the let-7a was around 80 min, obviously less than that of most of electrochemical DNA sensors reported previously. The biosensor showed a linear relationship of the current response to the let-7a in the range of 10 fM to 50 nM with a limit of detection (LOD) of 5.1 fM. Our biosensors were further tested using human serum spiked with the let-7a and the extracts of the breast adenocarcinoma cells spiked with and without the let-7a, respectively. Satisfied results were obtained. This study shows a potential promising future of development of electrochemical biosensors for rapid detection of miRNAs in the application of clinical practice.
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Affiliation(s)
- Xiaoyu Hua
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China
| | - Jingjing Fan
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China
| | - Lingzhi Yang
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen, 518037, PR China.
| | - Jun Wang
- Department of Biomedicine and Biopharmacology, Hubei University of Technology, Wuhan, 430068, PR China
| | - Yongqiang Wen
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China
| | - Lei Su
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, 518037, PR China.
| | - Xueji Zhang
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, 518037, PR China
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19
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Ouyang Y, Liu Y, Deng Y, He H, Huang J, Ma C, Wang K. Recent advances in biosensor for DNA glycosylase activity detection. Talanta 2021; 239:123144. [PMID: 34923254 DOI: 10.1016/j.talanta.2021.123144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/09/2021] [Accepted: 12/11/2021] [Indexed: 10/19/2022]
Abstract
Base excision repair (BER) is vital for maintaining the integrity of the genome under oxidative damage. DNA glycosylase initiates the BER pathway recognizes and excises the mismatched substrate base leading to the apurinic/apyrimidinic site generation, and simultaneously breaks the single-strand DNA. As the aberrant activity of DNA glycosylase is associated with numerous diseases, including cancer, immunodeficiency, and atherosclerosis, the detection of DNA glycosylase is significant from bench to bedside. In this review, we summarized novel DNA strategies in the past five years for DNA glycosylase activity detection, which are classified into fluorescence, colorimetric, electrochemical strategies, etc. We also highlight the current limitations and look into the future of DNA glycosylase activity monitoring.
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Affiliation(s)
- Yuzhen Ouyang
- School of Life Sciences, Central South University, Changsha, 410013, China; Clinical Medicine Eight-year Program, Xiangya School of Medicine, Central South University, Changsha, 410078, China
| | - Yifan Liu
- School of Life Sciences, Central South University, Changsha, 410013, China; Clinical Medicine Eight-year Program, Xiangya School of Medicine, Central South University, Changsha, 410078, China
| | - Yuan Deng
- School of Life Sciences, Central South University, Changsha, 410013, China
| | - Hailun He
- School of Life Sciences, Central South University, Changsha, 410013, China
| | - Jin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, China.
| | - Changbei Ma
- School of Life Sciences, Central South University, Changsha, 410013, China.
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, China
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20
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Huang X, He Z, Zhou K, Zhi H, Yang J. Fabrication of bifunctional G-quadruplex-hemin DNAzymes for colorimetric detection of apurinic/apyrimidinic endonuclease 1 and microRNA-21. Analyst 2021; 146:7379-7385. [PMID: 34816841 DOI: 10.1039/d1an01603b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
G-quadruplex-based complexes have been widely used in various analytical methods due to their outstanding capabilities of generating colorimetric, fluorescent or electrochemical signals. However, since loop sequences in traditional G-quadruplex structures are quite short, it is difficult to establish biosensors solely using G-quadruplex-based complexes. Herein, we attempted to lengthen the loop sequences of G-quadruplex structures and found that G-quadruplex-hemin DNAzymes (G-DNAzymes) with long loops (even 30 nucleotides) maintain high peroxidase activity. In addition, the peroxidase activity is not affected by the hybridization of the long loop with its complementary counterpart. Consequently, G-DNAzyme can be endowed with an additional function by taking the long loop as a recognition element, which may facilitate the construction of diverse colorimetric biosensors. Furthermore, by designing an apurinic/apyrimidinic site or a complementary sequence of microRNA-21 (miRNA-21) in long loops, bifunctional G-DNAzymes can be split in the presence of apurinic/apyrimidinic endonuclease 1 (APE1) or miRNA-21, decreasing their peroxidase activities. Accordingly, APE1 and miRNA-21 are quantified using 3,3',5,5'-tetramethylbenzidine as a chromophore. Using the G-DNAzyme, APE1 can be detected in a linear range from 2.5 to 22.5 U mL-1 with a LOD of 1.8 U mL-1. It is to be noted that benefitting from duplex-specific nuclease-induced signal amplification, the linear range of the miRNA-21 biosensor is broadened to 5 orders of magnitude, while the limit of detection is as low as 73 fM. This work demonstrates that G-DNAzymes with long loops can both generate signals and recognize targets, providing an alternative strategy to design G-quadruplex-based analytical methods.
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Affiliation(s)
- Xiaodong Huang
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials and Jiangsu Key Laboratory of Biofunctional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
| | - Zhenni He
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials and Jiangsu Key Laboratory of Biofunctional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
| | - Kejie Zhou
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials and Jiangsu Key Laboratory of Biofunctional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
| | - Huizhen Zhi
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials and Jiangsu Key Laboratory of Biofunctional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
| | - Jinfei Yang
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials and Jiangsu Key Laboratory of Biofunctional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
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21
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Mazzarotta A, Caputo TM, Battista E, Netti PA, Causa F. Hydrogel Microparticles for Fluorescence Detection of miRNA in Mix-Read Bioassay. SENSORS (BASEL, SWITZERLAND) 2021; 21:7671. [PMID: 34833752 PMCID: PMC8624599 DOI: 10.3390/s21227671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/12/2021] [Accepted: 11/16/2021] [Indexed: 11/20/2022]
Abstract
Herein we describe the development of a mix-read bioassay based on a three-dimensional (3D) poly ethylene glycol-(PEG)-hydrogel microparticles for the detection of oligonucleotides in complex media. The key steps of hydrogels synthesis and molecular recognition in a 3D polymer network are elucidated. The design of the DNA probes and their density in polymer network were opportunely optimized. Furthermore, the diffusion into the polymer was tuned adjusting the polymer concentration and consequently the characteristic mesh size. Upon parameters optimization, 3D-PEG-hydrogels were synthetized in a microfluidic system and provided with fluorescent probe. Target detection occurred by double strand displacement assay associated to fluorescence depletion within the hydrogel microparticle. Proposed 3D-PEG-hydrogel microparticles were designed for miR-143-3p detection. Results showed 3D-hydrogel microparticles with working range comprise between 10-6-10-12 M, had limit of detection of 30 pM and good specificity. Moreover, due to the anti-fouling properties of PEG-hydrogel, the target detection occurred in human serum with performance comparable to that in buffer. Due to the approach versatility, such design could be easily adapted to other short oligonucleotides detection.
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Affiliation(s)
- Alessia Mazzarotta
- Center for Advanced Biomaterials for Healthcare, Istituto Italiano di Tecnologia, L.go Barsanti e Matteucci, 53, 80125 Naples, Italy; (A.M.); (T.M.C.); (P.A.N.); (F.C.)
| | - Tania Mariastella Caputo
- Center for Advanced Biomaterials for Healthcare, Istituto Italiano di Tecnologia, L.go Barsanti e Matteucci, 53, 80125 Naples, Italy; (A.M.); (T.M.C.); (P.A.N.); (F.C.)
| | - Edmondo Battista
- Interdisciplinary Research Centre on Biomaterials (CRIB), Università degli Studi di Napoli “Federico II”, P.le Tecchio 80, 80125 Naples, Italy
| | - Paolo Antonio Netti
- Center for Advanced Biomaterials for Healthcare, Istituto Italiano di Tecnologia, L.go Barsanti e Matteucci, 53, 80125 Naples, Italy; (A.M.); (T.M.C.); (P.A.N.); (F.C.)
- Interdisciplinary Research Centre on Biomaterials (CRIB), Università degli Studi di Napoli “Federico II”, P.le Tecchio 80, 80125 Naples, Italy
- Dipartimento di Ingegneria Chimica del Materiali e della Produzione Industriale, Università degli Studi di Napoli “Federico II”, P.le Tecchio 80, 80125 Naples, Italy
| | - Filippo Causa
- Center for Advanced Biomaterials for Healthcare, Istituto Italiano di Tecnologia, L.go Barsanti e Matteucci, 53, 80125 Naples, Italy; (A.M.); (T.M.C.); (P.A.N.); (F.C.)
- Interdisciplinary Research Centre on Biomaterials (CRIB), Università degli Studi di Napoli “Federico II”, P.le Tecchio 80, 80125 Naples, Italy
- Dipartimento di Ingegneria Chimica del Materiali e della Produzione Industriale, Università degli Studi di Napoli “Federico II”, P.le Tecchio 80, 80125 Naples, Italy
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22
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Chen J, Zhu D, Huang T, Yang Z, Liu B, Sun M, Chen JX, Dai Z, Zou X. Isothermal Self-Primer EXPonential Amplification Reaction (SPEXPAR) for Highly Sensitive Detection of Single-Stranded Nucleic Acids and Proteins. Anal Chem 2021; 93:12707-12713. [PMID: 34491714 DOI: 10.1021/acs.analchem.1c02588] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Development of versatile sensing methods for sensitive and specific detection of clinically relevant nucleic acids and proteins is of great value for disease monitoring and diagnosis. In this work, we propose a novel isothermal Self-primer EXPonential Amplification Reaction (SPEXPAR) strategy based on a rationally engineered structure-switchable Metastable Hairpin template (MH-template). The MH-template initially keeps inactive with its self-primer overhanging a part of target recognition region to inhibit polymerization. The present targets can specifically compel the MH-template to transform into an "activate" conformation that primes a target-recyclable EXPAR. The method is simple and sensitive, can accurately and facilely detect long-chain single-stranded nucleic acids or proteins without the need of exogenous primer probes, and has a high amplification efficiency theoretically more than 2n. For a proof-of-concept demonstration, the SPEXPAR method was used to sensitively detect the characteristic sequence of the typical swine fever virus (CSFV) RNA and thrombin, as nucleic acid and protein models, with limits of detection down to 43 aM and 39 fM, respectively, and even the CSFV RNA in attenuated vaccine samples and thrombin in diluted serum samples. The SPEXPAR method may serve as a powerful technique for the biological research of single-stranded nucleic acids and proteins.
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Affiliation(s)
- Jun Chen
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, P. R. China
| | - Daozhong Zhu
- Guangzhou Customs Technology Center, Guangzhou 510623, P. R. China
| | - Ting Huang
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, P. R. China
| | - Zizhong Yang
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, P. R. China
| | - Birong Liu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, P. R. China
| | - Mengxu Sun
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, P. R. China
| | - Jin-Xiang Chen
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, P. R. China
| | - Zong Dai
- Key Laboratory of Sensing Techno logy and Biomedical Instrument of Guangdong Province, School of Biomedical Engineering, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Xiaoyong Zou
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P. R. China
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