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Han H, Jang SH, Ahn JK, Lee CY. DNA repair-retarded isothermal CRISPR amplification for rapid, sensitive base excision repair enzyme assay. Anal Chim Acta 2024; 1314:342799. [PMID: 38876521 DOI: 10.1016/j.aca.2024.342799] [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: 03/08/2024] [Revised: 05/05/2024] [Accepted: 05/29/2024] [Indexed: 06/16/2024]
Abstract
BACKGROUND As a core enzyme in the base excision repair system, uracil DNA glycosylase (UDG) is indispensable in maintaining genomic integrity and normal cell cycles. Its abnormal activity intervenes in cancers and neurodegerative diseases. Previous UDG assays based on isothermal amplification and Clustered Regularly Interspaced Short Palindromic Repeats/Cas (CRISPR/Cas) system were fine in sensitivity, but exposed to complications in assay flow, time, and probe design. After isothermal amplification, a CRISPR/Cas reagent should be separately added with extra manual steps and its guide RNA (gRNA) should be designed, considering the presence of protospacer adjacent motif (PAM) site. RESULTS We herein describe a UDG-REtarded CRISPR Amplification assay, termed 'URECA'. In URECA, isothermal nucleic acid (NA) amplification and CRISPR/Cas12a system were tightly combined to constitute a one-pot, isothermal CRISPR amplification system. Isothermal NA amplification for a UDG substrate (US) with uracil (U) bases was designed to activate and boost CRISPR/Cas12a reaction. Such scheme enabled us to envision that UDG would halt the isothermal CRISPR amplification reaction by excising U bases and messing up the US. Based on this principle, the assay detected the UDG activity down to 9.17 x 10-4 U/mL in 50 min. With URECA, we fulfilled the recovery test of UDG activities in plasma and urine with high precision and reproducibility and reliably determined UDG activities in cell extracts. Also, we verified its capability to screen candidate UDG inhibitors, showing its potentials in practical application as well as drug discovery. SIGNIFICANCE URECA offers further merits: i) the assay is seamless. Following target recognition, the reactions proceed in one-step without any intervening steps, ii) probe design is simple. Unlike the conventional CRISPR/Cas12a-based assays, URECA does not consider the PAM site in probe design as Cas12a activation relies on instantaneous gRNA binding to single-stranded DNA strands. By rationally designing an enzyme substrate probe to be specific to other enzymes, while keeping a role as a template for isothermal CRISPR amplification, the detection principle of URECA will be expanded to devise biosensors for various enzymes of biological, clinical significance.
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Affiliation(s)
- Hyogu Han
- User Convenience Technology R&D Department, Korea Institute of Industrial Technology (KITECH), Ansan, 15588, South Korea; Department of Chemistry, Gangneung-Wonju National University, Gangneung, 25457, South Korea
| | - Se Hee Jang
- User Convenience Technology R&D Department, Korea Institute of Industrial Technology (KITECH), Ansan, 15588, South Korea; Department of Medical Device Engineering and Management, College of Medicine, Yonsei University, Seoul 03722, South Korea
| | - Jun Ki Ahn
- User Convenience Technology R&D Department, Korea Institute of Industrial Technology (KITECH), Ansan, 15588, South Korea.
| | - Chang Yeol Lee
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea.
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2
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Yun W, Wang W, Lin Y, Wang R, Ha X, Yang L, Jiang Y, Zhang X. Catalytic hairpin self-assembly amplification fluorescence detection of chloramphenicol based on cross-shaped DNA and UiO-66. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 313:124110. [PMID: 38452462 DOI: 10.1016/j.saa.2024.124110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/25/2024] [Accepted: 03/02/2024] [Indexed: 03/09/2024]
Abstract
A catalytic hairpin self-assembly (CHA) amplification method was developed for CAP detection based on cross-shaped DNA and UiO-66. MOF was used to quench the fluorescent signal of FAM labeled DNA. Cross-shaped DNA with four fluorophore group (FAM) was utilized to enhance the fluorescent intensity. CAP could open hairpin structure of H-apt and induce CHA reaction. The product of CHA hybridized with cross-shaped DNA, resulting its leaving from the surface of UiO-66 and recovery of fluorescent signal. The limit of detection (LOD) was low to 0.87 pM. This method had been successfully applied for the detection of CAP in actual samples. Importantly, the high sensitivity was attributed to the great amplification efficiency of CHA, strong fluorescent intensity of cross-shaped DNA structure and great fluorescent quenched efficiency of UiO-66.
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Affiliation(s)
- Wen Yun
- Chongqing Key Laboratory of Catalysis and New Environmental Materials, College of Environment and Resources, Chongqing Technology and Business University, Chongqing 400067, China.
| | - Wanshan Wang
- Chongqing Key Laboratory of Catalysis and New Environmental Materials, College of Environment and Resources, Chongqing Technology and Business University, Chongqing 400067, China
| | - Yiyan Lin
- Chongqing Key Laboratory of Catalysis and New Environmental Materials, College of Environment and Resources, Chongqing Technology and Business University, Chongqing 400067, China
| | - Ruiqi Wang
- Chongqing Key Laboratory of Catalysis and New Environmental Materials, College of Environment and Resources, Chongqing Technology and Business University, Chongqing 400067, China
| | - Xia Ha
- Chongqing Key Laboratory of Catalysis and New Environmental Materials, College of Environment and Resources, Chongqing Technology and Business University, Chongqing 400067, China
| | - Li Yang
- The Third Hospital of Mianyang/Sichuan Mental Health Center, Mianyang, Sichuan 621000, China
| | - Yue Jiang
- Chongqing Nan'an District Ecological Environment Monitoring Station, Chongqing 401336, China.
| | - Xin Zhang
- The Third Hospital of Mianyang/Sichuan Mental Health Center, Mianyang, Sichuan 621000, China.
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3
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An experimental and Theoretical Approach of Coordination compounds derived from meso-tetra(thiophen-2-yl)porphyrin: DNA interactions and cytotoxicity. INORG CHEM COMMUN 2022. [DOI: 10.1016/j.inoche.2022.110135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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4
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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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5
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Ma F, Liu YZ, Liu M, Qiu JG, Zhang CY. Transcriptionally amplified synthesis of fluorogenic RNA aptamers for label-free DNA glycosylase assay. Chem Commun (Camb) 2022; 58:10229-10232. [PMID: 36004508 DOI: 10.1039/d2cc03628b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We demonstrate for the first time the utilization of fluorogenic RNA aptamers for label-free uracil-DNA glycosylase (UDG) assay. Through rationally engineering the transcription machine with dU substitution, this assay requires only a single probe to simultaneously sense and amplify the UDG signal, achieving a low detection limit of 6.3 × 10-6 U mL-1. Moreover, it can be applied for screening UDG inhibitors and measuring endogenous UDG activity in different cells.
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Affiliation(s)
- Fei Ma
- 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
| | - Ya-Zhen Liu
- 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.
| | - Jian-Ge Qiu
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China.
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China.
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6
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Wang L, Zhang H, Chen W, Chen H, Xiao J, Chen X. Recent advances in DNA glycosylase assays. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.10.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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7
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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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Guo X, Yang F, Jing L, Li J, Li Y, Ding R, Duan B, Zhang X. In-situ generation of highly active and four-in-one CoFe 2O 4/H 2PPOP nanozyme: Mechanism and its application for fast colorimetric detection of Cr (VI). JOURNAL OF HAZARDOUS MATERIALS 2022; 431:128621. [PMID: 35359113 DOI: 10.1016/j.jhazmat.2022.128621] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/22/2022] [Accepted: 03/01/2022] [Indexed: 05/28/2023]
Abstract
Nanozymes have been widely utilized in colorimetric sensors and developing nanomaterials with multienzyme functions have more application prospects due to their cascaded catalytic efficiency. Here, a unique organic-inorganic nanocomposite CoFe2O4/H2PPOP was synthesized by depositing CoFe2O4 nanocubes on a fully conjugated porphyrin-based porous organic polymer (H2PPOP) in situ. CoFe2O4/H2PPOP revealed outstanding tetra-enzyme-like activities, namely oxidase-like, peroxidase-like, catalase-like and superoxide dismutase-like activities. Compared with pure CoFe2O4 nanocubes, the catalytic activities of CoFe2O4/H2PPOP were significantly boosted because of the large surface area and extended conjugated structure of H2PPOP, abundant active substances (CoFe2O4) on the surface and the effective electronic transfer between CoFe2O4 and H2PPOP. Based on the oxidase-like activity of CoFe2O4/H2PPOP, a colorimetric platform was constructed for Cr (VI) with a wide linear range (0.6-100 μM) and a low detection limit (26 nΜ). Further utilizing the double oxidase-like and peroxidase-like activities, a more sensitive colorimetric platform with a faster detection speed for Cr (VI) was realized with the LOD as low as 2 nΜ. This work opens up a new way to prepare multi-enzyme active nanozyme and excavates its potential for detecting environmental pollutants.
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Affiliation(s)
- Xiaojun Guo
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong Province 250100, China
| | - Fei Yang
- School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong Province 250012, China.
| | - Lu Jing
- Geological and Mineral Exploration Institute of Shandong Province, Jinan, Shandong Province 250100, China
| | - Jie Li
- Geological and Mineral Exploration Institute of Shandong Province, Jinan, Shandong Province 250100, China
| | - Yanhong Li
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong Province 250100, China
| | - Rui Ding
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong Province 250100, China
| | - Binqiu Duan
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong Province 250100, China
| | - Xiaomei Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong Province 250100, China.
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9
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Zhang Q, Li CC, Ma F, Luo X, Zhang CY. Catalytic single-molecule Förster resonance energy transfer biosensor for uracil-DNA glycosylase detection and cellular imaging. Biosens Bioelectron 2022; 213:114447. [PMID: 35679648 DOI: 10.1016/j.bios.2022.114447] [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: 04/07/2022] [Revised: 05/21/2022] [Accepted: 05/30/2022] [Indexed: 11/02/2022]
Abstract
Uracil-DNA glycosylase (UDG) is essential to the maintenance of genomic integrity due to its critical role in base excision repair pathway. However, existing UDG assays suffer from laborious procedures, poor specificity, and limited sensitivity. In this research, we construct a catalytic single-molecule Föster resonance energy transfer (FRET) biosensor for in vitro and in vivo biosensing of UDG activity. Target UDG can remove uracil base from the detection probe and cause the cleavage of detection probe by apurinic/apyrimidinic endonuclease (APE1), which exposes its toehold domain and initiates catalytic assembly of two fluorescently labeled hairpin probes via toehold-meditated strand displacement reaction (SDA) to generate abundant DNA duplexes with amplified FRET signal. In this assay, target UDG signal is amplified via enzyme-free catalytic reaction and the whole reaction may be completed in one step, which greatly simplifies the assay procedure, reduces the assay time, and facilitates the cellular imaging. This biosensor enables specific and sensitive measurement of UDG down to 0.00029 U/mL, and it is suitable for analyzing kinetic parameters, screening inhibitors, and even imaging endogenous UDG in live cells. Importantly, this biosensor can visually quantify various DNA repair enzymes by rationally altering DNA substrates.
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Affiliation(s)
- Qian Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China
| | - Chen-Chen Li
- College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Fei Ma
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China.
| | - Xiliang Luo
- College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China.
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10
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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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Liu T, Li Z, Chen M, Zhao H, Zheng Z, Cui L, Zhang X. Sensitive electrochemical biosensor for Uracil-DNA glycosylase detection based on self-linkable hollow Mn/Ni layered doubled hydroxides as oxidase-like nanozyme for cascade signal amplification. Biosens Bioelectron 2021; 194:113607. [PMID: 34507096 DOI: 10.1016/j.bios.2021.113607] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/11/2021] [Accepted: 08/29/2021] [Indexed: 02/06/2023]
Abstract
Nanozymes have been widely used in biosensors instead of natural enzymes because of low cost, high stability and ease of storage. However, few works use oxidase-like nanozymes to fabricate electrochemical biosensors. Herein, we proposed a sensitive electrochemical biosensor to detect uracil-DNA glycosylase (UDG) based on the hollow Mn/Ni layered doubled hydroxides (h-Mn/Ni LDHs) as oxidase-like nanozyme. Briefly, the h-Mn/Ni LDHs, which was prepared by a facile hydrothermal method, exhibited excellent oxidase-like activity because the hollow structure provided rich active sites and high specific surface area. Then, the signal probes were constructed by assembling the hairpin DNA (hDNA), single DNA1 and DNA2 on the h-Mn/Ni LDHs, respectively. In the presence of UDG, the uracil bases in the stem of hDNA were specifically excised, generating apyrimidinic (AP) sites and inducing the unwinding of the hDNA. Afterwards, the h-Mn/Ni LDHs@Au-hDNA/DNA1 was connected on the electrode via hybridization between unwinded hDNA and capture DNA (cDNA). Subsequently, the self-linking process allowed the retention of numerous h-Mn/Ni LDHs through simple DNA hybridization to amplify the signal of o-phenylenediamine (o-PD). Unlike many peroxidase-like nanozyme-based electrochemical biosensors, there is no need to add H2O2 during the experimental process, which effectively reduced the background signal as well as improved the stability of the biosensor. As expected, the biosensor exhibited excellent performance with a wide linear range and a low detection limit. This work highlights an appealing opportunity to develop a no H2O2 platform based on h-Mn/Ni LDHs for future application in biological analysis and clinical diagnosis.
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Affiliation(s)
- Tingting Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, 250100, China
| | - Zhiwen Li
- School of Chemistry and Pharmaceutical Engineering, Shandong First Medical University & Shandong Academy of Medical Science, Taian, 271016, PR China
| | - Mohan Chen
- Jinan Foreign Language School, Jinan, Shandong Province, 250353, China
| | - Huijuan Zhao
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, 250100, China
| | - Zekun Zheng
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, 250100, China
| | - Lin Cui
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, Shandong, 250014, China.
| | - Xiaomei Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, 250100, China.
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12
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Yu X, Zhang S, Guo W, Li B, Yang Y, Xie B, Li K, Zhang L. Recent Advances on Functional Nucleic-Acid Biosensors. SENSORS (BASEL, SWITZERLAND) 2021; 21:7109. [PMID: 34770415 PMCID: PMC8587875 DOI: 10.3390/s21217109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/17/2021] [Accepted: 10/23/2021] [Indexed: 02/07/2023]
Abstract
In the past few decades, biosensors have been gradually developed for the rapid detection and monitoring of human diseases. Recently, functional nucleic-acid (FNA) biosensors have attracted the attention of scholars due to a series of advantages such as high stability and strong specificity, as well as the significant progress they have made in terms of biomedical applications. However, there are few reports that systematically and comprehensively summarize its working principles, classification and application. In this review, we primarily introduce functional modes of biosensors that combine functional nucleic acids with different signal output modes. In addition, the mechanisms of action of several media of the FNA biosensor are introduced. Finally, the practical application and existing problems of FNA sensors are discussed, and the future development directions and application prospects of functional nucleic acid sensors are prospected.
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Affiliation(s)
| | | | | | | | | | | | | | - Li Zhang
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.Y.); (S.Z.); (W.G.); (B.L.); (Y.Y.); (B.X.); (K.L.)
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13
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A Cu2O/PEDOT/graphene-modified electrode for the enzyme-free detection and quantification of glucose. J Electroanal Chem (Lausanne) 2021. [DOI: 10.1016/j.jelechem.2021.115558] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Yang Y, Liu X, Zhang N, Jiang W. The dumbbell probe mediated triple cascade signal amplification strategy for sensitive and specific detection of uracil DNA glycosylase activity. Talanta 2021; 234:122680. [PMID: 34364480 DOI: 10.1016/j.talanta.2021.122680] [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: 05/28/2021] [Revised: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 10/21/2022]
Abstract
Uracil DNA glycosylase (UDG) is a key base excision repair (BER) enzyme and its abnormal expression is nearly relevant to several diseases including cancer. The sensitive detection of UDG activity is beneficial for biomedical studies and clinic diagnosis. In this work, we proposed a dumbbell probe mediated triple cascade signal amplification strategy for sensitive and specific detection of UDG activity. The specially designed dumbbell probe contained two uracil bases, two recognition sites for nicking enzyme and a split sequence of DNAzyme. Unsealed dumbbell probes were first connected into sealed dumbbell probes by T4 DNA ligase, and then the unsealed probes were hydrolyzed by exonuclease to ensure the purity of probes. Under the influence of UDG, two uracil bases were removed to produce two apyrimidinic (AP) sites, which were subsequently cleaved by Endo.IV. The probes after cleavage acted as primers and templates for double nicking sites strand displacement amplification (SDA) to produce a mass of two products. The products of SDA continued to act as primers and templates for rolling circle amplification (RCA) to produce repeats containing complete DNAzyme sequences. The DNAzyme repeatedly cleaved multiple molecular beacons (MB), resulting in remarkable fluorescence enhancement. Benefiting from the triple cascade signal amplification, the sensitivity was improved and the detection limit was 7.2 × 10-5 U mL-1. The method could well distinguish UDG from other interfering enzymes and detect UDG activity in real biological samples, showing good specificity. In addition, this method could be used for screening inhibitors. The above results suggested that the method provided a promising analytical means for UDG related biomedical research and clinic diagnosis.
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Affiliation(s)
- Yayun Yang
- School of Chemistry and Chemical Engineering, Shandong University, 250100, Jinan, PR China
| | - Xiaoting Liu
- School of Chemistry and Chemical Engineering, Shandong University, 250100, Jinan, PR China; Department of Oncology, Research Center of Basic Medicine, Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, 250012, Jinan, PR China
| | - Nan Zhang
- Department of Oncology, Research Center of Basic Medicine, Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, 250012, Jinan, PR China.
| | - Wei Jiang
- School of Chemistry and Chemical Engineering, Shandong University, 250100, Jinan, PR China.
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Jiang C, Wang F, Zhang K, Min T, Chen D, Wen Y. Distance-Based Biosensor for Ultrasensitive Detection of Uracil-DNA Glycosylase Using Membrane Filtration of DNA Hydrogel. ACS Sens 2021; 6:2395-2402. [PMID: 34048234 DOI: 10.1021/acssensors.1c00624] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the deoxyribonucleic acid (DNA) repair pathways, DNA repair enzymes have great significance for genomic integrity. As one important initiator of the base-excision repair pathway, the aberrant activity of uracil-DNA glycosylase (UDG) is closely associated with many diseases. Herein, we developed a simple distance-based device for visual detection of UDG activity using a load-free DNA hydrogel. The DNA hydrogel consists of polyacrylamide-DNA chains being bridged by a single-stranded DNA crosslinker containing a responsive uracil base site. UDG can recognize and remove the uracil, resulting in the cleavage effect of the DNA crosslinker strand with the assistance of endonuclease IV (Endo IV). Plugging one end of the capillary tube, the DNA hydrogel acting as a filter membrane separator would control molecules to flow into the tube. The integrity of the DNA hydrogel networks is affected by the excision of UDG. Therefore, taking full advantage of membrane filtration of the DNA hydrogel, the activity of UDG can be quantitatively detected via reading the distance of the red indicator solution in the capillary tube. Without any instruments and complicated procedures, this method realizes high sensitivity and specificity for the detection of UDG as low as 0.02 mU/mL and can even measure UDG in complex cell samples. Additionally, this method is simple, universal, and can be used to screen inhibitors, which shows great potential for point-of-care testing, clinical diagnosis, and drug discovery.
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Affiliation(s)
- Chao Jiang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, People’s Republic of China
| | - Fangfang Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, People’s Republic of China
| | - Kexin Zhang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, People’s Republic of China
| | - Tiantian Min
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, People’s Republic of China
| | - Desheng Chen
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, People’s Republic of China
| | - Yongqiang Wen
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Daxing Research Institute, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, People’s Republic of China
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Li BR, Tang H, Yu RQ, Jiang JH. Single-Nanoparticle ICP-MS for Sensitive Detection of Uracil-DNA Glycosylase Activity. Anal Chem 2021; 93:8381-8385. [PMID: 34100608 DOI: 10.1021/acs.analchem.1c01447] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Single-nanoparticle inductively coupled plasma mass spectrometry (SP-ICP-MS) has demonstrated unique advantages for the detection of biological samples. However, methods for enzyme activity detection based on SP-ICP-MS technology have been rarely explored. Here we report the development of a novel SP-ICP-MS assay for uracil-DNA glycosylase (UDG) activity detection based on its ability to specifically recognize and remove uracil to induce the cleavage of the DNA probe. Our design allows the generation of single gold nanoparticles correlated to the specific enzymatic reaction for a highly sensitive SP-ICP-MS measurement. The developed assay enables sensitive UDG activity detection with a detection limit of 0.0003 U/mL. The cell lysate analysis by the developed assay reveals its applicability for the detection of UDG activity in real samples. It is envisioned that our design may provide a new paradigm for developing the SP-ICP-MS assay for enzyme activity detection in biological samples.
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Affiliation(s)
- Bang-Rui Li
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Hao Tang
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Ru-Qin Yu
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Jian-Hui Jiang
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
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Interactions of porphyrins with DNA: A review focusing recent advances in chemical modifications on porphyrins as artificial nucleases. J Inorg Biochem 2021; 219:111434. [PMID: 33819802 DOI: 10.1016/j.jinorgbio.2021.111434] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/18/2021] [Accepted: 03/18/2021] [Indexed: 12/14/2022]
Abstract
The advance of porphyrins as artificial nucleases along the years have developed a class of compounds having potential therapeutic applications. Being an extrovert of chemistry, a variety of chemical modifications have been done on porphyrin macrocycle in order to improve the spectroscopic properties and to adapt as artificial receptors that can recognize molecules. The last twenty years has witnessed broad research in the arena of porphyrin- DNA interactions and their evolution from simple to more complex entities. In this review, we summarize the recent advances in the porphyrin-based structural modifications, with a specific emphasis on various effects of porphyrin on DNA cleavage potency. We particularly detailed the nuclease activity of cationic and anionic porphyrins, porphyrin dimers and conjugates as well as heme proteins till the third generation porphyrins as artificial nucleases.
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Chen Y, Fang Y, Yu J, Gao W, Zhao H, Zhang X. A silsesquioxane-porphyrin-based porous organic polymer as a highly efficient and recyclable absorbent for wastewater treatment. JOURNAL OF HAZARDOUS MATERIALS 2021; 406:124769. [PMID: 33316666 DOI: 10.1016/j.jhazmat.2020.124769] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/10/2020] [Accepted: 12/01/2020] [Indexed: 06/12/2023]
Abstract
Effective capture of pollutants from wastewater is crucial for protecting the environment and human health. An azo-based porous organic polymer (AzoPPOP) containing porphyrin and inorganics cage polyhedral oligomeric silsesquioxane units was synthesized via a catalyst-free coupling reaction. Results showed that AzoPPOP possess a high surface area, a hierarchically porous structure, good thermal stability, abundant adsorption sites, and an electronegative nature. Based on these properties, AzoPPOP had an extremely high adsorption capacity (1357.58 mg g-1) for RhB, a fast adsorption rate, and good selectivity. Study of the mechanism revealed that in addition to electrostatic interactions, the high specific surface area, existence of -NH2, and the strong π-π interaction between AzoPPOP and RhB also play important roles for the adsorption of RhB. AzoPPOP also displayed excellent adsorption properties for heavy metal ions (230.45, 192.24 and 162.11 mg g-1 for Ag+, Hg2+, and Pb2+, respectively). More importantly, simulation of the purification experiment of waste water and the recycling regeneration experiment revealed that AzoPPOP has good high-level recyclability and could remove multi-pollutants in one pass through a simple adsorption column.
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Affiliation(s)
- Yanli Chen
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yishan Fang
- School of Food Science and Engineering, Qilu University of Technology, Jinan, Shandong 250353, China
| | - Jingkun Yu
- Jinan Shanda Experimental High School, Jinan, Shandong 250353, China
| | - Wenqiang Gao
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Huijuan Zhao
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Xiaomei Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China.
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Xu L, Li J, Shi W, Bao N, Yu C. Immobilization of hemoglobin on MnCO 3 sphere-loaded Au nanoparticles as highly efficient sensing platform towards hydrogen peroxide. NANOTECHNOLOGY 2021; 32:025503. [PMID: 32932239 DOI: 10.1088/1361-6528/abb8a5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this paper, we report the synthesis of MnCO3-Au hybrid microspheres and their application on the electrochemical biosensing of hydrogen peroxide (H2O2) based on the immobilization of hemoglobin (Hb). The characterization of MnCO3-Au microspheres revealed that an abundance of Au nanoparticles (AuNPs) has been absorbed on the surface of the spherical MnCO3 by the electrostatic assembly. The combined unique properties of MnCO3-Au microspheres are beneficial for the realization of the direct electron transfer of Hb. Hb immobilized on the microspheres maintained its biological activity, showing a surface-controlled process with the heterogeneous electron transfer rate constant (k s) of 2.63 s-1. The fabricated biosensor displayed an excellent performance for the electrocatalytic reduction of H2O2. The linear range for the determination of H2O2 was from 0.06-40.0 μM with a detection limit of 0.015 µM (S/N = 3). The biosensor also exhibited high selectivity, good repeatability and long-term stability, which offers great potential for H2O2 detection in real sample analysis.
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Affiliation(s)
- Linyi Xu
- School of Public Health, Nantong University, Nantong 226019, People's Republic of China
| | - Jing Li
- School of Public Health, Nantong University, Nantong 226019, People's Republic of China
| | - Weishan Shi
- School of Public Health, Nantong University, Nantong 226019, People's Republic of China
| | - Ning Bao
- School of Public Health, Nantong University, Nantong 226019, People's Republic of China
| | - Chunmei Yu
- School of Public Health, Nantong University, Nantong 226019, People's Republic of China
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Terminal deoxynucleotidyl transferase combined CRISPR-Cas12a amplification strategy for ultrasensitive detection of uracil-DNA glycosylase with zero background. Biosens Bioelectron 2021; 171:112734. [DOI: 10.1016/j.bios.2020.112734] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/10/2020] [Accepted: 10/13/2020] [Indexed: 12/26/2022]
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21
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Hao L, Zhao L, Li G, Li Y, Ma L, Liu Y, Wang W, Kong J. Ultrasensitive detection of CYFRA 21-1 DNA via SI-RAFT based in-situ metallization signal amplification. Microchem J 2020. [DOI: 10.1016/j.microc.2020.105216] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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