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Wang Y, Rong Y, Ma T, Li L, Li X, Zhu P, Zhou S, Yu J, Zhang Y. Photoelectrochemical sensors based on paper and their emerging applications in point-of-care testing. Biosens Bioelectron 2023; 236:115400. [PMID: 37271095 DOI: 10.1016/j.bios.2023.115400] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/01/2023] [Accepted: 05/14/2023] [Indexed: 06/06/2023]
Abstract
Point-of-care testing (POCT) technology is urgently required owing to the prevalence of the Internet of Things and portable electronics. In light of the attractive properties of low background and high sensitivity caused by the complete separation of excitation source and detection signal, the paper-based photoelectrochemical (PEC) sensors, featured with fast in analysis, disposable and environmental-friendly have become one of the most promising strategies in POCT. Therefore, in this review, the latest advances and principal issues in the design and fabrication of portable paper-based PEC sensors for POCT are systematically discussed. Primarily, the flexible electronic devices that can be constructed by paper and the reasons why they can be used in PEC sensors are expounded. Afterwards, the photosensitive materials involved in paper-based PEC sensor and the signal amplification strategies are emphatically introduced. Subsequently, the application of paper-based PEC sensors in medical diagnosis, environmental monitoring and food safety are further discussed. Finally, the main opportunities and challenges of paper-based PEC sensing platforms for POCT are briefly summarized. It provides a distinct perspective for researchers to construct paper-based PEC sensors with portable and cost-effective, hoping to enlighten the fast development of POCT soon after, as well as benefit human society.
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Affiliation(s)
- Yixiang Wang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, China
| | - Yumeng Rong
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, China
| | - Tinglei Ma
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, China
| | - Lin Li
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, China
| | - Xu Li
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, China
| | - Peihua Zhu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, China
| | - Shuang Zhou
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, China.
| | - Jinghua Yu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, China.
| | - Yan Zhang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, 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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2
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Recent advance in nucleic acid amplification-integrated methods for DNA methyltransferase assay. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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3
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Xue W, Song K, Chang Y, Liu M. Colorimetric Detection of DNase Type I 3'OH DNA Ends Using an Isothermal Amplification-Assisted Paper-Based Analytical Device. BIOSENSORS 2022; 12:1012. [PMID: 36421130 PMCID: PMC9688845 DOI: 10.3390/bios12111012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 06/16/2023]
Abstract
The generation of DNase type I 3'OH DNA ends is closely related to the harm of endogenous reactive oxygen species (ROS) and environmental genotoxic agents. The evaluation of this type of DNA damage plays an important role in clinical intervention and environmental toxicity assessment. Terminal deoxynucleotidyl transferase (TdT)-assisted isothermal amplification (TAIA) offers a facile and versatile way to detect DNase type I 3'OH DNA ends. Its ability of templated-independent isothermal amplification is one unique feature. Here, we reported a paper-based analytical device (PAD) coupled with a smartphone for the detection of DNase type I 3'OH DNA ends using TAIA and colorimetric signal readout. We achieved the integration of cell lysis, DNA extraction, TAIA, horseradish peroxidase (HRP)-enabled colorimetric reaction, and signal readout. This device could achieve a limit of detection of 264 cells with a total assay time of less than 45 min. By combining PAD with a smartphone, the integrated platform could be used for the visual and quantitative analysis of DNA damages with the advantages of ease-to-use, fast response, inexpensive, and instrument free. Furthermore, successful assessment of the genotoxicity in wastewater effluents suggested the great promise of the integrated platform for on-site testing in practical applications.
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4
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A sensing strategy combining T7 promoter-contained DNA probe with CRISPR/Cas13a for detection of bacteria and human methyltransferase. Anal Chim Acta 2022; 1227:340266. [DOI: 10.1016/j.aca.2022.340266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 08/03/2022] [Accepted: 08/12/2022] [Indexed: 11/21/2022]
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5
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A rapid and high sensitivity RNA detection based on NASBA and G4-ThT fluorescent biosensor. Sci Rep 2022; 12:10076. [PMID: 35710925 PMCID: PMC9203706 DOI: 10.1038/s41598-022-14107-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/01/2022] [Indexed: 11/15/2022] Open
Abstract
In recent years, various newly emerged and re-emerged RNA viruses have seriously threatened the global public health. There is a pressing need for rapid and reliable nucleic acid–based assays for detecting viral RNA. Here, we successfully developed a highly sensitive, easy-to-operate G4-ThT-NASBA system to detect viral RNA that no need for labeled primers and probes. Next, we tested the system for detecting the Classical Swine Fever Virus (CSFV), an RNA virus that causes a highly contagious disease in domestic pigs and wild boar and easily causes huge economic losses. Results showed that the system, integrated the G4-ThT fluorescent biosensor and NASBA (Nuclear acid sequence-based amplification),is capable to detect as little as 2 copies/μL of viral RNA without interfering by other swine viral RNA. Moreover, we were able to detect CSFV RNA within 2 h in serum samples taken from the field in a real-time mode. These findings indicate that the G4-ThT-NASBA system is a rapid, high sensitivity and easy-to-operate technique for RNA detection. The method also has the real-time detection capability which may be easily integrated in a highly automated system such as microfluidic chips.
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6
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Han Y, Wang C, Zou X, Zhang Y, Xu Q, Zhang CY. Construction of an APE1-Mediated Cascade Signal Amplification Platform for Homogeneously Sensitive and Rapid Measurement of DNA Methyltransferase in Escherichia coli Cells. Anal Chem 2022; 94:5980-5986. [PMID: 35394287 DOI: 10.1021/acs.analchem.2c00439] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
DNA methylation is an essential genomic epigenetic behavior in both eukaryotes and prokaryotes. Deregulation of DNA methyltransferase (Dam MTase) can change the DNA methylation level and cause various diseases. Herein, we develop an apurinic/apyrimidinic endonuclease 1 (APE1)-mediated cascade signal amplification platform for homogeneously sensitive and rapid measurement of Dam MTase in Escherichia coli cells. This assay involves a partial double-stranded DNA (dsDNA) substrate and two hairpin signal probes (HP1 and HP2) that are modified with Cy5 and BHQ2 at two ends, respectively. When Dam MTase is present, it methylates the dsDNA substrate, and subsequently, endonuclease DpnI cleaves the methylated substrate, yielding trigger probe 1. Hybridization of trigger probe 1 with HP1 forms a partial dsDNA containing an apurinic/apyrimidinic (AP) site, which is cleaved by APE1 to induce the cyclic cleavage of HP1 and the production of abundant trigger probe 2. Subsequent hybridization of trigger probe 2 with HP2 forms a partial dsDNA with an AP site, inducing the cyclic cleavage of HP2 by APE1. Consequently, cyclic cleavage of HP1 and HP2 induces the generation of abundant Cy5 molecules, which are easily measured by single-molecule imaging. This assay can be performed homogeneously and rapidly within 2 h, which is the shortest among the reported amplification-based assays. Moreover, it exhibits good selectivity and high sensitivity, and it can discriminate Dam MTase from other enzymes and screen inhibitors. Importantly, it can accurately measure the Dam MTase activity in serum and E. coli cells, with promising applications in clinical diagnosis and drug discovery.
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Affiliation(s)
- Yun Han
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Chen Wang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Xiaoran Zou
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Yan Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.,College of Chemistry and Chemical Engineering, Qilu Normal University, Jinan 250200, China
| | - Qinfeng Xu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, 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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Wang Y, Sun W, Wang J, Wang X, Xu Y, Guo Y, Wang Y, Zhang M, Jiang L, Liu S, Huang J. Ultrasensitive Uracil-DNA Glycosylase Activity Assay and Its Inhibitor Screening Based on Primer Remodeling Jointly via Repair Enzyme and Polymerase. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:3868-3875. [PMID: 35298179 DOI: 10.1021/acs.langmuir.2c00115] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The development of isothermal nucleic acid amplification techniques has great significance for highly sensitive biosensing in modern biology and biomedicine. A facile and robust exponential rolling circle amplification (RCA) strategy is proposed based on primer-remodeling amplification jointly via a repair enzyme and polymerase, and uracil-DNA glycosylase (UDG) is selected as a model analyte. Two kinds of complexes, complex I and complex II, are preprepared by hybridizing a circular template (CT) with a uracil-containing hairpin probe and tetrahydrofuran abasic site mimic (AP site)-embedded fluorescence-quenched probe (AFP), respectively. The target UDG specifically binds to complex I, resulting in the generation of an AP site, followed by cleavage via endonuclease IV (Endo IV) and the successive trimming of unmatched 3' terminus via phi29 DNA polymerase, thus producing a useable primer-CT complex that actuates the primary RCA. Then, numerous complex II anneal with the first-generation RCA product (RP), generating a complex II-RP assembly containing AP sites within the DNA duplex. With the aid of Endo IV and phi29, AFP, as a pre-primer in complex II, is converted into a mature primer to initiate additional rounds of RCA. So, countless AFPs are cleaved, releasing remarkably strong fluorescent signals. The biosensor is demonstrated to enable rapid and accurate detection of the UDG activity with an improved detection limit as low as 4.7 × 10-5 U·mL-1. Moreover, this biosensor is successfully applied for UDG inhibitor screening and complicated biological samples analysis. Compared to the previous exponential RCA methods, our proposed strategy offers additional advantages, including excellent stability, optional design of CT, and simplified operating steps. Therefore, this proposed strategy may create a useful and practical platform for ultrasensitive detection of low levels of analytes in clinical diagnosis and fundamental biomedicine research.
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Affiliation(s)
- Yu Wang
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P. R. China
| | - Wenyu Sun
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P. R. China
| | - Jingfeng Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Xu Wang
- Shandong Institute of Metrology and Science, Jinan 250014, P. R. China
| | - Yicheng Xu
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P. R. China
| | - Yuanzhen Guo
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P. R. China
| | - Yeru Wang
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P. R. China
| | - Manru Zhang
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, P. R. China
| | - Long Jiang
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, P. R. China
| | - Su Liu
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, P. R. China
| | - Jiadong Huang
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P. R. China
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8
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Pradhan A, Lahare P, Sinha P, Singh N, Gupta B, Kuca K, Ghosh KK, Krejcar O. Biosensors as Nano-Analytical Tools for COVID-19 Detection. SENSORS (BASEL, SWITZERLAND) 2021; 21:7823. [PMID: 34883826 PMCID: PMC8659776 DOI: 10.3390/s21237823] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/11/2021] [Accepted: 11/18/2021] [Indexed: 12/24/2022]
Abstract
Selective, sensitive and affordable techniques to detect disease and underlying health issues have been developed recently. Biosensors as nanoanalytical tools have taken a front seat in this context. Nanotechnology-enabled progress in the health sector has aided in disease and pandemic management at a very early stage efficiently. This report reflects the state-of-the-art of nanobiosensor-based virus detection technology in terms of their detection methods, targets, limits of detection, range, sensitivity, assay time, etc. The article effectively summarizes the challenges with traditional technologies and newly emerging biosensors, including the nanotechnology-based detection kit for COVID-19; optically enhanced technology; and electrochemical, smart and wearable enabled nanobiosensors. The less explored but crucial piezoelectric nanobiosensor and the reverse transcription-loop mediated isothermal amplification (RT-LAMP)-based biosensor are also discussed here. The article could be of significance to researchers and doctors dedicated to developing potent, versatile biosensors for the rapid identification of COVID-19. This kind of report is needed for selecting suitable treatments and to avert epidemics.
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Affiliation(s)
- Anchal Pradhan
- Center for Basic Sciences, Department of Chemistry, Pt. Ravishankar Shukla University, Raipur 492010, India; (A.P.); (P.L.); (P.S.); (K.K.G.)
| | - Preeti Lahare
- Center for Basic Sciences, Department of Chemistry, Pt. Ravishankar Shukla University, Raipur 492010, India; (A.P.); (P.L.); (P.S.); (K.K.G.)
| | - Priyank Sinha
- Center for Basic Sciences, Department of Chemistry, Pt. Ravishankar Shukla University, Raipur 492010, India; (A.P.); (P.L.); (P.S.); (K.K.G.)
| | - Namrata Singh
- Ramrao Adik Institute of Technology, DY Patil University, Nerul, Navi Mumbai 400706, India
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 50003 Hradec Kralove, Czech Republic
| | - Bhanushree Gupta
- Center for Basic Sciences, Department of Chemistry, Pt. Ravishankar Shukla University, Raipur 492010, India; (A.P.); (P.L.); (P.S.); (K.K.G.)
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 50003 Hradec Kralove, Czech Republic
- Biomedical Research Center, University Hospital, Sokolska 581, 50005 Hradec Kralove, Czech Republic
| | - Kallol K. Ghosh
- Center for Basic Sciences, Department of Chemistry, Pt. Ravishankar Shukla University, Raipur 492010, India; (A.P.); (P.L.); (P.S.); (K.K.G.)
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur 492010, India
| | - Ondrej Krejcar
- Center for Basic and Applied Research, Faculty of Informatics and Management, University of Hradec Kralove, Rokitanskeho 62, 50003 Hradec Kralove, Czech Republic;
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Liu H, You Y, Zhu Y, Zheng H. Recent advances in the exonuclease III-assisted target signal amplification strategy for nucleic acid detection. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:5103-5119. [PMID: 34664562 DOI: 10.1039/d1ay01275d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The detection of nucleic acids has become significantly important in molecular diagnostics, gene therapy, mutation analysis, forensic investigations and biomedical development, and so on. In recent years, exonuclease III (Exo III) as an enzyme in the 3'-5' exonuclease family has evolved as a frequently used technique for signal amplification of low level DNA target detection. Different from the traditional target amplification strategies, the Exo III-assisted amplification strategy has been used for target DNA detection through directly amplifying the amounts of signal reagents. The Exo III-assisted amplification strategy has its unique advantages and characters, because the character of non-specific recognition of Exo III can overcome the limitation of a target-to-probe ratio of 1 : 1 in the traditional nucleic acid hybridization assay and acquire higher sensitivity. In this review, we selectively discuss the recent advances in the Exo III-assisted amplification strategy, including the amplification strategy integrated with nanomaterials, biosensors, hairpin probes and other nucleic acid detection methods. We also discuss the strengths and limitations of each strategy and methods to overcome the limitations.
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Affiliation(s)
- Hongyu Liu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, P. R. China.
| | - Yuhao You
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, P. R. China.
| | - Youzhuo Zhu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, P. R. China.
| | - Heng Zheng
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, P. R. China.
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Z-DNA as a Tool for Nuclease-Free DNA Methyltransferase Assay. Int J Mol Sci 2021; 22:ijms222111990. [PMID: 34769422 PMCID: PMC8585049 DOI: 10.3390/ijms222111990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/29/2021] [Accepted: 10/30/2021] [Indexed: 01/16/2023] Open
Abstract
Methylcytosines in mammalian genomes are the main epigenetic molecular codes that switch off the repertoire of genes in cell-type and cell-stage dependent manners. DNA methyltransferases (DMT) are dedicated to managing the status of cytosine methylation. DNA methylation is not only critical in normal development, but it is also implicated in cancers, degeneration, and senescence. Thus, the chemicals to control DMT have been suggested as anticancer drugs by reprogramming the gene expression profile in malignant cells. Here, we report a new optical technique to characterize the activity of DMT and the effect of inhibitors, utilizing the methylation-sensitive B-Z transition of DNA without bisulfite conversion, methylation-sensing proteins, and polymerase chain reaction amplification. With the high sensitivity of single-molecule FRET, this method detects the event of DNA methylation in a single DNA molecule and circumvents the need for amplification steps, permitting direct interpretation. This method also responds to hemi-methylated DNA. Dispensing with methylation-sensitive nucleases, this method preserves the molecular integrity and methylation state of target molecules. Sparing methylation-sensing nucleases and antibodies helps to avoid errors introduced by the antibody’s incomplete specificity or variable activity of nucleases. With this new method, we demonstrated the inhibitory effect of several natural bio-active compounds on DMT. All taken together, our method offers quantitative assays for DMT and DMT-related anticancer drugs.
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Cai Y, Zhang Y, Wang H, Lin X, Yu K, Li C, Jie G. Cyclometalated Iridium(III) Complex-Sensitized NiO-Based-Cathodic Photoelectrochemical Platform for DNA Methyltransferase Assay. ACS APPLIED BIO MATERIALS 2021; 4:6103-6111. [PMID: 35006914 DOI: 10.1021/acsabm.1c00445] [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] [Indexed: 12/14/2022]
Abstract
This work reports an efficient [(C6)2Ir(dppz)]+PF6- (C6 = coumarin 6 and dppz = dipyridophenazine)-sensitized NiO photocathode and its application in photoelectrochemical (PEC) bioanalysis field for the first time. This dye-sensitized NiO photocathode was found to exhibit a markedly enhanced cathodic photocurrent. A sensitive cathodic PEC platform was proposed integrating the as-prepared photocathode with enzyme-free cascaded amplification strategies of the catalytic hairpin assembly (CHA) and the hybridization chain reaction (HCR) for DNA methyltransferase (MTase) assay. A hairpin DNA(HDam) with specific recognition site of Dam MTase in its stem was designed. The site of HDam was methylated in the presence of Dam MTase and then cut by endonuclease DpnI. The released loop fragment, as an initiator, triggered the CHA circuit and the follow-up HCR circuit, resulting in long dsDNA concatemers on the ITO electrode. Numerous [(C6)2Ir(dppz)]+PF6- were intercalated into dsDNA, and highly efficient signal amplification was realized. Benefiting from the superior iridium(III) complex-sensitized NiO photocathode and effective amplification strategy, a detection limit of 0.0028 U/mL for the determination of Dam MTase was achieved. Moreover, this work further demonstrated that these proposed tactics could be applied to screen Dam MTase activity inhibitors.
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Affiliation(s)
- Yueyuan Cai
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Yingtao Zhang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Huan Wang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Xiaojia Lin
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Kunpeng Yu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Chunxiang Li
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Guifen Jie
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
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12
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Wang X, Zhou S, Chu C, Yang M, Huo D, Hou C. Dual Methylation-Sensitive Restriction Endonucleases Coupling with an RPA-Assisted CRISPR/Cas13a System (DESCS) for Highly Sensitive Analysis of DNA Methylation and Its Application for Point-of-Care Detection. ACS Sens 2021; 6:2419-2428. [PMID: 34019391 DOI: 10.1021/acssensors.1c00674] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
High-performance detection of DNA methylation possesses great significance for the diagnosis and therapy of cancer. Herein, for the first time, we present a digestion strategy based on dual methylation-sensitive restriction endonucleases coupling with a recombinase polymerase amplification (RPA)-assisted CRISPR/Cas13a system (DESCS) for accurate and sensitive determination of site-specific DNA methylation. This dual methylation-sensitive restriction endonuclease system selectively digests the unmethylated target but exhibits no response to methylated DNA. Therefore, the intact methylated DNA target triggers the RPA reaction for rapid signal amplification. In contrast, the digested unmethylated target initiates no RPA reaction. RPA products with a T7 promoter can execute the T7 transcription in the presence of T7 RNA polymerase to generate a large number of single-stranded RNA (ssRNA). This ssRNA can be recognized by CRISPR/Cas13a to induce the ssRNase activity of Cas13a, showing the indiscriminate cleavage of the collateral FQ reporter to release the fluorescence signal. With such a design, by combining the unique features of dual methylation-sensitive restriction endonucleases with RPA-assisted CRISPR/Cas13a, the DESCS system not only presents the rapid and powerful signal amplification for the determination of methylated DNA with ultrahigh sensitivity but also effectively eliminates the false positive influences from incomplete digestion of the unmethylated target. More importantly, 0.01% methylation level can be effectively distinguished with the existence of excess unmethylated DNA. In addition, the DESCS assay is integrated into the lateral flow biosensor (LFB) for the point-of-care determination of DNA methylation. In view of the superiorities in high sensitivity, outstanding selectivity, and ease of operation, the DESCS system will provide a reliable assay for site-specific analysis of methylation.
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Affiliation(s)
- Xianfeng Wang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Shiying Zhou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Chengxiang Chu
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Mei Yang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
- Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing 400044, P. R. China
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
- Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing 400044, P. R. China
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13
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Tao G, Xu X, Li RS, Liu F, Li N. Nonamplification Multiplexed Assay of Endonucleases and DNA Methyltransferases by Colocalized Particle Counting. ACS Sens 2021; 6:1321-1329. [PMID: 33496573 DOI: 10.1021/acssensors.0c02665] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Restriction endonucleases (ENases) and DNA methyltransferases (MTases) are important enzymes in biological processes, and detection of ENases/MTases activity is significant for biological and pharmaceutical studies. However, available nonamplification methods with a versatile design, desirable sensitivity, and signal production mode of unbiased quantification toward multiple nucleases are rare. By combining deliberately designed hairpin DNA probes with the colocalized particle counting technique, we present a nonamplification, separation-free method for multiplexed detection of ENases and MTases. In the presence of target ENases, the hairpin DNA is cleaved and the resulting DNA sequence forms a sandwich structure to tie two different-colored fluorescent microbeads together to generate a colocalization signal that can be easily detected using a standard fluorescence microscope. The multiplexed assay is realized via different color combinations. For the assay of methyltransferase, methylation by MTases prevents cleavage of the hairpin by the corresponding ENase, leading to decreased colocalization events. Three ENases can be simultaneously detected with high selectivity, minimal cross-talk, and detection limits of (4.1-6.4) × 10-4 U/mL, and the corresponding MTase activity can be measured without a change of the probe design. The potential for practical application is evaluated with human serum samples and different ENase and MTase inhibitors with satisfactory results. The proposed method is separation-free, unbiased toward multiple targets, and easy to implement, and the strategy has the potential to be extended to other targets.
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Affiliation(s)
- Guangyu Tao
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiao Xu
- Environmental Metrology Center, National Institute of Metrology, Beijing 100029, China
| | - Rong Sheng Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Feng Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Na Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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14
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Li Z, Zou S, Wu S, Miao X, Ma DL. Polymerase chain reaction-based ultrasensitive detection of HBV DNA via G-quadruplex selective iridium(III) complex luminescent probe. Talanta 2021; 221:121661. [DOI: 10.1016/j.talanta.2020.121661] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/07/2020] [Accepted: 09/09/2020] [Indexed: 12/20/2022]
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15
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Xu L, Duan J, Chen J, Ding S, Cheng W. Recent advances in rolling circle amplification-based biosensing strategies-A review. Anal Chim Acta 2020; 1148:238187. [PMID: 33516384 DOI: 10.1016/j.aca.2020.12.062] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/09/2020] [Accepted: 12/28/2020] [Indexed: 01/12/2023]
Abstract
Rolling circle amplification (RCA) is an efficient enzymatic isothermal reaction that using circular probe as a template to generate long tandem single-stranded DNA or RNA products under the initiation of short DNA or RNA primers. As a simplified derivative of natural rolling circle replication which synthesizes copies of circular nucleic acids molecules such as plasmids, RCA amplifies the circular template rapidly without thermal cycling and finds various applications in molecular biology. Compared with other amplification strategies, RCA has many obvious advantages. Firstly, because of the strict complementarity required in ligation of a padlock probe, it endows the RCA reaction with high specificity and can even be utilized to distinguish single base mismatches. Secondly, through the introduction of multiple primers, exponential amplification can be achieved easily and leads to a good sensitivity. Thirdly, RCA products can be customized by manipulating circular templates to generate functional nucleic acids such as aptamer, DNAzymes and restriction enzyme sites. Moreover, the RCA has good biocompatibility and is especially suitable for in situ detection. Therefore, RCA has attracted considerable attention as an efficient and potential tool for highly sensitive detection of biomarkers. Herein, we comprehensively introduce the fundamental principles of RCA technology, summarize it from three aspects including initiation mode, amplification mode and signal output mode, and discuss the recent application of RCA-based biosensor in this review.
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Affiliation(s)
- Lulu Xu
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Jiaxin Duan
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Junman Chen
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China.
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16
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Luo X, Kang T, Zhu J, Wu P, Cai C. Sensitivity-Improved SERS Detection of Methyltransferase Assisted by Plasmonically Engineered Nanoholes Array and Hybridization Chain Reaction. ACS Sens 2020; 5:3639-3648. [PMID: 33147006 DOI: 10.1021/acssensors.0c02016] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Detection of methyltransferase (MTase) activity is of great significance in methylation-related disease diagnosis and drug screening. Herein, we present a dual-amplification sensing strategy that is assisted by plasmonically enhanced Raman intensity at engineered nanoholes array, along with signal amplification by the hybridization chain reaction (HCR) for the ultrasensitive detection of M.SssI MTase activity and inhibitor screening. An engineered surface-enhanced Raman scattering (SERS) substrate, namely, a structured nanoholes array (NHA) with wavelength-matched surface plasmon resonance (SPR) at the wavelength of laser excitation (785 nm), was rationally designed through finite-difference time-domain (FDTD) simulations, precisely fabricated through master-assisted replication, and then used as a sensing platform. Uniform and intense SERS signals were achieved by turning on the plasmonic enhancement under the excitation of SPR. Probe DNA was designed to hybridize with target DNA (a BRCA1 gene fragment), and the formed dsDNA with the recognition site of M.SssI was assembled on the NHA. In the presence of M.SssI, the HCR process was triggered upon adding DNAs labeled with the Raman reporter Cy5, leading to an amplified SERS signal of Cy5. The intensity of Cy5 increases with increasing M.SssI activity, which establishes the basis of the assay for M.SssI. The developed assay displays an ultrasensitivity that has a broad linear range (0.002-200 U/mL) and a low detection limit (2 × 10-4 U/mL), which is superior to that of the reported SERS-based detection methods. Moreover, it can selectively detect M.SssI in human serum samples and evaluate the efficiency of M.SssI inhibitors.
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Affiliation(s)
- Xiaojun Luo
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Tuli Kang
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Jingtian Zhu
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Ping Wu
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Chenxin Cai
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
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17
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Wu J, Hu Q, Chen Q, Dai J, Wu X, Wang S, Lou X, Xia F. Modular DNA-Incorporated Aggregation-Induced Emission Probe for Sensitive Detection and Imaging of DNA Methyltransferase. ACS APPLIED BIO MATERIALS 2020; 3:9002-9011. [DOI: 10.1021/acsabm.0c01249] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jun Wu
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, China
| | - Qinyu Hu
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, China
| | - Qing Chen
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, China
| | - Jun Dai
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xia Wu
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, China
| | - Shixuan Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiaoding Lou
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, China
| | - Fan Xia
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, China
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18
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Yan XL, Xue XX, Deng XM, Jian YT, Luo J, Jiang MM, Zheng XJ. Chemiluminescence strategy induced by HRP-sandwich structure based on strand displacement for sensitive detection of DNA methyltransferase. Microchem J 2020. [DOI: 10.1016/j.microc.2020.105183] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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19
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Chen X, Cao G, Wang X, Ji Z, Xu F, Huo D, Luo X, Hou C. Terminal deoxynucleotidyl transferase induced activators to unlock the trans-cleavage of CRISPR/Cpf 1 (TdT-IU- CRISPR/Cpf 1): An ultrasensitive biosensor for Dam MTase activity detection. Biosens Bioelectron 2020; 163:112271. [DOI: 10.1016/j.bios.2020.112271] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/13/2020] [Accepted: 05/01/2020] [Indexed: 12/14/2022]
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20
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Wang LJ, Han X, Qiu JG, Jiang B, Zhang CY. Cytosine-5 methylation-directed construction of a Au nanoparticle-based nanosensor for simultaneous detection of multiple DNA methyltransferases at the single-molecule level. Chem Sci 2020; 11:9675-9684. [PMID: 34094232 PMCID: PMC8161687 DOI: 10.1039/d0sc03240a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/25/2020] [Indexed: 12/28/2022] Open
Abstract
DNA methylation at cytosine/guanine dinucleotide islands (CpGIs) is the most prominent epigenetic modification in prokaryotic and eukaryotic genomes. DNA methyltransferases (MTases) are responsible for genomic methylation, and their aberrant activities are closely associated with various diseases including cancers. However, the specific and sensitive detection of multiple DNA MTases has remained a great challenge due to the specificity of the methylase substrate and the rareness of methylation-sensitive restriction endonuclease species. Here, we demonstrate for the first time the cytosine-5 methylation-directed construction of a Au nanoparticle (AuNP)-based nanosensor for simultaneous detection of multiple DNA MTases at the single-molecule level. We used the methyl-directed endonuclease GlaI to cleave the site-specific 5-methylcytosine (5-mC). In the presence of CpG and GpC MTases (i.e., M.SssI and M.CviPI), their hairpin substrates are methylated at cytosine-5 to form the catalytic substrates for GlaI, respectively, followed by simultaneous cleavage by GlaI to yield two capture probes. These two capture probes can hybridize with the Cy5/Cy3-signal probes which are assembled on the AuNPs, respectively, to form the double-stranded DNAs (dsDNAs). Each dsDNA with a guanine ribonucleotide can act as the catalytic substrate for ribonuclease (RNase HII), inducing recycling cleavage of signal probes to liberate large numbers of Cy5 and Cy3 molecules from the AuNPs. The released Cy5 and Cy3 molecules can be simply quantified by total internal reflection fluorescence (TIRF)-based single-molecule imaging for simultaneous measurement of M.SssI and M.CviPI MTase activities. This method exhibits good specificity and high sensitivity with a detection limit of 2.01 × 10-3 U mL-1 for M.SssI MTase and 3.39 × 10-3 U mL-1 for M.CviPI MTase, and it can be further applied for discriminating different kinds of DNA MTases, screening potential inhibitors, and measuring DNA MTase activities in human serum and cell lysate samples, holding great potential in biomedical research, clinical diagnosis, drug discovery and cancer therapeutics.
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Affiliation(s)
- Li-Juan Wang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University Jinan 250014 China
| | - Xiao Han
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University Jinan 250014 China
| | - Jian-Ge Qiu
- Academy of Medical Sciences, Zhengzhou University Zhengzhou 450000 China
| | - BingHua Jiang
- Academy of Medical Sciences, Zhengzhou University Zhengzhou 450000 China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University Jinan 250014 China
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21
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Li J, Mohammed-Elsabagh M, Paczkowski F, Li Y. Circular Nucleic Acids: Discovery, Functions and Applications. Chembiochem 2020; 21:1547-1566. [PMID: 32176816 DOI: 10.1002/cbic.202000003] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/13/2020] [Indexed: 12/14/2022]
Abstract
Circular nucleic acids (CNAs) are nucleic acid molecules with a closed-loop structure. This feature comes with a number of advantages including complete resistance to exonuclease degradation, much better thermodynamic stability, and the capability of being replicated by a DNA polymerase in a rolling circle manner. Circular functional nucleic acids, CNAs containing at least a ribozyme/DNAzyme or a DNA/RNA aptamer, not only inherit the advantages of CNAs but also offer some unique application opportunities, such as the design of topology-controlled or enabled molecular devices. This article will begin by summarizing the discovery, biogenesis, and applications of naturally occurring CNAs, followed by discussing the methods for constructing artificial CNAs. The exploitation of circular functional nucleic acids for applications in nanodevice engineering, biosensing, and drug delivery will be reviewed next. Finally, the efforts to couple functional nucleic acids with rolling circle amplification for ultra-sensitive biosensing and for synthesizing multivalent molecular scaffolds for unique applications in biosensing and drug delivery will be recapitulated.
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Affiliation(s)
- Jiuxing Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Mostafa Mohammed-Elsabagh
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Freeman Paczkowski
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Yingfu Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
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22
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Wang LJ, Lu YY, Zhang CY. Construction of a self-directed replication system for label-free and real-time sensing of repair glycosylases with zero background. Chem Sci 2020; 11:587-595. [PMID: 32206275 PMCID: PMC7069502 DOI: 10.1039/c9sc04738g] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 11/25/2019] [Indexed: 12/17/2022] Open
Abstract
Genomic DNA damage and repair are involved in multiple fundamental biological processes, including metabolism, disease, and aging. Inspired by the natural repair mechanism in vivo, we demonstrate for the first time the construction of a self-directed replication system for label-free and real-time sensing of repair glycosylases with zero background. The presence of DNA glycosylase can catalyze the excision repair of the damaged base, successively autostarting the self-directed replication through recycling polymerization extension and strand-displacement DNA synthesis for the generation of exponentially amplified dsDNAs. The resultant dsDNA products can be label-free and real-time monitored with SYBR Green I as the fluorescent indicator. Owing to the high efficiency of self-directed exponential replication and the absolute zero background resulting from the efficient inhibition of nonspecific amplification induced by multiple primer-dependent amplification, this strategy exhibits high sensitivity with a detection limit of 1 × 10-8 U μL-1 in vitro and 1 cell in vivo, and it can be further used to screen inhibitors, quantify DNA glycosylase from diverse cancer cells, and even monitor various repair enzymes by simply changing the specific damaged base in the DNA template. Importantly, this assay can be performed in a label-free, real-time and isothermal manner with the involvement of only a single type of polymerase, providing a simple, robust and universal platform for repair enzyme-related biomedical research and clinical therapeutics.
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Affiliation(s)
- Li-Juan Wang
- College of Chemistry , Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86-531-86186033
| | - Ying-Ying Lu
- College of Chemistry , Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86-531-86186033
| | - Chun-Yang Zhang
- College of Chemistry , Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86-531-86186033
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23
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Gao X, Niu S, Ge J, Luan Q, Jie G. 3D DNA nanosphere-based photoelectrochemical biosensor combined with multiple enzyme-free amplification for ultrasensitive detection of cancer biomarkers. Biosens Bioelectron 2020; 147:111778. [DOI: 10.1016/j.bios.2019.111778] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 10/08/2019] [Accepted: 10/09/2019] [Indexed: 11/16/2022]
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Li Y, Sun S, Tian X, Qiu JG, Jiang B, Zhang CY. A dumbbell probe-based dual signal amplification strategy for sensitive detection of multiple DNA methyltransferases. Chem Commun (Camb) 2020; 56:13627-13630. [DOI: 10.1039/d0cc05991a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Integration of a dumbbell probe with dual signal amplification enables simultaneously sensitive detection of multiple DNA methyltransferases.
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Affiliation(s)
- Yueying Li
- College of Chemistry, Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
- Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals
| | - Shuli Sun
- College of Chemistry, Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
- Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals
| | - Xiaorui Tian
- College of Chemistry, Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
- Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals
| | - Jian-Ge Qiu
- Academy of Medical Sciences
- Zhengzhou University
- Zhengzhou 450000
- China
| | - BingHua Jiang
- Academy of Medical Sciences
- Zhengzhou University
- Zhengzhou 450000
- China
| | - Chun-yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
- Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals
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25
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Zhang Y, Hao L, Zhao Z, Yang X, Wang L, Liu S. Immuno-DNA binding directed template-free DNA extension and enzyme catalysis for sensitive electrochemical DNA methyltransferase activity assay and inhibitor screening. Analyst 2020; 145:3064-3072. [DOI: 10.1039/d0an00008f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A new electrochemical immuno-DNA sensing platform for DNA methyltransferase activity assay and inhibitor screening.
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Affiliation(s)
- Ying Zhang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Lijie Hao
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Zhen Zhao
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Xiaoyan Yang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Li Wang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Shufeng Liu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
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26
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Du YC, Wang SY, Li XY, Wang YX, Tang AN, Kong DM. Terminal deoxynucleotidyl transferase-activated nicking enzyme amplification reaction for specific and sensitive detection of DNA methyltransferase and polynucleotide kinase. Biosens Bioelectron 2019; 145:111700. [DOI: 10.1016/j.bios.2019.111700] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/28/2019] [Accepted: 09/11/2019] [Indexed: 12/19/2022]
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27
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Kosman J, Juskowiak B. Bioanalytical Application of Peroxidase-Mimicking DNAzymes: Status and Challenges. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 170:59-84. [PMID: 28474157 DOI: 10.1007/10_2017_7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNAzymes with peroxidase-mimicking activity are a new class of catalytically active DNA molecules. This system is formed as a complex of hemin and a G-quadruplex structure created by oligonucleotides rich in guanine. Considering catalytic activity, this DNAzyme mimics horseradish peroxidase, the enzyme most commonly used for signal generation in bioassays. Because DNAzymes exhibit many advantages over protein enzymes (thermal stability, easy and cheap synthesis and purification) they can successfully replace HRP in bioanalytical applications. HRP-like DNAzymes have been applied in the detection of several DNA sequences. Many amplification techniques have been conjugated with DNAzyme systems, resulting in ultrasensitive bioassays. On the other hand, the combination of aptamers and DNAzymes has led to the development of aptazymes for specific targets. An up-to-date summary of the most interesting DNAzyme-based assays is presented here. The elaborated systems can be used in medical diagnosis or chemical and biological studies.
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Affiliation(s)
- J Kosman
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Poznan, Poland.
| | - B Juskowiak
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Poznan, Poland
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28
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Li Y, Wang L, Ding C, Luo X. Highly selective ratiometric electrogenerated chemiluminescence assay of DNA methyltransferase activity via polyaniline and anti-fouling peptide modified electrode. Biosens Bioelectron 2019; 142:111553. [DOI: 10.1016/j.bios.2019.111553] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 07/25/2019] [Accepted: 07/29/2019] [Indexed: 10/26/2022]
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29
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Zhang J, Yang Y, Jiang X, Dong C, Song C, Han C, Wang L. Ultrasensitive SERS detection of nucleic acids via simultaneous amplification of target-triggered enzyme-free recycling and multiple-reporter. Biosens Bioelectron 2019; 141:111402. [DOI: 10.1016/j.bios.2019.111402] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/21/2019] [Accepted: 05/31/2019] [Indexed: 01/28/2023]
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30
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Wang Z, Dong B, Feng G, Shan H, Huan Y, Fei Q. Water-soluble Hemin-mPEG-enhanced Luminol Chemiluminescence for Sensitive Detection of Hydrogen Peroxide and Glucose. ANAL SCI 2019; 35:1135-1140. [PMID: 31281131 DOI: 10.2116/analsci.19p150] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In the present study, we synthesized a water-soluble substance (Hemin-mPEG) at room temperature by using hemin and poly(ethylene glycol) methyl ether (mPEG). It was found that the Hemin-mPEG maintained the excellent catalytic activity inherited from hemin, and was first used to catalyze a luminol-H2O2 chemiluminescence (CL) system to generate an intense and slow CL signal. The results of a mechanism research showed that the presence of Hemin-mPEG could promote the production of oxygen-relative radicals from H2O2 and dissolved oxygen in solution. Based on this mechanism, an ultra-sensitive, cheap and simply practical sensor for detecting glucose and H2O2 was developed. Under the most optimal experimental conditions, H2O2 and glucose detection results exhibited a good linear range from 0.002 to 3 μM and from 0.02 to 4 μM, respectively, and the detection limits were 1.8 and 10 nM, respectively. This approach has been successfully used to detect glucose in actual biological samples, and achieved good results.
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Affiliation(s)
- Ze Wang
- Department of Analytical Chemistry, College of Chemistry, Jilin University
| | - Bin Dong
- Department of Analytical Chemistry, College of Chemistry, Jilin University
| | - Guodong Feng
- Department of Analytical Chemistry, College of Chemistry, Jilin University
| | - Hongyan Shan
- Department of Analytical Chemistry, College of Chemistry, Jilin University
| | - Yanfu Huan
- Department of Analytical Chemistry, College of Chemistry, Jilin University
| | - Qiang Fei
- Department of Analytical Chemistry, College of Chemistry, Jilin University
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Chen Y, Meng XZ, Gu HW, Yi HC, Sun WY. A dual-response biosensor for electrochemical and glucometer detection of DNA methyltransferase activity based on functionalized metal-organic framework amplification. Biosens Bioelectron 2019; 134:117-122. [DOI: 10.1016/j.bios.2019.03.051] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/16/2019] [Accepted: 03/26/2019] [Indexed: 11/16/2022]
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32
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Li H, Wang J, Wang X, Lin H, Li F. Perylene-Based Photoactive Material as a Double-Stranded DNA Intercalating Probe for Ultrasensitive Photoelectrochemical Biosensing. ACS APPLIED MATERIALS & INTERFACES 2019; 11:16958-16964. [PMID: 30993969 DOI: 10.1021/acsami.9b04299] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Photoelectrochemical (PEC) sensing techniques have attracted considerable concerns because of the intrinsic merit of complete separation between the excitation light and responsive current but still remain a great challenge for further potential application. It is assigned to the scarcity of photoactive materials with narrow band gap, good biosafety, and high photon-to-electron conversion efficiency and unfavorable processing methods for photoactive materials on indium tin oxide. Herein, we employed a perylene-based polymer (PTC-NH2) with exceptional photoelectrical properties to develop a red-light-driven PEC sensor for ultrasensitive biosensing based on its superior electrostatic intercalation efficiency in double-stranded DNA to that in single-stranded DNA, with DNA adenine methyltransferase (Dam MTase) as the model target. The prepared PTC-NH2 was characterized by Fourier transform infrared spectroscopy, ultraviolet-visible spectroscopy, and PEC techniques, and the results demonstrated that PTC-NH2 rather than metal oxides/metal sulfides/C3N4/metal complexes enjoyed the prominent capacity of converting light to current. Benefiting from the unique PEC properties of PTC-NH2 and target-initiated hybridization chain reaction (HCR) signal amplification, ultrasensitive detection of Dam MTase was accessibly realized with the detection limit of 0.015 U/mL, which is lower than that of PEC, electrochemical, or fluorescent biosensors previously reported. Furthermore, the proposed PEC sensor has been also applied in screening Dam MTase activity inhibitors. Therefore, the perylene-based PEC sensor exhibits great potential in early accurate diagnosis of DNA methylation-related diseases.
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Affiliation(s)
- Haiyin Li
- College of Chemistry and Pharmaceutical Sciences , Qingdao Agricultural University , Qingdao 266109 , People's Republic of China
| | - Jiao Wang
- College of Chemistry and Pharmaceutical Sciences , Qingdao Agricultural University , Qingdao 266109 , People's Republic of China
| | - Xin Wang
- College of Chemistry and Pharmaceutical Sciences , Qingdao Agricultural University , Qingdao 266109 , People's Republic of China
| | - Haiyang Lin
- College of Chemistry and Pharmaceutical Sciences , Qingdao Agricultural University , Qingdao 266109 , People's Republic of China
| | - Feng Li
- College of Chemistry and Pharmaceutical Sciences , Qingdao Agricultural University , Qingdao 266109 , People's Republic of China
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33
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Zhang H, Wang L, Xie Y, Zuo X, Chen H, Chen X. Base excision repair mediated cascading triple-signal amplification for the sensitive detection of human alkyladenine DNA glycosylase. Analyst 2019; 144:3064-3071. [PMID: 30916676 DOI: 10.1039/c9an00200f] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
DNA glycosylase (DG) plays a significant role in repairing DNA lesions, and the dysregulation of DG activity is associated with a variety of human pathologies. Thus, the detection of DG activity is essential for biomedical research and clinical diagnosis. Herein, we develop a facile fluorometric method based on the base excision repair (BER) mediated cascading triple-signal amplification for the sensitive detection of DG. The presence of human alkyladenine DNA glycosylase (hAAG) can initiate the cleavage of the substrate at the mismatched deoxyinosine site by endonuclease IV (Endo IV), resulting in the breaking of the DNA substrate. The cleaved DNA substrate functions as both a primer and a template to initiate strand displacement amplification (SDA) to release primers. The released primers can further bind to a circular template to induce an exponential primer generation rolling circle amplification (PG-RCA) reaction, producing a large number of primers. The primers that resulted from the SDA and PG-RCA reaction can induce the subsequent recycling cleavage of signal probes, leading to the generation of a fluorescence signal. Taking advantage of the high amplification efficiency of triple-signal amplification and the low background signal resulting from single uracil repair-mediated inhibition of nonspecific amplification, this method exhibits a low detection limit of 0.026 U mL-1 and a large dynamic range of 4 orders of magnitude for hAAG. Moreover, this method has distinct advantages of simplicity and low cost, and it can further quantify the hAAG activity from HeLa cell extracts, holding great potential in clinical diagnosis and biomedical research.
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Affiliation(s)
- Huige Zhang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China.
| | - Lili Wang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China.
| | - Yi Xie
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xianwei Zuo
- Key Laboratory of Sensor and Sensing Technology of Gansu Province, Gansu Academy of Sciences, Lanzhou 730000, China
| | - Hongli Chen
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China.
| | - Xingguo Chen
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China.
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Enhanced chemiluminescence enzyme‐linked immunoassay for the determination of DNA methyltransferase 1 in human serum. LUMINESCENCE 2019; 34:368-374. [DOI: 10.1002/bio.3619] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/12/2019] [Accepted: 01/30/2019] [Indexed: 12/16/2022]
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35
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Zhang J, Chai X, He XP, Kim HJ, Yoon J, Tian H. Fluorogenic probes for disease-relevant enzymes. Chem Soc Rev 2019; 48:683-722. [PMID: 30520895 DOI: 10.1039/c7cs00907k] [Citation(s) in RCA: 357] [Impact Index Per Article: 71.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Traditional biochemical methods for enzyme detection are mainly based on antibody-based immunoassays, which lack the ability to monitor the spatiotemporal distribution and, in particular, the in situ activity of enzymes in live cells and in vivo. In this review, we comprehensively summarize recent progress that has been made in the development of small-molecule as well as material-based fluorogenic probes for sensitive detection of the activities of enzymes that are related to a number of human diseases. The principles utilized to design these probes as well as their applications are reviewed. Specific attention is given to fluorogenic probes that have been developed for analysis of the activities of enzymes including oxidases and reductases, those that act on biomacromolecules including DNAs, proteins/peptides/amino acids, carbohydrates and lipids, and those that are responsible for translational modifications. We envision that this review will serve as an ideal reference for practitioners as well as beginners in relevant research fields.
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Affiliation(s)
- Junji Zhang
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Rd., Shanghai 200237, P. R. China.
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36
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Cui YX, Feng XN, Wang YX, Pan HY, Pan H, Kong DM. An integrated-molecular-beacon based multiple exponential strand displacement amplification strategy for ultrasensitive detection of DNA methyltransferase activity. Chem Sci 2019; 10:2290-2297. [PMID: 30881654 PMCID: PMC6385671 DOI: 10.1039/c8sc05102j] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 12/19/2018] [Indexed: 12/16/2022] Open
Abstract
DNA methylation is a significant epigenetic mechanism involving processes of transferring a methyl group onto cytosine or adenine. Such DNA modification catalyzed by methyltransferase (MTase) plays important roles in the modulation of gene expression and other cellular activities. Herein, we develop a simple and sensitive biosensing platform for the detection of DNA MTase activity by using only two oligonucleotides. The fluorophore labeled molecular beacon (MB) can be methylated by MTase and subsequently cleaved by endonuclease DpnI at the stem, giving a shortened MB. The shortened MB can then hybridize with a primer DNA, initiating a cycle of strand displacement amplification (SDA) reactions. The obtained SDA products can unfold new MB and initiate another cycle of SDA reaction. Therefore, continuous enlargement of SDA and exponential amplification of the fluorescence signal are achieved. Because the triple functions of substrate, template and probe are elegantly integrated in one oligonucleotide, only two oligonucleotides are necessary for multiple amplification cycles, which not only reduces the complexity of the system, but also overcomes the laborious and cumbersome operation that is always a challenge in conventional methods. This platform exhibits an extremely low limit of detection of 3.3 × 10-6 U mL-1, which is the lowest to our knowledge. The proposed MTase-sensing platform was also demonstrated to perform well in a real-time monitoring mode, which can achieve a further simplified and high-throughput detection. The sensing strategy might be extended to the activity detection of other enzymes, thus showing great application potential in bioanalysis and clinical diagnosis.
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Affiliation(s)
- Yun-Xi Cui
- State Key Laboratory of Medicinal Chemical Biology , Tianjin Key Laboratory of Biosensing and Molecular Recognition , Research Centre for Analytical Sciences , College of Chemistry , Nankai University , Tianjin 300071 , P. R. China .
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin , 300071 , P. R. China
| | - Xue-Nan Feng
- State Key Laboratory of Medicinal Chemical Biology , Tianjin Key Laboratory of Biosensing and Molecular Recognition , Research Centre for Analytical Sciences , College of Chemistry , Nankai University , Tianjin 300071 , P. R. China .
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin , 300071 , P. R. China
| | - Ya-Xin Wang
- State Key Laboratory of Medicinal Chemical Biology , Tianjin Key Laboratory of Biosensing and Molecular Recognition , Research Centre for Analytical Sciences , College of Chemistry , Nankai University , Tianjin 300071 , P. R. China .
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin , 300071 , P. R. China
| | - Hui-Yu Pan
- State Key Laboratory of Medicinal Chemical Biology , Tianjin Key Laboratory of Biosensing and Molecular Recognition , Research Centre for Analytical Sciences , College of Chemistry , Nankai University , Tianjin 300071 , P. R. China .
| | - Hua Pan
- State Key Laboratory of Medicinal Chemical Biology , Tianjin Key Laboratory of Biosensing and Molecular Recognition , Research Centre for Analytical Sciences , College of Chemistry , Nankai University , Tianjin 300071 , P. R. China .
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology , Tianjin Key Laboratory of Biosensing and Molecular Recognition , Research Centre for Analytical Sciences , College of Chemistry , Nankai University , Tianjin 300071 , P. R. China .
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin , 300071 , P. R. China
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Ge J, Zhao Y, Li C, Jie G. Versatile Electrochemiluminescence and Electrochemical “On–Off” Assays of Methyltransferases and Aflatoxin B1 Based on a Novel Multifunctional DNA Nanotube. Anal Chem 2019; 91:3546-3554. [DOI: 10.1021/acs.analchem.8b05362] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Junjun Ge
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, People’s Republic of China
| | - Yu Zhao
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, People’s Republic of China
| | - Chunli Li
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, People’s Republic of China
| | - Guifen Jie
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, People’s Republic of China
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38
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Mittal S, Thakur S, Mantha AK, Kaur H. Bio-analytical applications of nicking endonucleases assisted signal-amplification strategies for detection of cancer biomarkers -DNA methyl transferase and microRNA. Biosens Bioelectron 2019; 124-125:233-243. [DOI: 10.1016/j.bios.2018.10.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 09/27/2018] [Accepted: 10/01/2018] [Indexed: 12/31/2022]
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39
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Zhang H, Wang LJ, Wang L, Chen H, Chen X, Zhang CY. Development of a cascade isothermal amplification approach for the sensitive detection of DNA methyltransferase. J Mater Chem B 2018; 7:157-162. [PMID: 32254960 DOI: 10.1039/c8tb02096e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA methyltransferase (MTase) is an important epigenetic modification enzyme responsible for DNA methylation, and the dysregulation of DNA MTase activity is associated with various diseases in humans. Herein, we take advantage of the DNA lesion repair mechanism in vivo to develop a new fluorescence approach for the specific and sensitive detection of DNA methyltransferase (DNA MTase) on the basis of the DNA lesion repair-directed cascade isothermal amplification. Due to the high amplification efficiency of the uracil repair-mediated exponential isothermal amplification reaction (EXPAR), the efficient cleavage of endonuclease IV (Endo IV)-induced cyclic catalysis, and the low background signal caused by single uracil repair-mediated inhibition of nonspecific amplification, this approach exhibits high sensitivity with a detection limit of 0.014 U mL-1 for pure Dam MTase and 0.61 × 10-6 mg mL-1 for Dam MTase in E. coli cells and it can be further applied for the screening of DNA MTase inhibitors. More importantly, this approach can be applied to detect other DNA MTases by designing appropriate substrates, showing great potential in biomedical research and clinical diagnosis.
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Affiliation(s)
- Huige Zhang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China.
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40
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Liu H, Luo J, Fang L, Huang H, Deng J, Huang J, Zhang S, Li Y, Zheng J. An electrochemical strategy with tetrahedron rolling circle amplification for ultrasensitive detection of DNA methylation. Biosens Bioelectron 2018; 121:47-53. [DOI: 10.1016/j.bios.2018.07.055] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/23/2018] [Accepted: 07/25/2018] [Indexed: 12/20/2022]
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41
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Niu L, Wang X, Mao G, Li Z, Ji X, He Z. Sensitive fluorescent detection of methyltransferase based on thermosensitive poly(N-isopropylacrylamide). Talanta 2018; 189:579-584. [PMID: 30086963 DOI: 10.1016/j.talanta.2018.07.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 06/29/2018] [Accepted: 07/10/2018] [Indexed: 12/21/2022]
Abstract
DNA methyltransferase (MTase) has a crucial role in many biological processes, its abnormal expression level has been regarded as a predictive cancer biomarker. Herein, a sensitive fluorescence method based on thermosensitive poly (N-isopr-opylacrylamide) was developed to assay of M.SssI activity. When the M.SssI was introduced, dsDNA was methylated at palindromic sequence 5'-CmCGG-3' and became resistant to cleavage by the endonuclease HpaII. Therefore, a biotin modified ssDNA and a FAM modified ssDNA were designed including the recognized sites for both methyltransferase M.SssI and endonuclease HpaII. By SA-biotin intereaction, the DNA was conjugated to thermosensitive poly (N-isopropylacrylamide) modified by SA, the methylated substrate fluorescence was increased with the concentration of M.SssI increasing. The proposed method has a low detection limit of 0.18 U/mL. This simple method can be a useful tool to apply in diagnosis and biomedical research, which was successfully investigated in the serum sample.
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Affiliation(s)
- Longqing Niu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Xinxin Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Guobin Mao
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Zheng Li
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Xinghu Ji
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Zhike He
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China.
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42
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Xu Q, Zhang Y, Xiang D, Li CC, Zhang CY. A universal DNAzyme-based bioluminescent sensor for label-free detection of biomolecules. Anal Chim Acta 2018; 1043:81-88. [PMID: 30392672 DOI: 10.1016/j.aca.2018.08.059] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 08/27/2018] [Accepted: 08/30/2018] [Indexed: 12/28/2022]
Abstract
We demonstrate for the first time the development of a universal DNAzyme-based bioluminescent sensor for label-free detection of various biomolecules including DNAzyme and DNA. The presence of DNAzyme may induce the cyclic cleavage of riboadenosine (rA)-containing substrates, and the subsequent digestion of the cleaved substrates by exonuclease III (Exo III) releases abundant AMPs to initiate cyclic AMP pyrophosphorylation-ATP depyrophosphorylation for the generation of an enhanced bioluminescence signal. This sensor can real-time monitor the DNAzyme activity with a detection limit of 3.16 × 10-12 M. Moreover, the DNAzyme may be divided into two subunits for sensitive detection of target DNA. In the presence of target DNA, the two separated subunits may assemble into an active DNAzyme which can catalyze the cyclic cleavage of substrates and initiate the digestion of cleaved substrates by Exo III for the generation of an enhanced bioluminescence signal. This sensor can sensitively detect target DNA with a detection limit of 3.31 × 10-12 M. Importantly, this bioluminescent sensor can achieve a zero-background signal, and its output signal originates from the release of AMP for the generation of self-illuminating light emission without the requirement of either the external labels or the reporting reagents.
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Affiliation(s)
- Qinfeng Xu
- College of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Yan Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China
| | - Dongxue Xiang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China
| | - Chen-Chen Li
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China.
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43
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Kermani HA, Hosseini M, Miti A, Dadmehr M, Zuccheri G, Hosseinkhani S, Ganjali MR. A colorimetric assay of DNA methyltransferase activity based on peroxidase mimicking of DNA template Ag/Pt bimetallic nanoclusters. Anal Bioanal Chem 2018; 410:4943-4952. [DOI: 10.1007/s00216-018-1143-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/07/2018] [Accepted: 05/14/2018] [Indexed: 01/31/2023]
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44
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Wang LJ, Han X, Li CC, Zhang CY. Single-ribonucleotide repair-mediated ligation-dependent cycling signal amplification for sensitive and specific detection of DNA methyltransferase. Chem Sci 2018; 9:6053-6061. [PMID: 30079218 PMCID: PMC6053742 DOI: 10.1039/c8sc02215a] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 06/17/2018] [Indexed: 01/09/2023] Open
Abstract
Specific and sensitive detection of DNA MTase activity can be achieved by a single-ribonucleotide repair-mediated ligation-dependent cycling signal amplification approach.
DNA methylation is a predominant epigenetic modification that plays crucial roles in various cellular processes. DNA methyltransferase (MTase) is responsible for DNA methylation, and its dysregulation may induce aberrant methylation patterns that are closely related to cancers. Conventional methods for DNA MTase assay are usually cumbersome and laborious with poor sensitivity. Alternatively, some signal amplification strategies are employed to improve the sensitivity, but they suffer from poor specificity and consequently limited sensitivity due to the nonspecific amplification. Herein, we develop for the first time a new fluorescence method to specifically and sensitively detect DNA MTase activity on the basis of single-ribonucleotide repair-mediated ligation-dependent cycling signal amplification. In the presence of DNA MTase, the hairpin substrate is methylated and cleaved by endonuclease Dpn I, releasing a 24-nt cleavage product. The 24-nt cleavage product may function as a primer and adjacently hybridize with the ligation probes (LP1 and LP2) to form the template (LP1–LP2) for strand displacement amplification (SDA), initiating the single-ribonucleotide repair-mediated cyclic ligation-dependent SDA to produce a large number of reporter probes. The reporter probe can subsequently hybridize with the signal probe that is modified with FAM and BHQ1 to form a stable double-stranded DNA (dsDNA) duplex with a ribonucleotide mismatch. Ribonuclease HII (RNase HII) can excise the single ribonucleotide, resulting in the cyclic cleavage of signal probes and the generation of an enhanced fluorescence signal. Taking advantage of the high specificity of RNase HII-catalyzed single-ribonucleotide excision and the high amplification efficiency of cyclic ligation-dependent SDA, this assay exhibits the highest sensitivity reported so far with a detection limit of 4.8 × 10–6 U mL–1 and a large dynamic range of 5 orders of magnitude. Moreover, this method can be used for the discrimination of Dam MTase from other DNA MTases, the accurate quantification of Dam MTase activity in E. coli cells, and the screening of Dam MTase inhibitors, providing a new paradigm for biomedical research and clinical diagnosis.
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Affiliation(s)
- Li-Juan Wang
- College of Chemistry , Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86 531 86186033
| | - Xiao Han
- College of Chemistry , Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86 531 86186033
| | - Chen-Chen Li
- College of Chemistry , Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86 531 86186033
| | - Chun-Yang Zhang
- College of Chemistry , Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86 531 86186033
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Wang LJ, Ren M, Liang L, Zhang CY. Controllable fabrication of bio-bar codes for dendritically amplified sensing of human T-lymphotropic viruses. Chem Sci 2018; 9:4942-4949. [PMID: 29938021 PMCID: PMC5994793 DOI: 10.1039/c8sc01641k] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 05/09/2018] [Indexed: 01/10/2023] Open
Abstract
We demonstrate for the first time the controllable fabrication of bio-bar codes for dendritically amplified sensing of low-abundant HTLV-II DNA.
Human T-lymphotropic virus type II (HTLV-II) is an important type-C retrovirus, closely related to a variety of human diseases. Here, we demonstrate for the first time the controllable fabrication of bio-bar codes for dendritically amplified sensing of low-abundant HTLV-II DNA by the integration of terminal deoxynucleotidyl transferase (TdT)-catalyzed template-free polymerization extension with bio-bar-code amplification (BCA). HTLV-II DNA hybridizes with magnetic microparticle (MMP)-modified capture probe 1, forming a stable DNA duplex with a protruding 3′-hydroxylated sequence which may function as a primer to initiate the TdT-catalyzed first-step polymerization extension for the generation of a poly-thymidine (T) sequence. The resultant poly-T products may hybridize with poly-adenine (A) capture probe 2, inducing the self-assembly of multiple capture probe 2-/reporter probe-functionalized Au nanoparticles (AuNPs) onto the MMP. Subsequently, the reporter probes may act as the primers to initiate the TdT-catalyzed second-step polymerization extension, producing large numbers of G-rich DNAzymes for the generation of an enhanced chemiluminescence signal. Taking advantage of the efficient polymerization extension reaction catalyzed by TdT, the high amplification efficiency of BCA, and the intrinsically high sensitivity of G-rich DNAzyme-driven chemiluminescence, this method exhibits ultrahigh sensitivity with a limit of detection of as low as 0.50 aM and a large dynamic range of 9 orders of magnitude from 1 aM to 1 nM. Moreover, this method can be applied for the discrimination of a single-base mismatch and the measurement of HTLV-II DNA in both human serum and human T-lymphocytic leukemia cells, holding great potential in biomedical research and clinical diagnosis.
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Affiliation(s)
- Li-Juan Wang
- College of Chemistry, Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86 0531 86186033
| | - Ming Ren
- College of Chemistry, Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86 0531 86186033
| | - Li Liang
- Department of Tumor Chemotherapy and Radiation Sickness , Peking University Third Hospital , Beijing 100191 , China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science , Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong , Key Laboratory of Molecular and Nano Probes , Ministry of Education , Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals , Shandong Normal University , Jinan 250014 , China . ; ; Tel: +86 0531 86186033
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46
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A simple and universal electrochemical assay for sensitive detection of DNA methylation, methyltransferase activity and screening of inhibitors. J Electroanal Chem (Lausanne) 2018. [DOI: 10.1016/j.jelechem.2018.02.060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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47
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Chen S, Lv Y, Shen Y, Ji J, Zhou Q, Liu S, Zhang Y. Highly Sensitive and Quality Self-Testable Electrochemiluminescence Assay of DNA Methyltransferase Activity Using Multifunctional Sandwich-Assembled Carbon Nitride Nanosheets. ACS APPLIED MATERIALS & INTERFACES 2018; 10:6887-6894. [PMID: 29376630 DOI: 10.1021/acsami.7b17813] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
DNA methylation catalyzed by methylase plays a key role in many biological activities. However, developing a highly sensitive, simple, and reliable way for evaluation of DNA methyltransferase (MTase) activity is still a challenge. Here, we report a sandwich-assembled electrochemiluminescence (ECL) biosensor using multifunctional carbon nitride nanosheets (CNNS) to evaluate the Dam MTase activity. The CNNS could not only be used as an excellent substrate to conjugate a large amount of hairpin probe DNA to improve the sensitivity but also be utilized as an internal reliability checker and an analyte reporter in the bottom and top layers of the biosensor, respectively. Such a unique sandwich configuration of CNNS well coupled the advantages of ECL luminophor that were generally assembled in the bottom or top layer in a conventional manner. As a result, the biosensor exhibited an ultralow detection limit down to 0.043 U/mL and a linear range between 0.05 and 80 U/mL, superior to the MTase activity assay in most previous reports. We highlighted the great potential of emerging CNNS luminophor in developing highly sensitive and smart quality self-testable ECL sensing systems using a sandwiched configuration for early disease diagnosis, treatment, and management.
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Affiliation(s)
- Shiyu Chen
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Southeast University , Nanjing 211189, China
| | - Yanqin Lv
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Southeast University , Nanjing 211189, China
| | - Yanfei Shen
- Medical School, Southeast University , Nanjing 210009, China
| | - Jingjing Ji
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Southeast University , Nanjing 211189, China
| | - Qing Zhou
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Southeast University , Nanjing 211189, China
| | - Songqin Liu
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Southeast University , Nanjing 211189, China
| | - Yuanjian Zhang
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-Medical Research, School of Chemistry and Chemical Engineering, Southeast University , Nanjing 211189, China
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48
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Commercial glucometer as signal transducer for simple evaluation of DNA methyltransferase activity and inhibitors screening. Anal Chim Acta 2018; 1001:18-23. [DOI: 10.1016/j.aca.2017.11.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 07/31/2017] [Accepted: 11/14/2017] [Indexed: 12/20/2022]
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49
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Wang K, He MQ, Zhai FH, Wang J, He RH, Yu YL. Autonomous DNA nanomachine based on cascade amplification of strand displacement and DNA walker for detection of multiple DNAs. Biosens Bioelectron 2018; 105:159-165. [PMID: 29412940 DOI: 10.1016/j.bios.2018.01.044] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 01/18/2018] [Accepted: 01/19/2018] [Indexed: 01/06/2023]
Abstract
DNA can be modified to function as a scaffold for the construction of a DNA nanomachine, which can then be used in analytical applications if the DNA nanomachine can be triggered by the presence of a diagnostic DNA or some other analyte. We herein propose a novel and powerful DNA nanomachine that can detect DNA via combining the tandem strand displacement reactions and a DNA walker. Three different DNA sensing platforms are described, where the whole DNA machine was constructed on a gold electrode (GE). This cascade multiple amplification strategy exhibited an excellent sensitivity. Under optimal conditions, the electrochemical sensor could achieve a detection limit of 36 fM with a linear range from 50 to 500 fM. In particular, the electrochemical sensor could easily distinguish the base mutations. More interestingly, the DNA nanomachine could be used to construct analog AND and OR logic gates. We demonstrate that electrochemical signals generated from the different input combinations can be used to distinguish multiple target DNAs. The practical applicability of the present biosensor is demonstrated by the detection of target DNA in human serum with satisfactory results, which holds great potential for a future application in clinical diagnosis.
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Affiliation(s)
- Kun Wang
- Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Meng-Qi He
- Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Fu-Heng Zhai
- Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Jin Wang
- Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Rong-Huan He
- Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China.
| | - Yong-Liang Yu
- Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China.
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50
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Ma F, Wei SH, Leng J, Tang B, Zhang CY. A simple “mix-and-detection” method for the sensitive detection of telomerase from cancer cells under absolutely isothermal conditions. Chem Commun (Camb) 2018; 54:2483-2486. [DOI: 10.1039/c8cc00093j] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We develop a simple “mix-and-detection” method for the sensitive detection of telomerase from cancer cells under absolutely isothermal conditions.
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Affiliation(s)
- Fei Ma
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Shu-hua Wei
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Junhong Leng
- Jinan Maternity and Child Care Hospital
- Jinan 250000
- China
| | - Bo Tang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Chun-yang Zhang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
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