1
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Chen S, Zhao J, Xu C, Shi B, Xu J, Hu S, Zhao S. Lysosomes Initiating and DNAzyme-Assisted Intracellular Signal Amplification Strategy for Quantification of Alpha-Fetoprotein in a Single Cell. Anal Chem 2024; 96:85-91. [PMID: 38128902 DOI: 10.1021/acs.analchem.3c03152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Cellular trace proteins are critical for maintaining normal cell functions, with their quantitative analysis in individual cells aiding our understanding of the role of cell proteins in biological processes. This study proposes a strategy for the quantitative analysis of alpha-fetoprotein in single cells, utilizing a lysosome microenvironment initiation and a DNAzyme-assisted intracellular signal amplification technique based on electrophoretic separation. A nanoprobe targeting lysosomes was prepared, facilitating the intracellular signal amplification of alpha-fetoprotein. Following intracellular signal amplification, the levels of alpha-fetoprotein (AFP) in 20 HepG2 hepatoma cells and 20 normal HL-7702 hepatocytes were individually evaluated using microchip electrophoresis with laser-induced fluorescence detection (MCE-LIF). Results demonstrated overexpression of alpha-fetoprotein in hepatocellular carcinoma cells. This strategy represents a novel technique for single-cell protein analysis and holds significant potential as a powerful tool for such analyses.
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Affiliation(s)
- Shengyu Chen
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China
- Guangxi Key Laboratory of Urban Water Environment, Baise University, Baise 533000, China
| | - Jingjin Zhao
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China
| | - Chunhuan Xu
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China
| | - Bingfang Shi
- Guangxi Key Laboratory of Urban Water Environment, Baise University, Baise 533000, China
| | - Jiayao Xu
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China
| | - Shengqiang Hu
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China
| | - Shulin Zhao
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China
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2
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Bhuyan SK, Wang L, Jinata C, Kinghorn AB, Liu M, He W, Sharma R, Tanner JA. Directed Evolution of a G-Quadruplex Peroxidase DNAzyme and Application in Proteomic DNAzyme-Aptamer Proximity Labeling. J Am Chem Soc 2023. [PMID: 37276197 DOI: 10.1021/jacs.3c02625] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
DNAzymes have been limited in application by their low catalytic rates. Here, we evolved a new peroxidase DNAzyme mSBDZ-X-3 through a directed evolution method based on the capture of self-biotinylated DNA catalyzed by its intrinsic peroxidase activity. The mSBDX-X-3 DNAzyme has a parallel G-quadruplex structure and has more favorable catalytic properties than all previously reported peroxidase DNAzyme variants. We applied mSBDZ-X-3 in an aptamer-coupled proximity-based labeling proteomic assay to determine the proteins that bind to cell surface cancer biomarkers EpCAM and nucleolin. Confocal microscopy, western blot analysis, and LC-MS/MS showed that the hybrid DNAzyme aptamer-coupled proximity assay-labeled proteins associated with EpCAM and nucleolin within 6-12 min in fixed cancer cells. The labeled proteins were identified by mass spectrometry. This study provides a highly efficient peroxidase DNAzyme, a methodology for selection of such variants, and a method for its application in spatial proteomics using entirely nucleic acid-based tooling.
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Affiliation(s)
- Soubhagya K Bhuyan
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong SAR, China
| | - Lin Wang
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong SAR, China
| | - Chandra Jinata
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong SAR, China
| | - Andrew B Kinghorn
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Mengping Liu
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Weisi He
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Rakesh Sharma
- Proteomics and Metabolomics Core Facility, Centre for PanorOmic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Julian A Tanner
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong SAR, China
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3
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Yu H, Zhao Q. DNAzyme-Based Microscale Thermophoresis Sensor. Anal Chem 2023; 95:2152-2156. [PMID: 36657085 DOI: 10.1021/acs.analchem.2c04643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Microscale thermophoresis (MST) technology has emerged as a powerful growing method in a molecular interaction study by measuring fluorescence responses of molecules inside a capillary to infrared (IR) laser heating with the benefits of rapid ratiometric measurement, separation-free, no immobilization, and low sample consumption. Combining the advantages of RNA-cleaving DNAzymes in target recognition and enzymatic catalysis and the strength of MST technology for fluorescence signaling, here, we reported a DNAzyme-based MST method for sensitive target detection. We introduced a fluorescein terminal label at the RNA-cleaving DNAzyme, and the substrate was linked to DNAzyme together with a poly-T sequence in a unimolecular design or not conjugated with DNAzyme in a bimolecular design. The presence of the cofactor activated DNAzyme to catalytically cleave the substrate, causing molecular structure alteration and significant changes in MST signals. This DNAzyme MST sensor enabled sensitively detecting activator targets Pb2+ and l-histidine, with a detection limit of 49 pM Pb2+ and 3.9 μM l-histidine. This biosensing strategy is universal and promising for wide applications.
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Affiliation(s)
- Hao Yu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
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4
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Metal Ion-Directed Specific DNA Structures and Their Functions. Life (Basel) 2022; 12:life12050686. [PMID: 35629354 PMCID: PMC9145678 DOI: 10.3390/life12050686] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/01/2022] [Accepted: 05/02/2022] [Indexed: 11/17/2022] Open
Abstract
Various DNA structures, including specific metal ion complexes, have been designed based on the knowledge of canonical base pairing as well as general coordination chemistry. The role of metal ions in these studies is quite broad and diverse. Metal ions can be targets themselves in analytical applications, essential building blocks of certain DNA structures that one wishes to construct, or they can be responsible for signal generation, such as luminescence or redox. Using DNA conjugates with metal chelators, one can more freely design DNA complexes with diverse structures and functions by following the simple HSAB rule. In this short review, the authors summarize a part of their DNA chemistries involving specific metal ion coordination. It consists of three topics: (1) significant stabilization of DNA triple helix by silver ion; (2) metal ion-directed dynamic sequence edition through global conformational change by intramolecular complexation; and (3) reconstruction of luminescent lanthanide complexes on DNA and their analytical applications.
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5
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He YQ, Gao Y, Gu HW, Meng XZ, Yi HC, Chen Y, Sun WY. Target-induced activation of DNAzyme for sensitive detection of bleomycin by using a simple MOF-modified electrode. Biosens Bioelectron 2021; 178:113034. [DOI: 10.1016/j.bios.2021.113034] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 12/28/2020] [Accepted: 01/20/2021] [Indexed: 12/26/2022]
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6
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Xu J, Lee ES, Gye MC, Kim YP. Rapid and sensitive determination of bisphenol A using aptamer and split DNAzyme. CHEMOSPHERE 2019; 228:110-116. [PMID: 31026631 DOI: 10.1016/j.chemosphere.2019.04.110] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/12/2019] [Accepted: 04/14/2019] [Indexed: 06/09/2023]
Abstract
Despite the increasing concern regarding bisphenol A (BPA) as an endocrine disrupting chemical (EDC) upon environmental or human exposure, development of simple method for BPA detection has been hampered, due to the lack of a stable bioreceptor and signal generator. Here, we report a nucleic acid-based rapid and sensitive method for BPA detection, which constitutes a ssDNA aptamer and ssDNAzyme. When the peroxidase-like DNAzyme sequence was split into two parts (one incorporated into the anti-BPA aptamer as a target recognition element and the other into the complementary sequence as a bait), the presence of BPA hindered the association of the split DNA sequence, leading to a reduced signal in the DNAzyme-triggered chemiluminescence (CL). Thus, this NA-based CL measurement permitted the detection of BPA at as low as 5 nM with a broad dynamic range of five orders and with high selectivity towards BPA over other EDCs with structural similarity. With the development of aptamers, our detection method is expected to facilitate studies to monitor EDCs with high simplicity and sensitivity in the field of environmental science.
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Affiliation(s)
- Jing Xu
- Department of Environmental Sciences, Hanyang University, Seoul, 04763, Republic of Korea
| | - Eun-Song Lee
- Department of Life Science, Hanyang University, Seoul, 04763, Republic of Korea
| | - Myung Chan Gye
- Department of Life Science, Hanyang University, Seoul, 04763, Republic of Korea; Research Institute for Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea.
| | - Young-Pil Kim
- Department of Environmental Sciences, Hanyang University, Seoul, 04763, Republic of Korea; Department of Life Science, Hanyang University, Seoul, 04763, Republic of Korea; Research Institute for Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea; Institute of Nano Science and Technology, Hanyang University, Seoul, 04763, Republic of Korea; Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, Republic of Korea.
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7
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Fluorometric detection of silver(I) using cytosine-Ag(I)-cytosine pair formation, DNA assembly and the AND logic operation of a multiple-component DNAzyme. Mikrochim Acta 2019; 186:522. [DOI: 10.1007/s00604-019-3615-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 06/14/2019] [Indexed: 02/07/2023]
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8
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Yun W, You L, Li F, Wu H, Chen L, Yang L. Proximity ligation assay induced and DNAzyme powered DNA motor for fluorescent detection of thrombin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 207:39-45. [PMID: 30195184 DOI: 10.1016/j.saa.2018.08.062] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 08/23/2018] [Accepted: 08/30/2018] [Indexed: 06/08/2023]
Abstract
A novel DNA motor for thrombin detection was described here based on proximity ligation assay (PLA) induced DNAzyme recycling cleavage. Fluorophore labeled DNA is modified on gold nanoparticles (AuNPs) and the fluorescent signal is quenched by AuNPs. The PLA between target thrombin and two aptamers induces the forming of Mg2+-dependent DNAzyme. The fluorophore labeled DNA is cleaved circularly by the DNAzyme, releasing the fluorescent fragment from AuNPs surface. The cleavage and rebinding process create a processive walking along AuNPs surface track. As a result, the fluorescent intensity recovers significantly. A good linear relationship is obtained between the ratio of fluorescence intensity and thrombin concentration in the range from 10 pM to 10 nM. The limit of detection is calculated to be 4 pM. These results are comparable or even better than other amplification based methods.
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Affiliation(s)
- Wen Yun
- Chongqing Key Laboratory of Catalysis and New Environmental Materials, College of Environment and Resources, Chongqing Technology and Business University, Chongqing 400067, China.
| | - Linfeng You
- Chongqing Key Laboratory of Catalysis and New Environmental Materials, College of Environment and Resources, Chongqing Technology and Business University, Chongqing 400067, China
| | - Fukun Li
- Chongqing Key Laboratory of Catalysis and New Environmental Materials, College of Environment and Resources, Chongqing Technology and Business University, Chongqing 400067, China
| | - Hong Wu
- Chongqing Key Laboratory of Catalysis and New Environmental Materials, College of Environment and Resources, Chongqing Technology and Business University, Chongqing 400067, China
| | - Lin Chen
- State Key Laboratory of Environment-Friendly Energy Material, Southwest University of Science and Technology, Mianyang 621010, China.
| | - Lizhu Yang
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
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9
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Lu S, Wang S, Zhao J, Sun J, Yang X. Classical Triplex Molecular Beacons for MicroRNA-21 and Vascular Endothelial Growth Factor Detection. ACS Sens 2018; 3:2438-2445. [PMID: 30350592 DOI: 10.1021/acssensors.8b00996] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Triplex molecular beacons (tMBs) possess great potential in biological sensing because of the pH responsiveness and controllability of binding strength. Here, we systematically investigate and rationally design a classical tMB for convenient detection of microRNA-21, a well-known biomarker of cardio-cerebrovascular diseases. In the tMB, we employ the complementary sequence of miR-21 as the loop and the sequences of protonated cytosine-guanine-cytosine (C-G•C+) and thymine-adenine-thymine (T-A•T) as the triplex stem, in which both the Watson-Crick and Hoogsteen base-pairing control the binding strength in cooperation. It is demonstrated for the first time that the presence of miR-21 would only break the Hoogsteen base-pairing in the stem and hybridize with the tMB to form the rigid heterozygous hybrid duplex structure. These would hinder the fluorescence resonance energy transfer (FRET) between the fluorophore (FAM) and quencher (BHQ1) labeled at the ends of the oligonucleotide, and the fluorescence recovery degree of FAM can be used as the standard to quantitate the miR-21. More significantly, the excellent adjustability and sensitivity of our tMBs have been confirmed by constructing the corresponding duplex molecular beacon (dMB) for comparison. The fluorophore FAM in the tMB could be replaced by the fluorescent DNA/silver nanoclusters, which exhibits the universal applicability of energy donor and receptor selection for tMB. Furthermore, our proposed tMB could also be developed as an aptasensor for the detection of vascular endothelial growth factor (VEGF) by only introducing the complementary sequence of its aptamer into the tMB. This work is of great significance for the systematic study of tMBs for the detection of biomarkers such as nucleic acids and proteins.
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Affiliation(s)
- Shasha Lu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Shuang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jiahui Zhao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Sun
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Xiurong Yang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- University of Science and Technology of China, Hefei, Anhui 230026, China
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10
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Yun W, Wu H, Liu X, Fu M, Jiang J, Du Y, Yang L, Huang Y. Simultaneous fluorescent detection of multiple metal ions based on the DNAzymes and graphene oxide. Anal Chim Acta 2017; 986:115-121. [DOI: 10.1016/j.aca.2017.07.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 06/30/2017] [Accepted: 07/11/2017] [Indexed: 02/07/2023]
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11
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Portable aptamer biosensor of platelet-derived growth factor-BB using a personal glucose meter with triply amplified. Biosens Bioelectron 2017; 95:152-159. [PMID: 28445812 DOI: 10.1016/j.bios.2017.04.023] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 03/31/2017] [Accepted: 04/18/2017] [Indexed: 01/07/2023]
Abstract
Sensitive and rapid detection of platelet-derived growth factor BB (PDGF-BB), a cancer-related protein, could help early diagnosis, treatment, and prognosis of cancers. Although some methods have been developed to detect PDGF-BB, few can provide quantitative results using an affordable and portable device that is suitable for home use or field application. In this work, we report the first use of a portable kind of personal glucose meter (PGM) combining a catalytic and molecular beacon (CAMB) system with a cation exchange reaction (CX reaction) for ultrasensitive PDGF-BB assay. It realized the amplification of the detection in three ways, including greater aptamer payload on nanoparticles, CX reaction releasing thousands of Zn2+ and the cycle by the catalyzing cleavage of 8-17 DNAzyme. In the process, with the addition of PDGF-BB into the aptasensor, the specific recognition between aptamer and protein was initiated resulting in the combination of ZnS NNC for further CX reaction to release thousands of Zn2+, which could cleave the substrate DNA in the CAMB system realizing multiple cycle. The cleaved DNA fragment was designed with invertase-labeled could convert sucrose into glucose which could be detected and quantified by PGM accompanying with the change of color of the control window from yellow to green. The enhanced signal of the PGM has a relationship with the concentration of PDGF-BB in the range of 3.16×10-16M to 3.16×10-12M, and the detection limit is 0.11fM. Moreover, the catalytic and cleavage activities of 8-17 DNAzyme can be achieved in solution; thus, no enzyme immobilization is needed for detection. The triply amplified strategy showed high selectivity, stability, and applicability for detecting the desired protein.
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12
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Tram K, Manochehry S, Feng Q, Chang D, Salena BJ, Li Y. Colorimetric Detection of Bacteria Using Litmus Test. J Vis Exp 2016. [PMID: 27685457 DOI: 10.3791/54546] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
There are increasing demands for simple but still effective methods that can be used to detect specific pathogens for point-of-care or field applications. Such methods need to be user-friendly and produce reliable results that can be easily interpreted by both specialists and non-professionals. The litmus test for pH is simple, quick, and effective as it reports the pH of a test sample via a simple color change. We have developed an approach to take advantage of the litmus test for bacterial detection. The method exploits a bacterium-specific RNA-cleaving DNAzyme to achieve two functions: recognizing a bacterium of interest and providing a mechanism to control the activity of urease. Through the use of magnetic beads immobilized with a DNAzyme-urease conjugate, the presence of bacteria in a test sample is relayed to the release of urease from beads to solution. The released urease is transferred to a test solution to hydrolyze urea into ammonia, resulting in an increase of pH that can be visualized using the classic litmus test.
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Affiliation(s)
- Kha Tram
- Department of Biochemistry and Biomedical Sciences, McMaster University
| | - Sepehr Manochehry
- Department of Biochemistry and Biomedical Sciences, McMaster University
| | - Qian Feng
- Department of Chemistry and Chemical Biology, McMaster University
| | - Dingran Chang
- Department of Biochemistry and Biomedical Sciences, McMaster University
| | | | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University;
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13
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Wang Q, Gan X, Zang R, Chai Y, Yuan Y, Yuan R. An amplified electrochemical proximity immunoassay for the total protein of Nosema bombycis based on the catalytic activity of Fe3O4NPs towards methylene blue. Biosens Bioelectron 2016; 81:382-387. [DOI: 10.1016/j.bios.2016.02.063] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 02/18/2016] [Accepted: 02/23/2016] [Indexed: 10/22/2022]
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14
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Potent Intracellular Knock-Down of Influenza A Virus M2 Gene Transcript by DNAzymes Considerably Reduces Viral Replication in Host Cells. Mol Biotechnol 2016; 57:836-45. [PMID: 26021603 DOI: 10.1007/s12033-015-9876-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Influenza A virus has been known to be an important respiratory pathogen and cause of several epidemics and devastating pandemics leading to loss of life and resources across the globe. The M2 ion channel protein is highly conserved and essentially required during the trafficking, assembly, and budding processes of virus, thus an attractive target for designing antiviral drugs. We designed several 10-23 DNAzymes (Dz) targeting different regions of the M2 gene and analyzed their ability to specifically cleave the target RNA in both cell-free system as well as in cell culture using transient transfections. Dz114, among several others, directed against the predicted single-stranded bulge regions showed 70% inhibition of M2 gene expression validated by PCR and Western blot analysis. The activity was dependent on Mg(2+) (10-50 mM) in a dose-dependent manner. The mutant-Dz against M2 gene showed no down-regulation thereby illustrating high level of specificity of designed Dz114 towards the target RNA. Our findings suggest that Dz may be used as potential inhibitor of viral RNA replication and can be explored further for development of an effective therapeutic agent against influenza infection. These catalytic nucleic acid molecules may further be investigated as an alternative to the traditional influenza vaccines that require annual formulation.
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15
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Zhang Y, Fan J, Nie J, Le S, Zhu W, Gao D, Yang J, Zhang S, Li J. Timing readout in paper device for quantitative point-of-use hemin/G-quadruplex DNAzyme-based bioassays. Biosens Bioelectron 2015; 73:13-18. [DOI: 10.1016/j.bios.2015.04.081] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/23/2015] [Accepted: 04/24/2015] [Indexed: 12/31/2022]
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16
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Lable-free quadruple signal amplification strategy for sensitive electrochemical p53 gene biosensing. Biosens Bioelectron 2015; 77:157-63. [PMID: 26406456 DOI: 10.1016/j.bios.2015.09.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 08/22/2015] [Accepted: 09/04/2015] [Indexed: 11/21/2022]
Abstract
A versatile label-free quadruple signal amplification biosensing platform for p53 gene (target DNA) detection was proposed. The chitosan-graphene (CS-GR) modified electrode with excellent electron transfer ability could provide a large specific surface for high levels of AuNPs-DNA attachment. The large amount of AuNPs could immobilize more capture probes and enhance the electrochemical signal with the excellent electrocatalytic activity. Furthermore, with the assist of N.BstNB I (the nicking endonuclease), target DNA could be reused and more G-quadruplex-hemin DNAzyme could be formed, allowing significant signal amplification in the presence of H2O2. Such strategy can enhance the oxidation-reduction reaction of adsorbed methylene blue (MB) and efficiently improve the sensitivity of the proposed biosensor. The morphologies of materials and the stepwise biosensor were characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM) and cyclic voltammetry (CV). Differential pulse voltammetry (DPV) signals of MB provided quantitative measures of the concentrations of target DNA, with a linear calibration range of 1.0 × 10(-15)-1.0 × 10(-9)M and a detection limit of 3.0 × 10(-16)M. Moreover, the resulting biosensor also exhibited good specificity, acceptable reproducibility and stability, indicating that the present strategy was promising for broad potential application in clinic assay.
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17
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Hu R, Liu T, Zhang XB, Yang Y, Chen T, Wu C, Liu Y, Zhu G, Huan S, Fu T, Tan W. DLISA: A DNAzyme-Based ELISA for Protein Enzyme-Free Immunoassay of Multiple Analytes. Anal Chem 2015; 87:7746-53. [DOI: 10.1021/acs.analchem.5b01323] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Rong Hu
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Collaborative Innovation Center for Molecular Engineering
for Theranostics, Hunan University, Changsha 410082, China
- Department
of Chemistry and Department of Physiology and Functional Genomics,
Shands Cancer Center and UF Genetics Institute, Center for Research
at the Bio/Nano Interface, University of Florida, Gainesville, Florida 32611-7200, United States
- College
of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming 650092, China
| | - Tao Liu
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Collaborative Innovation Center for Molecular Engineering
for Theranostics, Hunan University, Changsha 410082, China
| | - Xiao-Bing Zhang
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Collaborative Innovation Center for Molecular Engineering
for Theranostics, Hunan University, Changsha 410082, China
| | - Yunhui Yang
- College
of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming 650092, China
| | - Tao Chen
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Collaborative Innovation Center for Molecular Engineering
for Theranostics, Hunan University, Changsha 410082, China
- Department
of Chemistry and Department of Physiology and Functional Genomics,
Shands Cancer Center and UF Genetics Institute, Center for Research
at the Bio/Nano Interface, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Cuichen Wu
- Department
of Chemistry and Department of Physiology and Functional Genomics,
Shands Cancer Center and UF Genetics Institute, Center for Research
at the Bio/Nano Interface, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Yuan Liu
- Department
of Chemistry and Department of Physiology and Functional Genomics,
Shands Cancer Center and UF Genetics Institute, Center for Research
at the Bio/Nano Interface, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Guizhi Zhu
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Collaborative Innovation Center for Molecular Engineering
for Theranostics, Hunan University, Changsha 410082, China
| | - Shuangyan Huan
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Collaborative Innovation Center for Molecular Engineering
for Theranostics, Hunan University, Changsha 410082, China
| | - Ting Fu
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Collaborative Innovation Center for Molecular Engineering
for Theranostics, Hunan University, Changsha 410082, China
- Department
of Chemistry and Department of Physiology and Functional Genomics,
Shands Cancer Center and UF Genetics Institute, Center for Research
at the Bio/Nano Interface, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Weihong Tan
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, College
of Biology, Collaborative Innovation Center for Molecular Engineering
for Theranostics, Hunan University, Changsha 410082, China
- Department
of Chemistry and Department of Physiology and Functional Genomics,
Shands Cancer Center and UF Genetics Institute, Center for Research
at the Bio/Nano Interface, University of Florida, Gainesville, Florida 32611-7200, United States
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18
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Zheng J, Yang R, Shi M, Wu C, Fang X, Li Y, Li J, Tan W. Rationally designed molecular beacons for bioanalytical and biomedical applications. Chem Soc Rev 2015; 44:3036-55. [PMID: 25777303 PMCID: PMC4431697 DOI: 10.1039/c5cs00020c] [Citation(s) in RCA: 248] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nucleic acids hold promise as biomolecules for future applications in biomedicine and biotechnology. Their well-defined structures and compositions afford unique chemical properties and biological functions. Moreover, the specificity of hydrogen-bonded Watson-Crick interactions allows the construction of nucleic acid sequences with multiple functions. In particular, the development of nucleic acid probes as essential molecular engineering tools will make a significant contribution to advancements in biosensing, bioimaging and therapy. The molecular beacon (MB), first conceptualized by Tyagi and Kramer in 1996, is an excellent example of a double-stranded nucleic acid (dsDNA) probe. Although inactive in the absence of a target, dsDNA probes can report the presence of a specific target through hybridization or a specific recognition-triggered change in conformation. MB probes are typically fluorescently labeled oligonucleotides that range from 25 to 35 nucleotides (nt) in length, and their structure can be divided into three components: stem, loop and reporter. The intrinsic merit of MBs depends on predictable design, reproducibility of synthesis, simplicity of modification, and built-in signal transduction. Using resonance energy transfer (RET) for signal transduction, MBs are further endowed with increased sensitivity, rapid response and universality, making them ideal for chemical sensing, environmental monitoring and biological imaging, in contrast to other nucleic acid probes. Furthermore, integrating MBs with targeting ligands or molecular drugs can substantially support their in vivo applications in theranositics. In this review, we survey advances in bioanalytical and biomedical applications of rationally designed MBs, as they have evolved through the collaborative efforts of many researchers. We first discuss improvements to the three components of MBs: stem, loop and reporter. The current applications of MBs in biosensing, bioimaging and therapy will then be described. In particular, we emphasize recent progress in constructing MB-based biosensors in homogeneous solution or on solid surfaces. We expect that such rationally designed and functionalized MBs will open up new and exciting avenues for biological and medical research and applications.
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Affiliation(s)
- Jing Zheng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China
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19
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Li L, Feng J, Fan Y, Tang B. Simultaneous Imaging of Zn2+ and Cu2+ in Living Cells Based on DNAzyme Modified Gold Nanoparticle. Anal Chem 2015; 87:4829-35. [DOI: 10.1021/acs.analchem.5b00204] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Lu 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, P. R. China
| | - Jie Feng
- 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, P. R. China
| | - Yuanyuan Fan
- 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, P. R. 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,
Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China
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20
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Gao F, Du L, Tang D, Lu Y, Zhang Y, Zhang L. A cascade signal amplification strategy for surface enhanced Raman spectroscopy detection of thrombin based on DNAzyme assistant DNA recycling and rolling circle amplification. Biosens Bioelectron 2015; 66:423-30. [DOI: 10.1016/j.bios.2014.12.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 11/11/2014] [Accepted: 12/01/2014] [Indexed: 11/28/2022]
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21
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Khanna M, Saxena L, Rajput R, Kumar B, Prasad R. Gene silencing: a therapeutic approach to combat influenza virus infections. Future Microbiol 2015; 10:131-40. [DOI: 10.2217/fmb.14.94] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
ABSTRACT Selective gene silencing technologies such as RNA interference (RNAi) and nucleic acid enzymes have shown therapeutic potential for treating viral infections. Influenza virus is one of the major public health concerns around the world and its management is challenging due to a rapid increase in antiviral resistance. Influenza vaccine also has its limitations due to the emergence of new strains that may escape the immunity developed by the previous year's vaccine. Antiviral drugs are the primary mode of prevention and control against a pandemic and there is an urgency to develop novel antiviral strategies against influenza virus. In this review, we discuss the potential utility of several gene silencing mechanisms and their prophylactic and therapeutic potential against the influenza virus.
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Affiliation(s)
- Madhu Khanna
- Department of Respiratory Virology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Latika Saxena
- Department of Respiratory Virology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Roopali Rajput
- Department of Respiratory Virology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Binod Kumar
- Department of Respiratory Virology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Rajendra Prasad
- Department of Pulmonary Medicine, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
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22
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Tian R, Chen X, Jiang N, Hao N, Xu L, Yao C. An electrochemical sensing strategy based on a three dimensional ordered macroporous polyaniline–platinum platform and a mercury(ii) ion-mediated DNAzyme functionalized nanolabel. J Mater Chem B 2015; 3:4805-4813. [DOI: 10.1039/c5tb00796h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An Hg2+-switched DNA biosensor using a three dimensional ordered macroporous polyaniline–platinum platform and a G-rich sequence recognition probe was developed, with the detection limit of 8.7 × 10−14 M.
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Affiliation(s)
- Rong Tian
- College of Sciences
- Nanjing Tech University
- Nanjing
- P. R. China
| | - Xiaojun Chen
- College of Sciences
- Nanjing Tech University
- Nanjing
- P. R. China
| | - Nan Jiang
- College of Sciences
- Nanjing Tech University
- Nanjing
- P. R. China
| | - Ning Hao
- Biotechnology and Pharmaceutical Engineering
- Nanjing Tech University
- Nanjing 211816
- P. R. China
| | - Lin Xu
- Biotechnology and Pharmaceutical Engineering
- Nanjing Tech University
- Nanjing 211816
- P. R. China
| | - Cheng Yao
- College of Sciences
- Nanjing Tech University
- Nanjing
- P. R. China
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23
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Gomez A, Miller N, Smolina I. Visual detection of bacterial pathogens via PNA-based padlock probe assembly and isothermal amplification of DNAzymes. Anal Chem 2014; 86:11992-8. [PMID: 25415469 PMCID: PMC4270401 DOI: 10.1021/ac5018748] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 11/21/2014] [Indexed: 12/12/2022]
Abstract
We have developed a self-reporting isothermal system for visual bacterial pathogen detection with single base resolution. The new DNA diagnostic is based on combination of peptide nucleic acid (PNA) technology, rolling circle amplification (RCA) and DNAzymes. PNAs are used as exceedingly selective chemical tools that bind genomic DNA at a predetermined sequence under nondenaturing conditions. After assembly of the PNA-DNA construct a padlock probe is circularized on the free strand. The probe incorporates a G-quadruplex structure flanked by nicking enzyme recognition sites. The assembled circle serves as a template for a novel hybrid RCA strategy that allows for exponential amplification and production of short single-stranded DNA pieces. These DNA fragments fold into G-quadruplex structures and when complexed with hemin become functional DNAzymes. The catalytic activity of each DNAzyme unit leads to colorimetric detection and provides the second amplification step. The combination of PNA, RCA, and DNAzymes allows for sequence-specific and highly sensitive detection of bacteria with a colorimetric output observed with the naked eye. Herein, we apply this method for the discrimination of Escherichia coli, Salmonella typhimurium, and Clostridium difficile genomes.
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Affiliation(s)
- Anastasia Gomez
- Department
of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
| | - Nancy
S. Miller
- Department
of Pathology and Laboratory Medicine, Boston
Medical Center and Boston University School of Medicine, 670 Albany Street, Boston, Massachusetts 02118, United States
| | - Irina Smolina
- Department
of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
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24
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Binding-induced and label-free colorimetric method for protein detection based on autonomous assembly of hemin/G-quadruplex DNAzyme amplification strategy. Biosens Bioelectron 2014; 64:572-8. [PMID: 25310491 DOI: 10.1016/j.bios.2014.09.096] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 09/30/2014] [Accepted: 09/30/2014] [Indexed: 11/21/2022]
Abstract
In this work, a new binding-induced and label-free colorimetric method for protein detection has been developed on the basis of an autonomous assembly of hemin/G-quadruplex DNAzyme amplification strategy. The system consists of two proximity probes carrying two aptamer sequences as recognition elements for target, and two hairpin structures include three-fourths and one-fourth of the G-quadruplex sequences in inactive configuration as functional elements. In the presence of target protein, two proximity probes bind to the protein simultaneously, forming a stable DNA-protein complex. Then the complex triggers an autonomous cross-opening of the two functional hairpin structures, leading to the formation of numerous hemin/G-quadruplex DNAzymes. The resulting DNAzymes catalyze the oxidation of colorless 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS(2-)) to the green-colored ABTS(•-) with the presence of H2O2, thus providing the amplified colorimetric detection of target. Using human α-thrombin as the protein target, this binding-induced DNAzyme amplification colorimetric method affords high sensitivity with a detection limit of 1.9 pM. Furthermore, this method might be further extended to sensitive detection of other proteins by simply replacing recognition elements of proximity probes.
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25
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Wang Q, Song Y, Chai Y, Pan G, Li T, Yuan Y, Yuan R. Electrochemical immunosensor for detecting the spore wall protein of Nosema bombycis based on the amplification of hemin/G-quadruplex DNAzyme concatamers functionalized Pt@Pd nanowires. Biosens Bioelectron 2014; 60:118-23. [DOI: 10.1016/j.bios.2014.03.075] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/29/2014] [Accepted: 03/31/2014] [Indexed: 11/26/2022]
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26
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Liu T, Zhang X, Zhu W, Liu W, Zhang D, Wang J. A G-quadruplex DNAzyme-based colorimetric method for facile detection of Alicyclobacillus acidoterrestris. Analyst 2014; 139:4315-21. [DOI: 10.1039/c4an00643g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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27
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Qian H, Tian C, Yu J, Guo F, Zheng MS, Jiang W, Dong QF, Mao C. Self-assembly of DNA nanotubes with defined diameters and lengths. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:855-858. [PMID: 24745047 DOI: 10.1002/smll.201301891] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Nanotubes with different sizes can be readily assembled from simple DNA nanomotifs, which consist of just a few unique DNA sequences. Such structurally well-defi ned DNA-nanotubes will have great potential in many technological applications ranging from drug delivery, to determination of biomacromolecular 3D structures, to nanoplasmonic devices.
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28
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Zhang J, Chai Y, Yuan R, Yuan Y, Bai L, Xie S, Jiang L. A novel electrochemical aptasensor for thrombin detection based on the hybridization chain reaction with hemin/G-quadruplex DNAzyme-signal amplification. Analyst 2013; 138:4558-64. [PMID: 23741737 DOI: 10.1039/c3an00396e] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this work, a novel signal amplification electrochemical aptasensor for the sensitive and selective detection of thrombin was successfully fabricated. The amplification method was based on the hybridization chain reaction (HCR) and a pseudobienzyme electrocatalytic system. HCR-based double-stranded DNA (dsDNA) polymers not only constructed an effective carrier for anchoring larger amounts of electron mediator methylene blue (MB) into the DNA duplexes to produce a strong differential pulse voltammetry (DPV) signal, but also resulted in the formation of hemin/G-quadruplex DNAzymes nanowires by intercalating hemin into two induced single-stranded DNA (ssDNA). With the addition of NADH into the electrolytic cell, the hemin/G-quadruplex acting as an NADH oxidase and HRP-mimicking DNAzyme for the pseudobienzyme amplifying system could in situ biocatalyze the formation of H₂O₂ with local concentrations and low transfer loss resulting in dramatic signal enhancements. The binding event can be detected by a decrease in the integrated charge of MB which electrostatically absorbed onto dsDNA polymers. In the presence of thrombin, the dsDNA polymers associated with MB and hemin/G-quadruplex structures were removed from the electrode surface, leading to a significant decrease of redox current. DPV signals of MB provided quantitative measures of the concentrations of thrombin, with a linear calibration range of 0.01-50 nM and a detection limit of 2 pM. Moreover, the resulting aptasensor also exhibited good specificity, acceptable reproducibility and stability, indicating that the present strategy was promising for broad potential application in clinic assay and various protein analyses.
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Affiliation(s)
- Juan Zhang
- Education Ministry Key Laboratory on Luminescence and Real-Time Analysis, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People's Republic of China
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29
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Zhao XH, Gong L, Zhang XB, Yang B, Fu T, Hu R, Tan W, Yu R. Versatile DNAzyme-based amplified biosensing platforms for nucleic acid, protein, and enzyme activity detection. Anal Chem 2013; 85:3614-20. [PMID: 23406194 DOI: 10.1021/ac303457u] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
DNAzymes have been widely applied as signal amplifiers for enzyme-free and highly sensitive detection of DNA. A few of them have also been employed for amplified detection of other biomolecules via a target-triggered assembly of split or mutated DNAzyme strategy. However, most of these designs adopt Mg(2+)-dependent DNAzyme as the catalytic unit, which suffered from low catalytic cleavage activity. Meanwhile, some DNAzymes with high catalytic activity are not suitable for these designs because the slight modification of the catalytic core might results in remarkably decreased or even no catalytic activity of these DNAzymes. On the basis of DNAzyme topological effect or the terminal protection of small-molecule-linked DNA, we developed two versatile sensing platforms for amplified detection of different biotargets. Since no modification is necessary for the catalytic core of the DNAzyme in these designs, they can employ any DNAzyme with high catalytic activity as amplified unit, which affords a high amplified efficiency for the sensing platform. A catalytic and molecular beacon design was further employed to realize the true enzymatic multiple turnover of DNAzyme. These designs together allow a high sensitivity for the biotargets, resulting in a detection limit of 20 pM, 0.2 U/mL, and 1 ng/mL for target DNA, DNA adenine methylation methyltransferase (Dam MTase), and streptavidin, respectively, much lower than previously reported biosensors. In addition, the proposed sensing strategy is versatile. By conjugating with various recognition units, it can be employed to detect a wide range of biotargets, varying from nucleic acids to proteins with high sensitivity.
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Affiliation(s)
- Xu-Hua Zhao
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, PR China
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30
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Tang S, Tong P, Li H, Gu F, Zhang L. The three-way junction DNAzyme based probe for label-free colorimetric detection of DNA. Biosens Bioelectron 2013; 41:397-402. [DOI: 10.1016/j.bios.2012.08.056] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Revised: 08/28/2012] [Accepted: 08/30/2012] [Indexed: 01/06/2023]
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31
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Wang HB, Wang L, Huang KJ, Xu SP, Wang HQ, Wang LL, Liu YM. A highly sensitive and selective biosensing strategy for the detection of Pb2+ ions based on GR-5 DNAzyme functionalized AuNPs. NEW J CHEM 2013. [DOI: 10.1039/c3nj00328k] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Deng H, Ren Y, Shen W, Gao Z. An ultrasensitive homogeneous chemiluminescent assay for microRNAs. Chem Commun (Camb) 2013; 49:9401-3. [DOI: 10.1039/c3cc44824j] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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Xie S, Chai Y, Yuan R, Bai L, Yuan Y, Wang Y. A dual-amplification aptasensor for highly sensitive detection of thrombin based on the functionalized graphene-Pd nanoparticles composites and the hemin/G-quadruplex. Anal Chim Acta 2012; 755:46-53. [PMID: 23146393 DOI: 10.1016/j.aca.2012.10.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 09/26/2012] [Accepted: 10/02/2012] [Indexed: 11/18/2022]
Abstract
In this work, an advanced sandwich-type electrochemical aptasensor for thrombin was proposed by integrating hemin/G-quadruplex with functionalized graphene-Pd nanoparticles composites (PdNPs-RGs). The hemin/G-quadruplex formed by intercalating hemin into thrombin binding aptamer (TBA), firstly acted as a NADH oxidase, assisting the oxidation of NADH to NAD(+) accompanying with the generation of H(2)O(2) in the presence of dissolved O(2). Subsequently, the hemin/G-quadruplex acted as HRP-mimicking DNAzyme that rapidly bioelectrocatalyze the reduction of the produced H(2)O(2). At the same time, the Pd nanoparticles supported on p-iodoaniline functionalized graphene were also adopted to catalyze the reduction of H(2)O(2). Thus, with the dual catalysis, a dramatically amplified electrochemical signal could be obtained. Besides, the avidin-biotin system for binding aptamer sequences on electrodes not only improved the sensitivity of thrombin analysis but also obtained an acceptable repeatability of the aptasensor. With several factors mentioned above, a wide linear ranged from 0.1 pM to 50 nM was acquired with a relatively low detection limit of 0.03 pM (defined as S/N=3). These excellent performances provided our approach a promising way for ultrasensitive assay in electrochemical aptasensors.
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Affiliation(s)
- Shunbi Xie
- Key Laboratory on Luminescence and Real-Time Analysis, Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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34
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Saha K, Agasti SS, Kim C, Li X, Rotello VM. Gold nanoparticles in chemical and biological sensing. Chem Rev 2012; 112:2739-79. [PMID: 22295941 PMCID: PMC4102386 DOI: 10.1021/cr2001178] [Citation(s) in RCA: 2742] [Impact Index Per Article: 228.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Krishnendu Saha
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, MA 01003, USA
| | - Sarit S. Agasti
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, MA 01003, USA
| | - Chaekyu Kim
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, MA 01003, USA
| | - Xiaoning Li
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, MA 01003, USA
| | - Vincent M. Rotello
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, MA 01003, USA
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35
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Nelson KE, Ihms HE, Mazumdar D, Bruesehoff PJ, Lu Y. The importance of peripheral sequences in determining the metal selectivity of an in vitro-selected Co(2+) -dependent DNAzyme. Chembiochem 2012; 13:381-91. [PMID: 22250000 PMCID: PMC3299816 DOI: 10.1002/cbic.201100724] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Indexed: 11/12/2022]
Abstract
DNAzymes are catalytically active DNA molecules that use metal cofactors for their enzymatic functions. While a growing number of DNAzymes with diverse functions and metal selectivities have been reported, the relationships between metal ion selectivity, conserved sequences and structures responsible for selectivity remain to be elucidated. To address this issue, we report biochemical assays of a family of previously reported in vitro selected DNAzymes. This family includes the clone 11 DNAzyme, which was isolated by positive and negative selection, and the clone 18 DNAzyme, which was isolated by positive selection alone. The clone 11 DNAzyme has a higher selectivity for Co(2+) over Pb(2+) compared with clone 18. The reasons for this difference are explored here through phylogenetic comparison, mutational analysis and stepwise truncation. A novel DNAzyme truncation method incorporated a nick in the middle of the DNAzyme to allow for truncation close to the nicked site while preserving peripheral sequences at both ends of the DNAzyme. The results demonstrate that peripheral sequences within the substrate binding arms, most notably the stem loop, loop II, are sufficient to restore its selectivity for Co(2+) over Pb(2+) to levels observed in clone 11. A comparison of these sequences' secondary structures and Co(2+) selectivities suggested that metastable structures affect metal ion selectivity. The Co(2+) selectivity of the clone 11 DNAzyme showed that the metal ion binding and selectivities of small, in vitro selected DNAzymes may be more complex than previously appreciated, and that clone 11 may be more similar to larger ribozymes than to other small DNAzymes in its structural complexity and behavior. These factors should be taken into account when metal-ion selectivity is required in rationally designed DNAzymes and DNAzyme-based biosensors.
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Affiliation(s)
- Kevin E. Nelson
- Department of Biochemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL 61801 (USA)
- Department of Pediatrics, Primary Children’s Medical Center, University of Utah, 100 North Mario Capecchi Drive, Salt Lake City, UT 84113 (USA)
| | - Hannah E. Ihms
- Department of Chemistry, University of Illinois, A322 Chemical and Life Sciences Laboratory, MC-712, Box 8–6, 600 South Mathews Avenue, Urbana, IL 61801 (USA)
| | - Debapriya Mazumdar
- Department of Chemistry, University of Illinois, A322 Chemical and Life Sciences Laboratory, MC-712, Box 8–6, 600 South Mathews Avenue, Urbana, IL 61801 (USA)
| | - Peter J. Bruesehoff
- Department of Chemistry, University of Illinois, A322 Chemical and Life Sciences Laboratory, MC-712, Box 8–6, 600 South Mathews Avenue, Urbana, IL 61801 (USA)
| | - Yi Lu
- Department of Biochemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL 61801 (USA)
- Department of Chemistry, University of Illinois, A322 Chemical and Life Sciences Laboratory, MC-712, Box 8–6, 600 South Mathews Avenue, Urbana, IL 61801 (USA)
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36
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Guga P, Koziołkiewicz M. Phosphorothioate nucleotides and oligonucleotides - recent progress in synthesis and application. Chem Biodivers 2012; 8:1642-81. [PMID: 21922655 DOI: 10.1002/cbdv.201100130] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Piotr Guga
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry, Sienkiewicza 112, PL-90-363 Łódź.
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37
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Nie D, Wu H, Zheng Q, Guo L, Ye P, Hao Y, Li Y, Fu F, Guo Y. A sensitive and selective DNAzyme-based flow cytometric method for detecting Pb2+ions. Chem Commun (Camb) 2012; 48:1150-2. [DOI: 10.1039/c2cc16635f] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Reducing background signal of G-quadruplex–hemin DNAzyme sensing platform by single-walled carbon nanotubes. Biosens Bioelectron 2011; 27:137-40. [DOI: 10.1016/j.bios.2011.06.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Revised: 06/01/2011] [Accepted: 06/26/2011] [Indexed: 11/23/2022]
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Zhang H, Jiang B, Xiang Y, Su J, Chai Y, Yuan R. DNAzyme-based highly sensitive electronic detection of lead via quantum dot-assembled amplification labels. Biosens Bioelectron 2011; 28:135-8. [PMID: 21803567 DOI: 10.1016/j.bios.2011.07.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Revised: 07/07/2011] [Accepted: 07/08/2011] [Indexed: 11/19/2022]
Abstract
An electronic DNAzyme sensor for highly sensitive detection of Pb(2+) is demonstrated by coupling the significant signal enhancement of the layer-by-layer (LBL) assembled quantum dots (QDs) with Pb(2+) specific DNAzymes. The presence of Pb(2+) cleaves the DNAzymes and releases the biotin-modified fragments, which further hybridize with the complementary strands immobilized on the gold substrate. The streptavidin-coated, QD LBL assembled nanocomposites were captured on the gold substrate through biotin-streptavidin interactions. Subsequent electrochemical signals of the captured QDs upon acid dissolution provide quantitative information on the concentrations of Pb(2+) with a dynamic range from 1 to 1000 nM. Due to the dramatic signal amplification by the numerous QDs, subnanomolar level (0.6 nM) of Pb(2+) can be detected. The proposed sensor also shows good selectivity against other divalent metal ions and thus holds great potential for the construction of general DNAzyme-based sensing platform for the monitoring of other heavy metal ions.
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Affiliation(s)
- Haixia Zhang
- Key Laboratory on Luminescence and Real-Time Analysis, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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Yi J, Liu C. Efficient silencing of gene expression by an ASON-bulge-DNAzyme complex. PLoS One 2011; 6:e18629. [PMID: 21490924 PMCID: PMC3072403 DOI: 10.1371/journal.pone.0018629] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 03/14/2011] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND DNAzymes are DNA molecules that can directly cleave cognate mRNA, and have been developed to silence gene expression for research and clinical purposes. The advantage of DNAzymes over ribozymes is that they are inexpensive to produce and exhibit good stability. The "10-23 DNA enzyme" is composed of a catalytic domain of 15 deoxynucleotides, flanked by two substrate-recognition domains of approximately eight nucleotides in each direction, which provides the complementary sequence required for specific binding to RNA substrates. However, these eight nucleotides might not afford sufficient binding energy to hold the RNA substrate along with the DNAzyme, which would interfere with the efficiency of the DNAzyme or cause side effects, such as the cleavage of non-cognate mRNAs. METHODOLOGY In this study, we inserted a nonpairing bulge at the 5' end of the "10-23 DNA enzyme" to enhance its efficiency and specificity. Different sizes of bulges were inserted at different positions in the 5' end of the DNAzyme. The non-matching bulge will avoid strong binding between the DNAzyme and target mRNA, which may interfere with the efficiency of the DNAzyme. CONCLUSIONS Our novel DNAzyme constructs could efficiently silence the expression of target genes, proving a powerful tool for gene silencing. The results showed that the six oligo bulge was the most effective when the six oligo bulge was 12-15 bp away from the core catalytic domain.
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Affiliation(s)
- Jianzhong Yi
- Institute of Animal Husbandry Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China.
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41
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Ma DL, Chan DSH, Man BYW, Leung CH. Oligonucleotide-based luminescent detection of metal ions. Chem Asian J 2011; 6:986-1003. [PMID: 21337527 DOI: 10.1002/asia.201000870] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Indexed: 01/20/2023]
Abstract
Metal ions are prevalent in biological systems and are critically involved in essential life processes. However, excess concentrations of metals can pose a serious danger to living organisms. Oligonucleotides represent a versatile sensing platform for the detection of various molecular entities including metal ions. This review summarizes the recent advances in the development of oligonucleotide-based luminescent detection methods for metal ions.
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Affiliation(s)
- Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, China.
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Li LD, Chen ZB, Zhao HT, Guo L. Electrochemical real-time detection of l-histidine via self-cleavage of DNAzymes. Biosens Bioelectron 2011; 26:2781-5. [DOI: 10.1016/j.bios.2010.10.041] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2010] [Revised: 10/23/2010] [Accepted: 10/25/2010] [Indexed: 12/01/2022]
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Liu Y, Stepanov VG, Strych U, Willson RC, Jackson GW, Fox GE. DNAzyme-mediated recovery of small recombinant RNAs from a 5S rRNA-derived chimera expressed in Escherichia coli. BMC Biotechnol 2010; 10:85. [PMID: 21134283 PMCID: PMC3019158 DOI: 10.1186/1472-6750-10-85] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 12/06/2010] [Indexed: 01/24/2023] Open
Abstract
Background Manufacturing large quantities of recombinant RNAs by overexpression in a bacterial host is hampered by their instability in intracellular environment. To overcome this problem, an RNA of interest can be fused into a stable bacterial RNA for the resulting chimeric construct to accumulate in the cytoplasm to a sufficiently high level. Being supplemented with cost-effective procedures for isolation of the chimera from cells and recovery of the recombinant RNA from stabilizing scaffold, this strategy might become a viable alternative to the existing methods of chemical or enzymatic RNA synthesis. Results Sequence encoding a 71-nucleotide recombinant RNA was inserted into a plasmid-borne deletion mutant of the Vibrio proteolyticus 5S rRNA gene in place of helix III - loop C segment of the original 5S rRNA. After transformation into Escherichia coli, the chimeric RNA (3×pen aRNA) was expressed constitutively from E. coli rrnB P1 and P2 promoters. The RNA chimera accumulated to levels that exceeded those of the host's 5S rRNA. A novel method relying on liquid-solid partitioning of cellular constituents was developed for isolation of total RNA from bacterial cells. This protocol avoids toxic chemicals, and is therefore more suitable for large scale RNA purification than traditional methods. A pair of biotinylated 8-17 DNAzymes was used to bring about the quantitative excision of the 71-nt recombinant RNA from the chimera. The recombinant RNA was isolated by sequence-specific capture on beads with immobilized complementary deoxyoligonucleotide, while DNAzymes were recovered by biotin affinity chromatography for reuse. Conclusions The feasibility of a fermentation-based approach for manufacturing large quantities of small RNAs in vivo using a "5S rRNA scaffold" strategy is demonstrated. The approach provides a route towards an economical method for the large-scale production of small RNAs including shRNAs, siRNAs and aptamers for use in clinical and biomedical research.
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Affiliation(s)
- Yamei Liu
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
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Li J, Wang N, Luo Q, Wan L. The 10-23 DNA enzyme generated by a novel expression vector mediate inhibition of taco expression in macrophage. Oligonucleotides 2010; 20:61-8. [PMID: 20059315 DOI: 10.1089/oli.2009.0217] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The 10-23 DNA enzyme (10-23 DNAzyme), a single-stranded DNA (ssDNA) molecule, can efficiently and specifically cleave almost any target RNA molecules. Therefore, it is regarded as one of the promising tools in gene therapy. However, there are still some obstacles, such as low efficiency of cellular uptake and instability in vivo, in its application. Taking advantage of the mechanism of Moloney mouse leukemia virus (MMLV) reverse transcriptase (RT), we investigate the construction of a novel ssDNA expression vector in this study. In order to improve the expression efficiency, the mmlv-rt gene and ODN-PMT (an oligodeoxynucleotide including other essential sequences for generating ssDNA) were cloned into a single plasmid under the control of 2 separated promoters. The ability of the vector to generate specific 10-23 DNAzyme in mammalian cell was tested by constructing a tryptophan-aspartate-containing coat protein (taco) gene-specific 10-23 DNAzyme expression plasmid. The potential of the expressed 10-23 DNAzyme to suppress TACO expression was also investigated. Our results indicated that this vector generates desired 10-23 DNAzyme in mammalian cells. The expressed 10-23 DNAzyme targeting taco gene can reduce TACO expression both at mRNA level (by 78.26%) and at protein level (by 75.30%).
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Affiliation(s)
- Junming Li
- Department of Clinical Laboratory, First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China.
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Bi S, Yan Y, Hao S, Zhang S. Colorimetric Logic Gates Based on Supramolecular DNAzyme Structures. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201000840] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Zhang C, Su M, He Y, Leng Y, Ribbe AE, Wang G, Jiang W, Mao C. Exterior modification of a DNA tetrahedron. Chem Commun (Camb) 2010; 46:6792-4. [DOI: 10.1039/c0cc02363a] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Yang X, Xu J, Tang X, Liu H, Tian D. A novel electrochemical DNAzyme sensor for the amplified detection of Pb2+ ions. Chem Commun (Camb) 2010; 46:3107-9. [DOI: 10.1039/c002137g] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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49
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Kong DM, Yang W, Wu J, Li CX, Shen HX. Structure-function study of peroxidase-like G-quadruplex-hemin complexes. Analyst 2009; 135:321-6. [PMID: 20098765 DOI: 10.1039/b920293e] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structure-function relationship of G-quadruplex-hemin complexes with peroxidase activity was studied by comparing peroxidase activity and circular dichroism (CD) spectra of 22 oligonucleotides with the sequence of d(G(2)T(n))(3)G(2), d(G(3)T(n))(3)G(3) (n = 1-4) and dG(3)T(i)G(3)T(j)G(3)T(k)G(3). According to the experimental results, some conclusions can be drawn, such as the addition of hemin may promote the conversion of some G-quadruplexes from antiparallel structures to parallel structures; the formation of G-quadruplexes is a crucial factor in determining the peroxidase activity of G-quadruplex-hemin complexes; and the complexes formed by hemin and parallel G-quadruplexes have much higher peroxidase activity than those formed by hemin and antiparallel G-quadruplexes.
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Affiliation(s)
- De-Ming Kong
- Key Laboratory of Functional Polymer Materials, Ministry of Education, Nankai University, Tianjin, 300071, People's Republic of China.
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50
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Li B, Du Y, Li T, Dong S. Investigation of 3,3′,5,5′-tetramethylbenzidine as colorimetric substrate for a peroxidatic DNAzyme. Anal Chim Acta 2009; 651:234-40. [DOI: 10.1016/j.aca.2009.09.009] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Revised: 09/07/2009] [Accepted: 09/08/2009] [Indexed: 01/29/2023]
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