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Effect of Distance from Catalytic Synergy Group to Iron Porphyrin Center on Activity of G-Quadruplex/Hemin DNAzyme. Molecules 2020; 25:molecules25153425. [PMID: 32731553 PMCID: PMC7435396 DOI: 10.3390/molecules25153425] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 07/16/2020] [Accepted: 07/27/2020] [Indexed: 11/17/2022] Open
Abstract
G-quadruplex/Hemin (G4/Hemin) complex has been widely used in biocatalysis and analytical applications. Meanwhile, compared with natural proteinous enzyme, its low catalytic activity is still limiting its applications. Even though several methods have been developed to enhance the peroxidation efficiency, the important core of the G4 design based enhancement mechanism is still indistinct. Here, we focus the mechanism study on the two most important microdomains: the iron porphyrin center and the catalytic synergy group within the 3' flanking. These microdomains not only provide the pocket for the combination of substrate, but also offer the axial coordination for the accelerated formation of Compound I (catalytic intermediate). In order to obtain a more suitable space layout to further accelerate the catalytic process, we have used the bases within the 3' flanking to precisely regulate the distance between microdomains. Finally, the position-dependent effect on catalytic enhancement is observed. When dC is positioned at the second-position of 3' flanking, the newly obtained DNAzyme achieves an order of magnitude improvement compared to parent G4/Hemin in catalytic activity. The results highlight the influence of the distance between the catalytic synergy group and iron porphyrin center on the activity of DNAzyme, and provide insightful information for the design of highly active DNAzymes.
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52
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Bai Y, Zhang H, Zhao L, Wang Y, Chen X, Zhai H, Tian M, Zhao R, Wang T, Xu H, Feng F. A novel aptasensor based on HCR and G-quadruplex DNAzyme for fluorescence detection of Carcinoembryonic Antigen. Talanta 2020; 221:121451. [PMID: 33076074 DOI: 10.1016/j.talanta.2020.121451] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 07/15/2020] [Accepted: 07/22/2020] [Indexed: 12/11/2022]
Abstract
In this paper, a rationally designed aptasensing platform based on Hybridization Chain Reaction (HCR) and G-quadruplex DNAzyme for the fluorescence detection of Carcinoembryonic Antigen (CEA) has been developed. In the presence of target CEA, the aptamer sequence in Aptamer Probe (AP) specifically bound to CEA, resulting in the AP conformation change and thus releasing initiator, which triggered the autonomous cross-opening of Hairpin 1 (H1) and Hairpin 2 (H2) that yielded extended nicked double-stranded DNA via HCR. Upon the addition of hemin, G-rich segments at the end of H1 and H2 self-assembled into the peroxidase-mimicking hemin/G-quadruplex DNAzymes, which catalyzed the hydrogen peroxide-mediated oxidation of thiamine to achieve fluorescence detection of CEA. The HCR product, and the formation and catalytic performance of DNAzyme were characterized by agarose gel electrophoresis, UV-vis spectroscopy and fluorescence spectroscopy, respectively. Under optimal conditions, the fluorescent aptasensor showed a linear relationship ranging from 0.25 to 1.5 nM toward CEA with a detection limit of 0.2 nM. In addition, this aptasensor exhibited high selectivity for CEA without being affected by other interfering proteins, such as IgG, AFP and PSA. Furthermore, this proposed aptasensor was successfully applied to CEA analysis in diluted human serum samples. It is believed that this strategy has a promising potential in biochemical analysis and clinic application.
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Affiliation(s)
- Yunfeng Bai
- College of Chemistry and Environmental Engineering, Shanxi Datong University, Datong, 037009, China.
| | - Huilin Zhang
- College of Chemistry and Environmental Engineering, Shanxi Datong University, Datong, 037009, China; College of Chemistry and Chemical Engineering, Shanxi University, Taiyuan, 030006, China
| | - Lu Zhao
- College of Chemistry and Environmental Engineering, Shanxi Datong University, Datong, 037009, China
| | - Yuzhen Wang
- College of Chemistry and Environmental Engineering, Shanxi Datong University, Datong, 037009, China
| | - Xiaoliang Chen
- College of Chemistry and Environmental Engineering, Shanxi Datong University, Datong, 037009, China
| | - Hong Zhai
- College of Chemistry and Environmental Engineering, Shanxi Datong University, Datong, 037009, China
| | - Maozhong Tian
- College of Chemistry and Environmental Engineering, Shanxi Datong University, Datong, 037009, China
| | - Ruirui Zhao
- College of Chemistry and Chemical Engineering, Shanxi University, Taiyuan, 030006, China
| | - Tao Wang
- College of Chemistry and Environmental Engineering, Shanxi Datong University, Datong, 037009, China
| | - Hui Xu
- College of Chemistry and Environmental Engineering, Shanxi Datong University, Datong, 037009, China
| | - Feng Feng
- College of Chemistry and Environmental Engineering, Shanxi Datong University, Datong, 037009, China; College of Chemistry and Chemical Engineering, Shanxi University, Taiyuan, 030006, China.
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53
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Cao Y, Li W, Ding P, Pei R. Acid-facilitated G-quadruplex/hemin DNAzymes: accompanied by the assembly of quadruplex supramolecules. Chem Commun (Camb) 2020; 56:8667-8670. [PMID: 32608405 DOI: 10.1039/d0cc03082a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Four types of quadruplex supramolecules containing G-quadruplex (G4)-I-motif interfaces were assembled under slightly acidic conditions, which can interact with hemin to form I-motif-linked G4/hemin DNAzymes. Our data demonstrated that some I-motif-linked DNAzymes are highly acid-dependent due to the stabilization of hemiprotonated cytosine-cytosine (C˙CH+) pairs for the G4 units.
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Affiliation(s)
- Yanwei Cao
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China.
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Arrabito G, Aleeva Y, Ferrara V, Prestopino G, Chiappara C, Pignataro B. On the Interaction between 1D Materials and Living Cells. J Funct Biomater 2020; 11:E40. [PMID: 32531950 PMCID: PMC7353490 DOI: 10.3390/jfb11020040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 01/08/2023] Open
Abstract
One-dimensional (1D) materials allow for cutting-edge applications in biology, such as single-cell bioelectronics investigations, stimulation of the cellular membrane or the cytosol, cellular capture, tissue regeneration, antibacterial action, traction force investigation, and cellular lysis among others. The extraordinary development of this research field in the last ten years has been promoted by the possibility to engineer new classes of biointerfaces that integrate 1D materials as tools to trigger reconfigurable stimuli/probes at the sub-cellular resolution, mimicking the in vivo protein fibres organization of the extracellular matrix. After a brief overview of the theoretical models relevant for a quantitative description of the 1D material/cell interface, this work offers an unprecedented review of 1D nano- and microscale materials (inorganic, organic, biomolecular) explored so far in this vibrant research field, highlighting their emerging biological applications. The correlation between each 1D material chemistry and the resulting biological response is investigated, allowing to emphasize the advantages and the issues that each class presents. Finally, current challenges and future perspectives are discussed.
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Affiliation(s)
- Giuseppe Arrabito
- Dipartimento di Fisica e Chimica—Emilio Segrè, University of Palermo, Viale delle Scienze, Ed.17, 90128 Palermo, Italy;
| | - Yana Aleeva
- INSTM UdR Palermo, Viale delle Scienze, Ed.17, 90128 Palermo, Italy; (Y.A.); (C.C.)
| | - Vittorio Ferrara
- Dipartimento di Scienze Chimiche, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy;
| | - Giuseppe Prestopino
- Dipartimento di Ingegneria Industriale, Università di Roma “Tor Vergata”, Via del Politecnico 1, I-00133 Roma, Italy;
| | - Clara Chiappara
- INSTM UdR Palermo, Viale delle Scienze, Ed.17, 90128 Palermo, Italy; (Y.A.); (C.C.)
| | - Bruno Pignataro
- Dipartimento di Fisica e Chimica—Emilio Segrè, University of Palermo, Viale delle Scienze, Ed.17, 90128 Palermo, Italy;
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55
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Zhou Z, Fan D, Willner I. Modeling Gene Expression Instability by Programmed and Switchable Polymerization/Nicking DNA Nanomachineries. ACS NANO 2020; 14:5046-5052. [PMID: 32250590 DOI: 10.1021/acsnano.0c01583] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Models for gene expression instability by noncanonical DNA-nanostructures are introduced. The systems consist of a promoter-template scaffold that acts as a polymerization/nicking machinery that models, in the presence of polymerase/Nt.BbvCI and dNTPs, the autonomous synthesis of displaced strands mimicking the native "genes". Incorporation of noncanonical DNA structures into the scaffolds consisting of Sr2+-ion-stabilized G-quadruplexes, T-A·T triplexes, or ATP-aptamer complexes results in the perturbation of the polymerization/nicking DNA machineries and the synthesis of displaced strands-"genes" exhibiting other structures. By the dissociation of the noncanonical blockage units, the regeneration of the synthesis of the original intact displaced strands-"genes" is demonstrated. The study introduces conceptual means to eliminate destructive gene expression instability pathways.
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Affiliation(s)
- Zhixin Zhou
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Daoqing Fan
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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56
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Effects of Molecular Crowding on G-Quadruplex-hemin Mediated Peroxidase Activity. Chem Res Chin Univ 2020. [DOI: 10.1007/s40242-020-0018-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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57
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58
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LIU ZL, TAO CA, WANG JF. Progress on Applications of G-quadruplex in Biochemical Analysis. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(19)61212-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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59
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Rafiee SD, Kocabey S, Mayer M, List J, Rüegg C. Detection of HER2 + Breast Cancer Cells using Bioinspired DNA-Based Signal Amplification. ChemMedChem 2020; 15:661-666. [PMID: 31943804 PMCID: PMC7187270 DOI: 10.1002/cmdc.201900697] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 12/17/2019] [Indexed: 01/25/2023]
Abstract
Circulating tumor cells (CTC) are promising biomarkers for metastatic cancer detection and monitoring progression. However, detection of CTCs remains challenging due to their low frequency and heterogeneity. Herein, we report a bioinspired approach to detect individual cancer cells, based on a signal amplification cascade using a programmable DNA hybridization chain reaction (HCR) circuit. We applied this approach to detect HER2+ cancer cells using the anti‐HER2 antibody (trastuzumab) coupled to initiator DNA eliciting a HCR cascade that leads to a fluorescent signal at the cell surface. At 4 °C, this HCR detection scheme resulted in highly efficient, specific and sensitive signal amplification of the DNA hairpins specifically on the membrane of the HER2+ cells in a background of HER2− cells and peripheral blood leukocytes, which remained almost non‐fluorescent. The results indicate that this system offers a new strategy that may be further developed toward an in vitro diagnostic platform for the sensitive and efficient detection of CTC.
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Affiliation(s)
- Sarah D Rafiee
- Department of Oncology, Microbiology and Immunology Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, PER17, 1700, Fribourg, Switzerland
| | - Samet Kocabey
- Department of Oncology, Microbiology and Immunology Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, PER17, 1700, Fribourg, Switzerland
| | - Michael Mayer
- BioPhysics, Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, PER 18, 1700, Fribourg, Switzerland
| | - Jonathan List
- BioPhysics, Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, PER 18, 1700, Fribourg, Switzerland.,Physics of Synthetic Biological Systems, Technical University Munich, Am Coulombwall 4a, 85748, Garching, Germany
| | - Curzio Rüegg
- Department of Oncology, Microbiology and Immunology Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, PER17, 1700, Fribourg, Switzerland
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60
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Sun X, Fei R, Zhang L, Huo B, Wang Y, Peng Y, Ning B, He J, Gao Z, Hu Y. Bio-barcode triggered isothermal amplification in a fluorometric competitive immunoassay for the phytotoxin abrin. Mikrochim Acta 2020; 187:127. [PMID: 31938848 DOI: 10.1007/s00604-019-3961-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 09/19/2019] [Indexed: 02/01/2023]
Abstract
Abrin is one of the most toxic phytotoxins to date, and is a potential biological warfare agent. A bio-barcode triggered isothermal amplification for fluorometric determination of abrin is described. Free abrin competes with abrin-coated magnetic microparticles (MMP) probes to bind to gold nanoparticle (AuNP) probes modified with abrin antibody and bio-barcoded DNA. Abundant barcodes are released from the MMP-AuNP complex via dithiothreitol treatment. This triggers an exponential amplification reaction (EXPAR) that is monitored by real-time fluorometry, at typical excitation/emission wavelengths of 495/520 nm. The EXPAR assay is easily operated, highly sensitive and specific. It was used to quantify abrin in spiked commercial samples. The detection limit (at S/N = 3; for n = 6) is 5.6 pg·mL-1 which is considerably lower than previous reports. This assay provides a universal sensing platform and has great potential for determination of various analytes, including small molecules, proteins, DNA, and cells. Graphical abstract Schematic representation of the bio-barcode triggered exponential amplification reaction (EXPAR) for a fluorometric competitive immunoassay for abrin. The limit of detection is 5.6 pg mL-1 with a large dynamic range from 10 pg mL-1 to 1 µg mL-1.
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Affiliation(s)
- Xuan Sun
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ruihua Fei
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lu Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bingyang Huo
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environment and Operational Medicine, Tianjin, 300050, China
| | - Yu Wang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environment and Operational Medicine, Tianjin, 300050, China
| | - Yuan Peng
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environment and Operational Medicine, Tianjin, 300050, China
| | - Baoan Ning
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environment and Operational Medicine, Tianjin, 300050, China
| | - Jing He
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhixian Gao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environment and Operational Medicine, Tianjin, 300050, China.
| | - Yonggang Hu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China.
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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61
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Li H, Jie G. A versatile dendritical amplification photoelectric biosensing platform based on Bi2S3 nanorods and a perylene-based polymer for signal “on” and “off” double detection of DNA. Analyst 2020; 145:5524-5531. [DOI: 10.1039/d0an01040e] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A novel versatile dendritical amplification photoelectric biosensing platform using Bi2S3 nanorods and a perylene-based polymer as double signal probes is proposed for the detection of trace target DNA.
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Affiliation(s)
- Hongkun 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
- PR 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
- PR China
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62
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Kumari S, Mandal S, Das P. Carbon dot mediated G quadruplex nano-network formation for enhanced DNAzyme activity and easy catalyst reclamation. RSC Adv 2019; 9:41502-41510. [PMID: 35541604 PMCID: PMC9076458 DOI: 10.1039/c9ra08290e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 12/01/2019] [Indexed: 02/01/2023] Open
Abstract
The significant application potential of the DNAzyme activity of G-quadruplex (G4)–hemin complexes has prompted considerable research efforts to amplify their peroxidase mimicking activity to match that of their enzymatic counterparts. However, concurrent improvements in the catalytic cycle and catalyst recovery remain elusive. Herein, we report the creation of a network array of G-quadruplex (G4)–hemin complexes crosslinked by carbon quantum dots (CDs) that not only significantly improves the G-quadruplex–hemin DNAzyme activity, stability, and catalytic cycle, but also points towards easy catalyst regeneration via a semi-heterogeneous catalysis approach. 5′-phosphate terminated G-rich single-stranded DNA molecules proficient in generating intermolecular and intramolecular G-quadruplexes were covalently conjugated to anthrarufin derived CDs through phosphoramidite chemistry. The network array was achieved through K+ mediated intermolecular G-quadruplex formation that readily complexes with hemin to give the catalytic core. The presence of CDs in close vicinity ensures a favorable microenvironment that helps in amplifying the DNAzyme activity in both the intermolecular CD–G-quadruplex network assembly and the intramolecular CD–G quadruplex conjugate, while the former is necessary for easy catalyst regeneration. The CD photophysics enable the monitoring of the DNAzyme recovery and reaction progress. Enhanced DNAzyme activity of G-quadruplex–hemin complex in carbon dot crosslinked nanonetwork with access to easy catalyst regeneration.![]()
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Affiliation(s)
- Sonam Kumari
- Department of Chemistry, Indian Institute of Technology Patna Bihta Patna 801103 Bihar India
| | - Saptarshi Mandal
- Department of Chemistry, Indian Institute of Technology Patna Bihta Patna 801103 Bihar India
| | - Prolay Das
- Department of Chemistry, Indian Institute of Technology Patna Bihta Patna 801103 Bihar India
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63
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Zhu L, Li G, Shao X, Huang K, Luo Y, Xu W. A colorimetric zinc(II) assay based on the use of hairpin DNAzyme recycling and a hemin/G-quadruplex lighted DNA nanoladder. Mikrochim Acta 2019; 187:26. [DOI: 10.1007/s00604-019-3996-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 11/03/2019] [Indexed: 11/28/2022]
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64
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Zhou Y, Yang L, Wei J, Ma K, Gong X, Shang J, Yu S, Wang F. An Autonomous Nonenzymatic Concatenated DNA Circuit for Amplified Imaging of Intracellular ATP. Anal Chem 2019; 91:15229-15234. [PMID: 31668059 DOI: 10.1021/acs.analchem.9b04126] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A robust ATP aptasensor has been successfully constructed for intracellular imaging via the autonomous nonenzymatic cascaded hybridization chain reaction (Ca-HCR) circuit. This compact aptasensor is easily assembled by integrating the sensing module and amplification module, and is furtherly introduced for selective adenosine triphosphate (ATP) assay and for the sensitive tracking of varied ATP expressions in living cells. The ATP-targeting aptamer-encoded sensing module can specifically recognize ATP and release the initiator strand for successively motivating the two-layered HCR (hybridization chain reaction) circuit via the FRET transduction mechanism. The synergistic reaction acceleration of the two HCRs contributes to the high signal gain (amplification efficiency of N2). The whole reaction process was modeled and simulated by MATLAB to deeply explore the underlying molecular reaction mechanism, implying that the cascade HCR is sufficient enough to guarantee the ATP-recognition and amplification processes. The Ca-HCR-amplified aptasensor shows high sensitivity and selectivity for in vitro ATP assay, and can monitor these varied ATP expressions in living cells via intracellular imaging technique. Furthermore, the present aptasensor can be easily extended for monitoring other low-abundance biomarkers, which is especially important for precisely understanding these related biological processes.
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Affiliation(s)
- Yangjie Zhou
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , P. R. China
| | - Lei Yang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , P. R. China
| | - Jie Wei
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , P. R. China
| | - Kang Ma
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , P. R. China
| | - Xue Gong
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , P. R. China
| | - Jinhua Shang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , P. R. China
| | - Shanshan Yu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , P. R. China
| | - Fuan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , P. R. China
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65
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Li H, Lin H, Wang X, Lv W, Li F. Dopamine-Based Paper Analytical Device for Truly Equipment-Free and Naked-Eye Biosensing Based on the Target-Initiated Catalyzed Oxidation. ACS APPLIED MATERIALS & INTERFACES 2019; 11:36469-36475. [PMID: 31544453 DOI: 10.1021/acsami.9b14859] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The development of low cost, portable, and disposable biosensors for equipment-free and naked-eye biosensing is in eager demand for their widespread application in biomedical field, but it is still a challenge. Herein, we propose a novel paper analytical device (PAD) for truly equipment-free and naked-eye biosensing using dopamine as the chromogenic agent based on target-initiated catalyzed oxidation reaction. The dopamine-functionalized PAD (DPAD) possesses a significant three-dimensional net structure, excellent hydrophilicity, and unique response toward G-quadruplex DNAs against other DNAs, benefiting the bio/chemo reaction occurrence to assay target biomolecules. In light of the exceptional properties, the fabricated DPAD was applied in the analysis of Dam MTase through target-triggered exponential isothermal amplification. The recognition and methylation of H1 by Dam MTase contribute to formation of abundant hemin/G-quadruplexes, which catalyze oxidation of dopamine into dopachrome and reduce the dopamine amount on the DPAD surface. In comparison with the case in which Dam MTase is absent, an evident deep pink signal originating from dopachrome is observed directly by the naked eye and relied on Dam MTase concentrations. Therefore, truly equipment-free and naked-eye detection of Dam MTase is achieved with a detection limit of 1.46 U/mL. The fabricated DPAD not only achieves Dam MTase-visualized detection but also permits the accurate determination of other analytes by varying recognizable DNA's sequences, thus offering a universal biosensor and depicting significant potential for widespread applications in biomedical field.
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Affiliation(s)
- Haiyin Li
- 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
| | - Xin Wang
- College of Chemistry and Pharmaceutical Sciences , Qingdao Agricultural University , Qingdao 266109 , People's Republic of China
| | - Wenxin Lv
- 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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66
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Li J, Lin L, Yu J, Zhai S, Liu G, Tian L. Fabrication and Biomedical Applications of “Polymer-Like” Nucleic Acids Enzymatically Produced by Rolling Circle Amplification. ACS APPLIED BIO MATERIALS 2019; 2:4106-4120. [DOI: 10.1021/acsabm.9b00622] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jing Li
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Li Lin
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Jiantao Yu
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Shiyao Zhai
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Guoyuan Liu
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Leilei Tian
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
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Zhang C, Miao P, Sun M, Yan M, Liu H. Progress in miRNA Detection Using Graphene Material-Based Biosensors. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1901867. [PMID: 31379135 DOI: 10.1002/smll.201901867] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 07/20/2019] [Indexed: 05/16/2023]
Abstract
MicroRNAs (miRNAs) are short, endogenous, noncoding RNAs that play critical roles in physiologic and pathologic processes and are vital biomarkers for several disease diagnostics and therapeutics. Therefore, rapid, low-cost, sensitive, and selective detection of miRNAs is of paramount importance and has aroused increasing attention in the field of medical research. Among the various reported miRNA sensors, devices based on graphene and its derivatives, which form functional supramolecular nanoassemblies of π-conjugated molecules, have been revealed to have great potential due to their extraordinary electrical, chemical, optical, mechanical, and structural properties. This Review critically and comprehensively summarizes the recent progress in miRNA detection based on graphene and its derivative materials, with an emphasis on i) the underlying working principles of these types of sensors, and the unique roles and advantages of graphene materials; ii) state-of-the-art protocols recently developed for high-performance miRNA sensing, including representative examples; and iii) perspectives and current challenges for graphene sensors. This Review intends to provide readers with a deep understanding of the design and future of miRNA detection devices.
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Affiliation(s)
- Congcong Zhang
- Institute for Advanced Interdisciplinary Research, Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, University of Jinan, Jinan, 250011, China
| | - Pei Miao
- Department of Chemistry, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250011, China
| | - Mingyuan Sun
- Institute for Advanced Interdisciplinary Research, Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, University of Jinan, Jinan, 250011, China
| | - Mei Yan
- Department of Chemistry, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250011, China
| | - Hong Liu
- Institute for Advanced Interdisciplinary Research, Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, University of Jinan, Jinan, 250011, China
- Center of Bio & Micro/Nano Functional Materials, State Key Laboratory of Crystal Materials, Shandong University, Jinan, 250100, China
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68
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Zhao LL, Cao T, Zhou QY, Zhang XH, Zhou YL, Yang L, Zhang XX. The Exploration of a New Stable G-Triplex DNA and Its Novel Function in Electrochemical Biosensing. Anal Chem 2019; 91:10731-10737. [DOI: 10.1021/acs.analchem.9b02161] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ling-Li Zhao
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ting Cao
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Qian-Yu Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiao-Hui Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Ying-Lin Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Lijiang Yang
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xin-Xiang Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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69
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Wu Q, Wang H, Gong K, Shang J, Liu X, Wang F. Construction of an Autonomous Nonlinear Hybridization Chain Reaction for Extracellular Vesicles-Associated MicroRNAs Discrimination. Anal Chem 2019; 91:10172-10179. [PMID: 31288510 DOI: 10.1021/acs.analchem.9b02181] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Extracellular vesicles (EVs) have emerged as promising tumor biomarkers for early cancer diagnosis, as primary tumor-secreted EVs carry characteristic molecular information on parent cells. It is thus desirable to realize the efficient discrimination of the signatured EVs-associated microRNAs (miRNAs) with low expression and subtle variation. Here, we introduce an autonomous nonlinear enzyme-free signal amplification paradigm for EVs discrimination through a highly sensitive and selective detection of their inherent miRNAs in situ. Our proposed amplifier consists of a modularized DNAzyme-amplified two-stage cascaded hybridization chain reaction (CHCR-DNAzyme) circuit, where the analyte-generated output of the preceding hybridization chain reaction (HCR1) stage serves as input to motivate the following hybridization chain reaction (HCR2) stage and the concomitant assembly of numerous DNAzyme biocatalysts. By incorporating a flexibly configurable sensing module, this modular CHCR-DNAzyme circuit can further extend to "plug-and-play" sensing mode that enables the miRNA assay with high specificity. The sophisticated design and the detecting performance of our CHCR-DNAzyme scheme were systematically investigated in vitro. The optimized CHCR-DNAzyme system was further applied for distinguishing EVs derived from different cells through the amplified detection of a putative miRNA biomarker in EVs. This compact CHCR-DNAzyme amplifier provides a universal and facile toolbox for highly efficient identification of multiple miRNAs-involved EVs and thus holds great potential for early cancer diagnosis.
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Affiliation(s)
- Qiong Wu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , 430072 , People's Republic of China
| | - Hong Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , 430072 , People's Republic of China
| | - Keke Gong
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , 430072 , People's Republic of China
| | - Jinhua Shang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , 430072 , People's Republic of China
| | - Xiaoqing Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , 430072 , People's Republic of China
| | - Fuan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , 430072 , People's Republic of China
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70
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Gong X, Li X, Qing T, Zhang P, Feng B. Amplified colorimetric detection of tetracycline based on an enzyme-linked aptamer assay with multivalent HRP-mimicking DNAzyme. Analyst 2019; 144:1948-1954. [PMID: 30694262 DOI: 10.1039/c8an02284d] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Tetracycline (TC) is widely used to treat bacterial infections in humans and animals due to its low price and good antibacterial properties. The abuse of tetracycline has led to TC residues in daily food that could seriously affect human health. Thus, it is imperative to develop highly sensitive and selective methods for TC detection. In this work, we developed a colorimetric method for TC detection based on an enzyme-linked aptamer assay (ELAA) with multivalent HRP-mimicking DNAzyme. An aptamer was used as an alternative recognition element in the enzyme-linked immunosorbent assay (ELISA). Multivalent HRP-mimicking DNAzyme, assembled via hybridization chain reactions (HCR), was used for catalytic substrate color rendering in ELAA. The multivalent HRP-mimicking DNAzyme exhibited enhanced catalytic capacity and improved the detection sensitivity greatly. The limit of detection was 8.1 × 10-2 ng mL-1 with a linear range from 1.0 × 10-2 ng mL-1 to 1.0 × 104 ng mL-1 toward TC in buffer. To challenge the practical application capability of this strategy, the detection of TC in milk samples was also investigated and showed similar linear relationships. Due to the introduction of an aptamer, this ELAA strategy shows high selectivity towards TC and has potential for the detection of a wide spectrum of analytes.
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Affiliation(s)
- Xin Gong
- College of Chemical Engineering, Xiangtan University, Xiangtan 411105, Hunan Province, China
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71
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Gyawali P, Gc K, Ma Y, Abeysirigunawardena S, Nagasawa K, Balci H. Impact of Small Molecules on Intermolecular G-Quadruplex Formation. Molecules 2019; 24:molecules24081570. [PMID: 31010019 PMCID: PMC6514588 DOI: 10.3390/molecules24081570] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 04/18/2019] [Accepted: 04/19/2019] [Indexed: 11/24/2022] Open
Abstract
We performed single molecule studies to investigate the impact of several prominent small molecules (the oxazole telomestatin derivative L2H2-6OTD, pyridostatin, and Phen-DC3) on intermolecular G-quadruplex (i-GQ) formation between two guanine-rich DNA strands that had 3-GGG repeats in one strand and 1-GGG repeat in the other (3+1 GGG), or 2-GGG repeats in each strand (2+2 GGG). Such structures are not only physiologically significant but have recently found use in various biotechnology applications, ranging from DNA-based wires to chemical sensors. Understanding the extent of stability imparted by small molecules on i-GQ structures, has implications for these applications. The small molecules resulted in different levels of enhancement in i-GQ formation, depending on the small molecule and arrangement of GGG repeats. The largest enhancement we observed was in the 3+1 GGG arrangement, where i-GQ formation increased by an order of magnitude, in the presence of L2H2-6OTD. On the other hand, the enhancement was limited to three-fold with Pyridostatin (PDS) or less for the other small molecules in the 2+2 GGG repeat case. By demonstrating detection of i-GQ formation at the single molecule level, our studies illustrate the feasibility to develop more sensitive sensors that could operate with limited quantities of materials.
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Affiliation(s)
- Prabesh Gyawali
- Department of Physics, Kent State University, Kent, OH 44242, USA.
| | - Keshav Gc
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA.
| | - Yue Ma
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan.
| | | | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan.
| | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH 44242, USA.
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72
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Park CR, Rhee WJ, Kim KW, Hwang BH. Colorimetric biosensor using dual‐amplification of enzyme‐free reaction through universal hybridization chain reaction system. Biotechnol Bioeng 2019; 116:1567-1574. [DOI: 10.1002/bit.26978] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 03/12/2019] [Accepted: 03/28/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Chae Rin Park
- Department of Bioengineering and Nano‐bioengineeringIncheon National UniversityIncheon Korea
| | - Won Jong Rhee
- Department of Bioengineering and Nano‐bioengineeringIncheon National UniversityIncheon Korea
- Division of BioengineeringIncheon National UniversityIncheon Korea
| | - Kyu Won Kim
- Department of ChemistryIncheon National UniversityIncheon Korea
| | - Byeong Hee Hwang
- Department of Bioengineering and Nano‐bioengineeringIncheon National UniversityIncheon Korea
- Division of BioengineeringIncheon National UniversityIncheon Korea
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73
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Shen R, Zou L, Wu S, Li T, Wang J, Liu J, Ling L. A novel label-free fluorescent detection of histidine based upon Cu 2+-specific DNAzyme and hybridization chain reaction. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 213:42-47. [PMID: 30682646 DOI: 10.1016/j.saa.2019.01.062] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 01/16/2019] [Accepted: 01/16/2019] [Indexed: 06/09/2023]
Abstract
A novel label-free fluorescent sensor for histidine was developed based upon Cu2+-specific DNAzyme, hybridization chain reaction(HCR) and triplex DNA. Cu2+ can bind to the histidine, in the presence of histidine, leading to the inhibition of the cleavage of substrate strand of Cu2+-dependent DNAzyme, then the intact substrate strand trigger the HCR between H1 and H2. The HCR product can be recognized by triplex-forming oligonucleotide (TFO) through triplex formation and reported by the fluorescence of berberine, the fluorescence intensity of the sensing system was proportional to the concentration of histidine during the range of 5.7-455 nmol L-1, with a detection limit of 2.0 nmol L-1.
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Affiliation(s)
- Ruidi Shen
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Li Zou
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Shixin Wu
- Maternal and Child Care Service Centre of Yunxi County, Shiyan 442600, PR China
| | - Tingting Li
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Jing Wang
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Jianmin Liu
- Department of Neurosurgery, the First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou 510405, PR China
| | - Liansheng Ling
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, PR China.
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74
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Li J, Kong C, Liu Q, Chen Z. Colorimetric ultrasensitive detection of DNA based on the intensity of gold nanoparticles with dark-field microscopy. Analyst 2019; 143:4051-4056. [PMID: 30059077 DOI: 10.1039/c8an00825f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We present an ultrasensitive colorimetric nucleic acid assay based on the intensity of gold nanoparticles (Au NPs) using dark field microscopy. In the absence of target DNA, two hairpin-like DNA strands with protruding single-stranded DNA (ssDNA) can be absorbed onto the Au NP surface via non-covalent interactions between the exposed nitrogen bases of ssDNA and Au NPs, which inhibits Au NPs from aggregating in a high concentration of salt media, while in the presence of target DNA, two hairpin DNA strands hybridize with target DNA to form double-stranded DNA (dsDNA). After hybridization chain reaction (HCR) amplification, rigid dsDNA polymers are formed, which results in serious Au NP aggregation in the salt environment. By measuring the intensity change of yellow and red dots on a dark-field image, the concentration of target DNA can be accurately quantified with a limit of detection (LOD) of 66 fM.
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Affiliation(s)
- Jingjing Li
- Department of Chemistry, Capital Normal University, Beijing, 100048, P. R. China.
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75
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Sakamoto T, Yamada R. Label‐Free in Situ Monitoring of the DNA Hybridization Chain Reaction by Using Sequence‐Selective Minor‐Groove‐Binding Fluorophores. Chembiochem 2019; 20:1242-1245. [DOI: 10.1002/cbic.201800738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Takashi Sakamoto
- Faculty of Systems EngineeringWakayama University 930 Sakaedani Wakayama 640-8510 Japan
| | - Rikuto Yamada
- Faculty of Systems EngineeringWakayama University 930 Sakaedani Wakayama 640-8510 Japan
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76
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Abstract
Multiplex detection of biomolecules is important in bionanotechnology and clinical diagnostics. Multiplexing using engineered solutions such as microarrays, synthetic nanopores, and DNA barcodes is promising, but they require sophisticated design/engineering and typically yield semiquantitative information. Single-molecule fluorescence resonance energy transfer (smFRET) is an attractive tool in this regard as it enables both sensitive and quantitative detection. However, multiplexing with smFRET remains a great challenge as it requires either multiple excitation sources, an antenna system created by multiple FRET pairs, or multiple acceptors of the donor fluorophore, which complicates not only the labeling schemes but also data analysis, due to overlapping of FRET efficiencies ( EFRET). Here, we address these currently outstanding issues by designing interconvertible hairpin-based sensors (iHabSs) with nonoverlapping EFRET utilizing a single donor/acceptor pair and demonstrate a high-confidence multiplex detection of unlabeled nucleic acid sequences. We validated the reliability of our approach by systematically omitting one target at a time. Further, we demonstrate that these iHabSs are fully recyclable, sensitive with a limit of detection of ∼200 pM, and able to discriminate against single base mismatches. The multiplexed approach developed here has the potential to benefit the fields of biosensing and diagnostics by allowing simultaneous and quantitative detection of unlabeled nucleic acid biomarkers.
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Affiliation(s)
- Anisa Kaur
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, Virginia 23284, United States
| | - Kumar Sapkota
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, Virginia 23284, United States
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, Virginia 23284, United States
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77
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Yao B, Zhu S, Xu X, Feng N, Tian Y, Zhou N. Ultrasensitive detection of the androgen receptor through the recognition of an androgen receptor response element and hybridization chain amplification. Analyst 2019; 144:2179-2185. [PMID: 30768083 DOI: 10.1039/c9an00034h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
An ultrasensitive electrochemical detection of the androgen receptor (AR) was developed based on the protection of a DNA duplex by the AR from restriction endonuclease-mediated digestion and a subsequent hybridization chain reaction (HCR). Two partially complementary DNA probes P1 and P2 were designed to form an androgen receptor binding probe (ARBP) through hybridization. The ARBP contains a duplex at one end and two single-stranded tails at the other end. The duplex part containing the recognition sites of the AR and NspI restriction endonuclease was immobilized on an Au electrode, whereas the single-stranded parts served as capture probes to activate the HCR. In the absence of the AR, NspI can cleave the duplex and release the capture probes, and thus, no HCR occurs. However, the AR can bind to the ARBP and protect the duplex from cleavage; therefore, the capture probes can trigger the HCR between four carefully designed G-quadruplex forming hairpin probes and the capture probes, resulting in the formation of numerous G-quadruplexes. Finally, differential pulse voltammetry (DPV) was carried out to quantify the AR. The assay revealed a detection limit of 7.64 fM. The verification of its high specificity and practicability in serum samples indicated its potential applications in the fields of clinical examination and disease diagnosis.
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Affiliation(s)
- Binbin Yao
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
| | - Sha Zhu
- Department of Oncology, The Affiliated Wuxi No. 2 People's Hospital of Nanjing Medical University, Wuxi 214002, China
| | - Xinyu Xu
- Department of Urology, The Affiliated Wuxi No. 2 People's Hospital of Nanjing Medical University, Wuxi 214002, China.
| | - Ninghan Feng
- Department of Urology, The Affiliated Wuxi No. 2 People's Hospital of Nanjing Medical University, Wuxi 214002, China.
| | - Yaping Tian
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
| | - Nandi Zhou
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
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78
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He H, Dai J, Dong G, Shi H, Wang F, Qiu Y, Liao R, Zhou C, Guo Y, Xiao D. Self-Replication-Assisted Rapid Preparation of DNA Nanowires at Room Temperature and Its Biosensing Application. Anal Chem 2019; 91:3043-3047. [PMID: 30667217 DOI: 10.1021/acs.analchem.8b05431] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A rapid room-temperature DNA nanowires preparation strategy on the basis of self-replicating catalyzed hairpin assembly (SRCHA) was reported. In this system, three hairpin probes (P1, P2, and P3) were well-designed and partially hybridize to each other, and two split trigger DNA sequences were integrated into P1 and P3, respectively. When the SRCHA was initiated by the trigger DNA, a series of DNA assembly steps based on the toehold-mediated DNA strand displacement were activated, and the Y shaped DNA (P1-P2-P3) was formed. In that case, the two split trigger DNA sequences will come into close-enough proximity to form the trigger DNA replicas, which can initiate the additional SRCHA reaction cycles for DNA nanowire preparation, and eventually a rapid room-temperature DNA nanowires preparation strategy without need of fuel strands was successfully developed. Furthermore, the prepared DNA nanowires have been used to develop a rapid and signal amplified sensing platform for sensitive adenosine triphosphate (ATP) detection.
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Affiliation(s)
- Hongfei He
- College of Chemistry , Sichuan University , Chengdu 610064 , China.,College of Life Sciences , Sichuan University , Chengdu 610065 , China
| | - Jianyuan Dai
- College of Chemistry , Sichuan University , Chengdu 610064 , China
| | - Guixiu Dong
- College of Chemistry , Sichuan University , Chengdu 610064 , China
| | - Hongli Shi
- College of Chemistry , Sichuan University , Chengdu 610064 , China
| | - Fang Wang
- College of Chemical Engineering , Sichuan University , Chengdu 610065 , China
| | - Yunran Qiu
- College of Chemistry , Sichuan University , Chengdu 610064 , China
| | - Ruoxing Liao
- College of Chemistry , Sichuan University , Chengdu 610064 , China
| | - Cuisong Zhou
- College of Chemistry , Sichuan University , Chengdu 610064 , China
| | - Yong Guo
- College of Chemistry , Sichuan University , Chengdu 610064 , China
| | - Dan Xiao
- College of Chemistry , Sichuan University , Chengdu 610064 , China.,College of Chemical Engineering , Sichuan University , Chengdu 610065 , China
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79
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Simmel FC, Yurke B, Singh HR. Principles and Applications of Nucleic Acid Strand Displacement Reactions. Chem Rev 2019; 119:6326-6369. [PMID: 30714375 DOI: 10.1021/acs.chemrev.8b00580] [Citation(s) in RCA: 356] [Impact Index Per Article: 71.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Dynamic DNA nanotechnology, a subfield of DNA nanotechnology, is concerned with the study and application of nucleic acid strand-displacement reactions. Strand-displacement reactions generally proceed by three-way or four-way branch migration and initially were investigated for their relevance to genetic recombination. Through the use of toeholds, which are single-stranded segments of DNA to which an invader strand can bind to initiate branch migration, the rate with which strand displacement reactions proceed can be varied by more than 6 orders of magnitude. In addition, the use of toeholds enables the construction of enzyme-free DNA reaction networks exhibiting complex dynamical behavior. A demonstration of this was provided in the year 2000, in which strand displacement reactions were employed to drive a DNA-based nanomachine (Yurke, B.; et al. Nature 2000, 406, 605-608). Since then, toehold-mediated strand displacement reactions have been used with ever increasing sophistication and the field of dynamic DNA nanotechnology has grown exponentially. Besides molecular machines, the field has produced enzyme-free catalytic systems, all DNA chemical oscillators and the most complex molecular computers yet devised. Enzyme-free catalytic systems can function as chemical amplifiers and as such have received considerable attention for sensing and detection applications in chemistry and medical diagnostics. Strand-displacement reactions have been combined with other enzymatically driven processes and have also been employed within living cells (Groves, B.; et al. Nat. Nanotechnol. 2015, 11, 287-294). Strand-displacement principles have also been applied in synthetic biology to enable artificial gene regulation and computation in bacteria. Given the enormous progress of dynamic DNA nanotechnology over the past years, the field now seems poised for practical application.
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Affiliation(s)
| | - Bernard Yurke
- Micron School of Materials Science and Engineering , Boise State University , Boise , ID 83725 , United States
| | - Hari R Singh
- Physics Department , TU München , 85748 Garching , Germany
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80
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Yang L, Wu Q, Chen Y, Liu X, Wang F, Zhou X. Amplified MicroRNA Detection and Intracellular Imaging Based on an Autonomous and Catalytic Assembly of DNAzyme. ACS Sens 2019; 4:110-117. [PMID: 30562005 DOI: 10.1021/acssensors.8b01000] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Abnormal microRNAs (miRNAs) expression is demonstrated to associate with various important biological processes, including tumorigenesis, metastasis, and progression. Given the low miRNA expression at the earlier stage of diseases, its amplified detection still requires more efforts. Inspired by the two-stage arithmetic amplifier of electric devices, we reported an autonomous and catalytic assembly of DNAzyme strategy by integrating a DNAzyme biocatalyst and catalytic hairpin assembly (CHA) circuit. Here the catalytically inactive DNAzyme subunits were respectively grafted into these metastable CHA hairpin reactants that were kinetically impeded without false cross-hybridizations. The target catalyzed the nonenzymatic CHA-mediated successive assembly of dumbbell-like bis-DNAzyme nanostructures, leading to the efficient DNAzyme-mediated cleavage of fluorophore/quencher-modified substrate and to the generation of an amplified fluorescence signal. The present CHA-DNAzyme amplifier can be employed as a versatile and general sensing platform for analyzing other analytes (e.g., miRNA) by introducing a sensing module into the present system. Moreover, the homogeneous CHA-DNAzyme method could realize the sensitive intracellular miRNA imaging in living cells, which is attributed to the inherently synergistic amplification property between DNAzyme and CHA reactions. Given the attractive analytical features of the autonomous CHA-DNAzyme system, the present strategy shows great promise for analyzing additional different analytes in clinical research fields.
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Affiliation(s)
- Lei Yang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Qiong Wu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yuqi Chen
- Key Laboratory of Biomedical Polymers (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Xiaoqing Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Fuan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Xiang Zhou
- Key Laboratory of Biomedical Polymers (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
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81
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Chronocoulometric aptamer based assay for staphylococcal enterotoxin B by target-triggered assembly of nanostructured dendritic nucleic acids on a gold electrode. Mikrochim Acta 2019; 186:109. [PMID: 30637509 DOI: 10.1007/s00604-019-3236-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 01/05/2019] [Indexed: 01/01/2023]
Abstract
A rapid and ultrasensitive method is described for the detection of staphylococcal enterotoxin B (SEB). It is based on the formation of a dendritic DNA superstructure by integrating (a) target-induced triggering of DNA release with (b) signal amplification by a hybridization chain reaction. Partially complementary pairing of aptamer and trigger DNA forms a duplex structure. The capture DNA is then placed on the surface of a gold electrode through gold-thiol chemistry. In the presence of SEB, the aptamer-target conjugate is compelled to form. This causes the release of trigger DNA owing to a strong competition with SEB. The trigger DNA is subsequently hybridized with the partial complementary sequences of the capture DNA to trigger HCR with three auxiliary DNA sequances (referred to as H1, H2, H3). Finally, the dendritic DNA superstructure is bound to hexaammineruthenium(III) cation by electrostatic adsorption and assembled onto the modified gold electrode. This produces an amplified electrochemical signal that is measured by chronocoulometry. Under optimal conditions, the charge difference increases linearly with the logarithm of the SEB concentrations in the range from 5 pg·mL-1 to 100 ng·mL-1 with a detection limit as low as 3 pg·mL-1 (at S/N = 3). Graphical abstract An electrochemical switching strategy is presented for the sensitive detection of Staphylococcus enterotoxin B based on target-triggered assembly of dendritic nucleic acid nanostructures.
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Abstract
DNA has played an early and powerful role in the development of bottom-up nanotechnologies, not least because of DNA's precise, predictable, and controllable properties of assembly on the nanometer scale. Watson-Crick complementarity has been used to build complex 2D and 3D architectures and design a number of nanometer-scale systems for molecular computing, transport, motors, and biosensing applications. Most of such devices are built with classical B-DNA helices and involve classical A-T/U and G-C base pairs. However, in addition to the above components underlying the iconic double helix, a number of alternative pairing schemes of nucleobases are known. This review focuses on two of these noncanonical classes of DNA helices: G-quadruplexes and the i-motif. The unique properties of these two classes of DNA helix have been utilized toward some remarkable constructions and applications: G-wires; nanostructures such as DNA origami; reconfigurable structures and nanodevices; the formation and utilization of hemin-utilizing DNAzymes, capable of generating varied outputs from biosensing nanostructures; composite nanostructures made up of DNA as well as inorganic materials; and the construction of nanocarriers that show promise for the therapeutics of diseases.
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Affiliation(s)
- Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering , Nanjing University , Nanjing 210023 , China.,ARNA Laboratory , Université de Bordeaux, Inserm U 1212, CNRS UMR5320, IECB , Pessac 33600 , France.,Institute of Biophysics of the CAS , v.v.i., Královopolská 135 , 612 65 Brno , Czech Republic
| | - Dipankar Sen
- Department of Molecular Biology & Biochemistry , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada.,Department of Chemistry , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada
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83
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Zhao XH, Zhang LZ, Zhao SY, Cui XH, Gong L, Zhao R, Yu BF, Xie J. Silver-ion-mediated Mg2+-dependent DNAzyme activity for amplified fluorescence detection of cysteine. Analyst 2019; 144:1982-1987. [DOI: 10.1039/c8an02308e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Schematic illustration of a DNAzyme-based fluorescent biosensor for amplified Cys detection.
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Affiliation(s)
- Xu-Hua Zhao
- Department of Biochemistry and Molecular Biology
- Shanxi Medical University
- Taiyuan 030001
- P. R. China
| | - Li-Zhuan Zhang
- Department of Biochemistry and Molecular Biology
- Shanxi Medical University
- Taiyuan 030001
- P. R. China
| | - Su-Ya Zhao
- Department of Biochemistry and Molecular Biology
- Shanxi Medical University
- Taiyuan 030001
- P. R. China
| | - Xiao-Hua Cui
- Department of Biochemistry and Molecular Biology
- Shanxi Medical University
- Taiyuan 030001
- P. R. China
| | - Liang Gong
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices
- College of Life Sciences and Chemistry
- Hunan University of Technology
- Zhuzhou 412007
- China
| | - Rong Zhao
- Department of Biochemistry and Molecular Biology
- Shanxi Medical University
- Taiyuan 030001
- P. R. China
| | - Bao-Feng Yu
- Department of Biochemistry and Molecular Biology
- Shanxi Medical University
- Taiyuan 030001
- P. R. China
| | - Jun Xie
- Department of Biochemistry and Molecular Biology
- Shanxi Medical University
- Taiyuan 030001
- P. R. China
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84
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Zhang J, Li X, Sun X, Liu Y, Hao J, Tan Y, Song A. G-Quadruplex based hydrogels stabilized by a cationic polymer as an efficient adsorbent of picric acid. NEW J CHEM 2019. [DOI: 10.1039/c9nj03143j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Hydrogels based on G-quadruplexes (G-hydrogels) were prepared using guanosine 5′-monophosphate disodium salt, GMP, with a hyperbranched poly(ethylenimine), PEI, containing abundant –NH2 groups.
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Affiliation(s)
- Jin Zhang
- Key Laboratory of Colloids and Interface Chemistry (Shandong University)
- Ministry of Education
- Jinan 250100
- China
| | - Xiaoyang Li
- Key Laboratory of Colloids and Interface Chemistry (Shandong University)
- Ministry of Education
- Jinan 250100
- China
| | - Xiuping Sun
- Key Laboratory of Colloids and Interface Chemistry (Shandong University)
- Ministry of Education
- Jinan 250100
- China
| | - Yihan Liu
- Key Laboratory of Colloids and Interface Chemistry (Shandong University)
- Ministry of Education
- Jinan 250100
- China
| | - Jingcheng Hao
- Key Laboratory of Colloids and Interface Chemistry (Shandong University)
- Ministry of Education
- Jinan 250100
- China
| | - Yebang Tan
- Key Laboratory of Colloids and Interface Chemistry (Shandong University)
- Ministry of Education
- Jinan 250100
- China
| | - Aixin Song
- Key Laboratory of Colloids and Interface Chemistry (Shandong University)
- Ministry of Education
- Jinan 250100
- China
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85
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Dutta S, Dutta Chowdhury A, Biswas S, Park EY, Agnihotri N, De A, De S. Development of an effective electrochemical platform for highly sensitive DNA detection using MoS2 - polyaniline nanocomposites. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.09.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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86
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Li C, Wang H, Shang J, Liu X, Yuan B, Wang F. Highly Sensitive Assay of Methyltransferase Activity Based on an Autonomous Concatenated DNA Circuit. ACS Sens 2018; 3:2359-2366. [PMID: 30350594 DOI: 10.1021/acssensors.8b00738] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Methyltransferase-involved DNA methylation is one of the most important epigenetic processes, making the ultrasensitive MTase assay highly desirable in clinical diagnosis as well as biomedical research. Traditional single-stage amplification means often achieve linear amplification that might not fulfill the increasing demands for detecting trace amount of target. It is desirable to construct multistage cascaded amplifiers that allow for enhanced signal amplifications. Herein, a powerful nonenzymatic MTase-sensing platform is successfully engineered based on a two-layered DNA circuit, in which the upstream catalytic hairpin assembly (CHA) circuit successively generates DNA product that could be used to activate the downstream hybridization chain reaction (HCR) circuit, resulting in the generation of a dramatically amplified fluorescence signal. In the absence of M.SssI MTase, HpaII endonuclease could specifically recognize the auxiliary hairpin substrate and then catalytically cleave the corresponding recognition site, releasing a DNA fragment that triggers the CHA-HCR-mediated FRET transduction. Yet the M.SssI-methylated hairpin substrate could not be cleaved by HpaII enzyme, and thus prohibits the CHA-HCR-mediated FRET generation, providing a substantial signal difference with that of MTase-absent system. Taking advantage of the high specificity of multiple-guaranteed recognitions of MTase/endonuclease and the synergistic amplification features of concatenated CHA-HCR circuit, this method enables an ultrasensitive detection of MTase and its inhibitors in serum and E. coli cells. Furthermore, the rationally assembled CHA-HCR also allows for probing other different biotransformations through a facile design of the corresponding substrates. It is anticipated that the infinite layer of multilayered DNA circuit could further improve the signal gain of the system for accurately detecting other important biomarkers, and thus holds great promise for cancerous treatment and biomedical research.
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Affiliation(s)
- Chunxiao Li
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Huimin Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Jinhua Shang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Xiaoqing Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Bifeng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Fuan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
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87
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Song J, Xu C, Huang S, Lei W, Ruan Y, Lu H, Zhao W, Xu J, Chen H. Ultrasmall Nanopipette: Toward Continuous Monitoring of Redox Metabolism at Subcellular Level. Angew Chem Int Ed Engl 2018; 57:13226-13230. [DOI: 10.1002/anie.201808537] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Juan Song
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Cong‐Hui Xu
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Shi‐Zhen Huang
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Wen Lei
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Yi‐Fan Ruan
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Hai‐Jie Lu
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Wei Zhao
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Jing‐Juan Xu
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Hong‐Yuan Chen
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
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88
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Wen G, Dong W, Liu B, Li Z, Fan L. A novel nonenzymatic cascade amplification for ultrasensitive photoelectrochemical DNA sensing based on target driven to initiate cyclic assembly of hairpins. Biosens Bioelectron 2018; 117:91-96. [DOI: 10.1016/j.bios.2018.05.054] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/26/2018] [Accepted: 05/28/2018] [Indexed: 12/25/2022]
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89
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Qu X, Bian F, Guo Q, Ge Q, Sun Q, Huang X. Ligation-Rolling Circle Amplification on Quantum Dot-Encoded Microbeads for Detection of Multiplex G-Quadruplex-Forming Sequences. Anal Chem 2018; 90:12051-12058. [DOI: 10.1021/acs.analchem.8b02820] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Xiaojun Qu
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Feika Bian
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qingsheng Guo
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qingjiang Sun
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Xuebin Huang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
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90
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Wu Q, Liao S, Yu G, Wu J, Mei W. High-order self-assembly of G-quadruplex DNA: Nano-network formation under the guidance of arene ruthenium(II) complexes. J Inorg Biochem 2018; 189:81-90. [PMID: 30243121 DOI: 10.1016/j.jinorgbio.2018.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 09/12/2018] [Accepted: 09/15/2018] [Indexed: 10/28/2022]
Affiliation(s)
- Qiong Wu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China; Guangdong Province Engineering Technology Center for Molecular Probe and Biomedical Imaging, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Siyan Liao
- School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou 510180, China
| | - Gengnan Yu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China; Guangdong Province Engineering Technology Center for Molecular Probe and Biomedical Imaging, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Jian Wu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China; Guangdong Province Engineering Technology Center for Molecular Probe and Biomedical Imaging, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Wenjie Mei
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China; Guangdong Province Engineering Technology Center for Molecular Probe and Biomedical Imaging, Guangdong Pharmaceutical University, Guangzhou 510006, China.
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91
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Park CR, Park SJ, Lee WG, Hwang BH. Biosensors Using Hybridization Chain Reaction - Design and Signal Amplification Strategies of Hybridization Chain Reaction. BIOTECHNOL BIOPROC E 2018. [DOI: 10.1007/s12257-018-0182-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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92
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Li Y, Yang P, Lei N, Ma Y, Ji Y, Zhu C, Wu Y. Assembly of DNA-Templated Bioluminescent Modules for Amplified Detection of Protein Biomarkers. Anal Chem 2018; 90:11495-11502. [DOI: 10.1021/acs.analchem.8b02734] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
| | | | | | | | - Yaoting Ji
- Key Lab for Oral Biomedical Engineering of Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, 430079, P. R. China
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93
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Song J, Xu C, Huang S, Lei W, Ruan Y, Lu H, Zhao W, Xu J, Chen H. Ultrasmall Nanopipette: Toward Continuous Monitoring of Redox Metabolism at Subcellular Level. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201808537] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Juan Song
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Cong‐Hui Xu
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Shi‐Zhen Huang
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Wen Lei
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Yi‐Fan Ruan
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Hai‐Jie Lu
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Wei Zhao
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Jing‐Juan Xu
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
| | - Hong‐Yuan Chen
- State Key Laboratory of Analytical Chemistry for, Life Science and Collaborative Innovation Center of, Chemistry for Life SciencesSchool of Chemistry and Chemical EngineeringNanjing University Nanjing 210023 China
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94
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Sui Z, Wu W, Komiyama M, Liang X. Highly Sensitive and Selective Detection of Food Toxin Using Three Functional DNA Hairpins. CHEM LETT 2018. [DOI: 10.1246/cl.180357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Zhe Sui
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Wei Wu
- Institute for Translational Medicine, Qingdao University, Qingdao 266021, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
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95
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Wang K, Feng M, He MQ, Zhai FH, Dai Y, He RH, Yu YL. DNA-fueled target recycling-induced two-leg DNA walker for amplified electrochemical detection of nucleic acid. Talanta 2018; 188:685-690. [PMID: 30029432 DOI: 10.1016/j.talanta.2018.06.049] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/11/2018] [Accepted: 06/13/2018] [Indexed: 12/13/2022]
Abstract
Taking advantage of the homogeneous and heterogeneous electrochemical biosensors, a simple, sensitive, and selective electrochemical biosensor is constructed by combining entropy-driven amplification (EDA) with DNA walker. This electrochemical biosensor realizes the biorecognition and EDA operation in homogeneous solution, which is beneficial to improve the recognition and amplification efficiency. A two-leg DNA walker generated by EDA can walk on the surface of gold electrode for cleaving the immobilized substrate DNA and releasing the electroactive labels, giving rise to a significant decrease of the electrochemical signal. The immobilization of the electroactive labels ensures the reproducibility and reliability of the biosensor. The present cascade amplification assay can be applied to detect target DNA with a detection limit of 0.29 fM, and base mutations can be easily distinguished. Moreover, the proposed electrochemical biosensor shows a satisfactory performance for the detection of target DNA in human serum. Thus, the novel electrochemical biosensor holds promising potential for a future application in disease diagnosis.
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Affiliation(s)
- Kun Wang
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Min Feng
- The first Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Meng-Qi He
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Fu-Heng Zhai
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Yu Dai
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Rong-Huan He
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China.
| | - Yong-Liang Yu
- Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China.
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96
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Wang H, Li C, Liu X, Zhou X, Wang F. Construction of an enzyme-free concatenated DNA circuit for signal amplification and intracellular imaging. Chem Sci 2018; 9:5842-5849. [PMID: 30079197 PMCID: PMC6050587 DOI: 10.1039/c8sc01981a] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 06/05/2018] [Indexed: 12/22/2022] Open
Abstract
A rationally and modularly engineered two-layered CHA–HCR circuit was constructed for amplified biosensing and bioimaging with high performance.
Nucleic acid circuits have shown promising potential for amplified detection of biomarkers with interest in biologically important engineering applications. In this work, by properly integrating two signal amplification approaches, catalytic hairpin assembly (CHA) and hybridization chain reaction (HCR), a concatenated CHA–HCR system was established as an isothermal enzyme-free amplification strategy for highly sensitive and selective nucleic acid assay. The target catalyzes the self-assembly of CHA hairpin substrates into dsDNA products, where the split segments of HCR trigger are successively connected to drive the subsequent autonomous cross-opening of HCR hairpins, leading to the construction of HCR tandem copolymeric dsDNA nanowires. The resulting HCR copolymer brings a fluorophore donor/acceptor pair into close proximity that allows an efficient generation of FRET readout signal. Moreover, the optimized CHA–HCR circuit, upon the incorporation of an auxiliary sensing module, can be converted into a universal sensing platform for detecting cancerous biomarkers (e.g., a well-known oncogene miR-21) through a convenient easy-to-integrate procedure. The concatenated CHA–HCR amplifier enables accurate intracellular miRNA imaging in living cells, which is especially suitable for in situ amplified detection of lowly expressed endogenous analytes. The inherent synergistically accelerated recognition and hybridization features of CHA–HCR circuit contribute to the amplified detection of endogenous RNAs in living cells. The flexible and programmable nature of the homogeneous CHA–HCR system provides a versatile and robust toolbox for a wide range of research fields, such as in vivo bioimaging, clinical diagnosis and environmental monitoring.
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Affiliation(s)
- Huimin Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
| | - Chunxiao Li
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
| | - Xiaoqing Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
| | - Xiang Zhou
- Key Laboratory of Biomedical Polymers-Ministry of Education , College of Chemistry and Molecular Sciences , Wuhan University , 430072 Wuhan , China
| | - Fuan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , P. R. China .
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97
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Ultrasensitive Faraday cage-type electrochemiluminescence assay for femtomolar miRNA-141 via graphene oxide and hybridization chain reaction-assisted cascade amplification. Biosens Bioelectron 2018. [DOI: 10.1016/j.bios.2018.02.062] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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98
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Zhou Z, Luo G, Wulf V, Willner I. Application of DNA Machineries for the Barcode Patterned Detection of Genes or Proteins. Anal Chem 2018; 90:6468-6476. [PMID: 29737162 DOI: 10.1021/acs.analchem.7b04916] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The study introduces an analytical platform for the detection of genes or aptamer-ligand complexes by nucleic acid barcode patterns generated by DNA machineries. The DNA machineries consist of nucleic acid scaffolds that include specific recognition sites for the different genes or aptamer-ligand analytes. The binding of the analytes to the scaffolds initiate, in the presence of the nucleotide mixture, a cyclic polymerization/nicking machinery that yields displaced strands of variable lengths. The electrophoretic separation of the resulting strands provides barcode patterns for the specific detection of the different analytes. Mixtures of DNA machineries that yield, upon sensing of different genes (or aptamer ligands), one-, two-, or three-band barcode patterns are described. The combination of nucleic acid scaffolds acting, in the presence of polymerase/nicking enzyme and nucleotide mixture, as DNA machineries, that generate multiband barcode patterns provide an analytical platform for the detection of an individual gene out of many possible genes. The diversity of genes (or other analytes) that can be analyzed by the DNA machineries and the barcode patterned imaging is given by the Pascal's triangle. As a proof-of-concept, the detection of one of six genes, that is, TP53, Werner syndrome, Tay-Sachs normal gene, BRCA1, Tay-Sachs mutant gene, and cystic fibrosis disorder gene by six two-band barcode patterns is demonstrated. The advantages and limitations of the detection of analytes by polymerase/nicking DNA machineries that yield barcode patterns as imaging readout signals are discussed.
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Affiliation(s)
- Zhixin Zhou
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Guofeng Luo
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Verena Wulf
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Itamar Willner
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
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Guo X, Wang J, Zhu Z, Zhang M, Li H, Liu J, Ling L. A colorimetric method for the sequence-specific recognition of double-stranded DNA on the surface of a silver-coated glass slide. CAN J CHEM 2018. [DOI: 10.1139/cjc-2017-0544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study, a colorimetric method for sequence-specific recognition of double-stranded DNA (dsDNA) was established on the surface of a silver-coated glass slide. Oligo-1 was assembled on the surface of a silver-coated glass slide through an Ag–S bond, and Oligo-2 as reporter was used to bind with streptavidin-horseradish peroxidase (SA–HRP). They could bind with target dsDNA that was composed of Oligo-3 and Oligo-4 on the surface of a silver-coated glass slide through triplex formation. The bound HRP could be moved into the solution by DNase I and catalyze the oxidation of 3,3′,5,5′-tetramethylbenzidine (TMB). Therefore, the concentration of target dsDNA could be determined with the colour change of TMB. Under the optimum conditions, the absorbance was proportional to the concentration of target dsDNA over the range of 100 pmol/L to 2.0 nmol/L, with a detection limit of 13 pmol/L. In addition, this method showed good sequence selectivity, enabling it to be further developed for the detection of other polymerase chain reaction (PCR) products.
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Affiliation(s)
- Xiaoting Guo
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Jing Wang
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Zhifang Zhu
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Manjun Zhang
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Haigang Li
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Jianmin Liu
- Department of Neurosurgery, the First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou 510405, P. R. China
| | - Liansheng Ling
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, P. R. China
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100
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Wang Y, Shan D, Wu G, Wang H, Ru F, Zhang X, Li L, Qian Y, Lu X. A novel “dual-potential” ratiometric electrochemiluminescence DNA sensor based on enhancing and quenching effect by G-quadruplex / hemin and Au-Luminol bifunctional nanoparticles. Biosens Bioelectron 2018; 106:64-70. [DOI: 10.1016/j.bios.2018.01.052] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/22/2018] [Accepted: 01/23/2018] [Indexed: 11/26/2022]
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