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Pang YH, Wang YY, Sun MM, Shen XF. Visual detection of CaMV35S promoter via target-triggered rolling circle amplification of DNAzyme. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2021.104304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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2
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Amidinium sulfonate hydrogen-bonded organic framework with fluorescence amplification function for sensitive aniline detection. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.01.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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3
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Mao J, Chen X, Xu H, Xu X. DNAzyme-driven DNA walker biosensor for amplified electrochemical detection of T4 polynucleotide kinase activity and inhibition. J Electroanal Chem (Lausanne) 2020. [DOI: 10.1016/j.jelechem.2020.114470] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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4
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Jin T, Zhang J, Zhao Y, Huang X, Tan C, Sun S, Tan Y. Magnetic bead-gold nanoparticle hybrids probe based on optically countable gold nanoparticles with dark-field microscope for T4 polynucleotide kinase activity assay. Biosens Bioelectron 2020; 150:111936. [DOI: 10.1016/j.bios.2019.111936] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 11/12/2019] [Accepted: 11/27/2019] [Indexed: 12/12/2022]
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5
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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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6
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Zhang Y, Wang L, Dong Y. A Label-free and Universal Platform for the Construction of Various Logic Circuits Based on Graphene Oxide and G-Quadruplex Structure. ANAL SCI 2019; 35:181-187. [PMID: 30745511 DOI: 10.2116/analsci.18p349] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Due to structual polymorphism, excellent binding activity and functional significances in biological regulation, G-quadruplex has become the focus of research as an innovated module for analytical chemistry and biomedicine. Meanwhile, in the biosensor fields, new nanomaterial graphene oxide (GO) has also received extensive attention due to its brilliant physical and chemical properties. Herein, we propose a non-label and enzyme-free logic operation platform based on G-quadruplex structure and GO instead of any expensive modification. Taking advantage of the quenching ability of GO to AgNCs and the fluorescence enhancement of NMM (N-methylmesoporphyrin IX) mediated by the split G-quadruplex, a series of binary logic gates (AND, OR, INHIBIT, XOR) have been constructed and verified by biological experiments. Subsequently, two combinatorial logic gates were successfully realized conceptually on the basis of the same BGG platform, including half adder and half subtractor. Taken together, such a universal platform has great potential in applications, such as biocomputing, bio-imaging and disease diagnosis, which cultivate a new view for future biological research.
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Affiliation(s)
| | - Luhui Wang
- College of Life Sciences, Shaanxi Normal University
| | - Yafei Dong
- College of Life Sciences, Shaanxi Normal University.,Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest of China
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Li J, Ma J, Zhang Y, Zhang Z, He G. A fluorometric method for determination of the activity of T4 polynucleotide kinase by using a DNA-templated silver nanocluster probe. Mikrochim Acta 2019; 186:48. [DOI: 10.1007/s00604-018-3157-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 12/07/2018] [Indexed: 12/31/2022]
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8
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Kumar S, Jain S, Dilbaghi N, Ahluwalia AS, Hassan AA, Kim KH. Advanced Selection Methodologies for DNAzymes in Sensing and Healthcare Applications. Trends Biochem Sci 2018; 44:190-213. [PMID: 30559045 DOI: 10.1016/j.tibs.2018.11.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/01/2018] [Accepted: 11/01/2018] [Indexed: 02/07/2023]
Abstract
DNAzymes have been widely explored owing to their excellent catalytic activity in a broad range of applications, notably in sensing and biomedical devices. These newly discovered applications have built high hopes for designing novel catalytic DNAzymes. However, the selection of efficient DNAzymes is a challenging process but one that is of crucial importance. Initially, systemic evolution of ligands by exponential enrichment (SELEX) was a labor-intensive and time-consuming process, but recent advances have accelerated the automated generation of DNAzyme molecules. This review summarizes recent advances in SELEX that improve the affinity and specificity of DNAzymes. The thriving generation of new DNAzymes is expected to open the door to several healthcare applications. Therefore, a significant portion of this review is dedicated to various biological applications of DNAzymes, such as sensing, therapeutics, and nanodevices. In addition, discussion is further extended to the barriers encountered for the real-life application of these DNAzymes to provide a foundation for future research.
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Affiliation(s)
- Sandeep Kumar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-Haryana, 125001, India; Department of Civil Engineering, College of Engineering, University of Nebraska at Lincoln, PO Box 886105, Lincoln, NE 68588-6105, USA.
| | - Shikha Jain
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-Haryana, 125001, India
| | - Neeraj Dilbaghi
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-Haryana, 125001, India
| | | | - Ashraf Aly Hassan
- Department of Civil Engineering, College of Engineering, University of Nebraska at Lincoln, PO Box 886105, Lincoln, NE 68588-6105, USA
| | - Ki-Hyun Kim
- Department of Civil and Environmental Engineering, Hanyang University, 222 Wangsimni-Ro, Seoul 04763, Republic of Korea.
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Wang S, Sun J, Zhao J, Lu S, Yang X. Photo-Induced Electron Transfer-Based Versatile Platform with G-Quadruplex/Hemin Complex as Quencher for Construction of DNA Logic Circuits. Anal Chem 2018; 90:3437-3442. [PMID: 29425022 DOI: 10.1021/acs.analchem.7b05145] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
G-quadruplex has been developed as an innovator for analytical chemistry and biomedicine due to its vibrant binding activity, structural polymorphism, and critical roles in biological regulation. Herein, a simple but versatile platform was obtained by integrating split G-quadruplex and fluorophore into a molecular beacon, where the photoinduced electron transfer could occur when the fluorophore approached the preformed G-quadruplex/hemin complexes. Such design subtly combined the G4 disruption-induced fluorescent turn-on strategy and the photoinduced electron transfer property into one platform for constructing the logic circuits. On the basis of such a universal platform, a series of binary logic gates (OR, INHIBIT, AND, and XOR), a combinatorial gate (INHIBIT-OR), and even a complex logic operation for discrimination of multiples of three from natural numbers less than ten have been successfully achieved only by employing such platform as work unit and single-strand DNAs as inputs. The set-reset function of this platform could be realized by alternatively introducing blocking and releasing strands. In addition, this platform could operate in a biological matrix stably and precisely. Therefore, such a universal platform lays the foundation for complicating the logic systems, realizing the biocomputing and also points out a new direction for target detection.
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Affiliation(s)
- Shuang Wang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Changchun , Jilin 130022 , China.,University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Jian Sun
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Changchun , Jilin 130022 , China
| | - Jiahui Zhao
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Changchun , Jilin 130022 , China.,University of Chinese Academy of Sciences , Beijing 100039 , China
| | - Shasha Lu
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Changchun , Jilin 130022 , China.,University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Xiurong Yang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Changchun , Jilin 130022 , China
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QIN SY, CHEN ND, WANG Q, HUANG J, HE XX, LIU JB, GUO QP, YANG XH, WANG KM. Application of Nucleic Acid Aptamers in Polypeptides Researches. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2017. [DOI: 10.1016/s1872-2040(17)61055-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Gao M, Guo J, Song Y, Zhu Z, Yang CJ. Detection of T4 Polynucleotide Kinase via Allosteric Aptamer Probe Platform. ACS APPLIED MATERIALS & INTERFACES 2017; 9:38356-38363. [PMID: 29027787 DOI: 10.1021/acsami.7b14185] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
As a vital enzyme in DNA phosphorylation and restoration, T4 polynucleotide kinase (T4 PNK) has aroused great interest in recent years. Therefore, numerous strategies have been established for highly sensitive detection of T4 PNK based on diverse signal amplification techniques. However, they often need sophisticated design, a variety of auxiliary reagents and enzymes, or cumbersome manipulations. We have designed a new kind of allosteric aptamer probe (AAP) consisting of streptavidin (SA) aptamer and the complementary DNA (cDNA) for simple detection of T4 PNK without signal amplification and with minimized interference in complex biological samples. When the 5'-terminus of the cDNA is phosphorylated by T4 PNK, the cDNA is degraded by lambda exonuclease to release the fluorescein amidite (FAM)-labeled SA aptamer, which subsequently binds to streptavidin beads. The enhancement of the fluorescence signal on SA beads can be detected precisely and easily by a microscope or flow cytometer. Our method performs well in complex biological samples as a result of the enrichment of the signaling molecules on beads, as well as simple manipulations to discard the background interference and nonbinding molecules. Without signal amplification techniques, our AAP method not only avoids complicated manipulations but also decreases the time required. With the advantages of ease of operation, reliability, and robustness for T4 PNK detection in buffer as well as real biological samples, the AAP has great potential for clinical diagnostics, inhibitor screening, and drug discovery.
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Affiliation(s)
- Mingxuan Gao
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Collaborative Innovation Centre of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, China
| | - Jingjing Guo
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Collaborative Innovation Centre of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, China
| | - Yanling Song
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Collaborative Innovation Centre of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, China
- The Key Lab of Analysis and Detection Technology for Food Safety of MOE, State Key Laboratory of Photocatalysis on Energy and Environment, College of Biological Science and Engineering, Fuzhou University , Fuzhou 350116, China
| | - Zhi Zhu
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Collaborative Innovation Centre of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, China
| | - Chaoyong James Yang
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Collaborative Innovation Centre of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Chronic Liver Disease and Hepatocellular Carcinoma of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, China
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A Dual-signal Amplification Method for DNA Detection Based on Exonuclease III and Fluorescence Quenching Ability of MoS 2 Nanosheet. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2017. [DOI: 10.1016/s1872-2040(17)60997-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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13
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ZHANG YY, CHENG H, SUN Y, WANG JE, WU ZY, PEI RJ. Engineering of Thiamine Pyrophosphate Fluorescent Biosensors Based on Ribozyme Switches in Mammalian Cells. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2017. [DOI: 10.1016/s1872-2040(16)60992-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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14
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Guo Y, Chen Q, Qi Y, Xie Y, Qian H, Yao W, Pei R. Label-free ratiometric DNA detection using two kinds of interaction-responsive emission dyes. Biosens Bioelectron 2017; 87:320-324. [DOI: 10.1016/j.bios.2016.08.041] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 08/03/2016] [Accepted: 08/13/2016] [Indexed: 11/17/2022]
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15
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Xu L, Hong S, Shen X, Zhou L, Wang J, Zhang J, Pei R. DNA Triplexes-Guided Assembly of G-Quadruplexes for Constructing Label-free Fluorescent Logic Gates. Chem Asian J 2016; 11:1892-5. [DOI: 10.1002/asia.201600626] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Indexed: 12/11/2022]
Affiliation(s)
- Lijun Xu
- Key Laboratory of Nano-Bio Interface; Division of Nanobiomedicine; Suzhou Institute of Nano-Tech and Nano-Bionics; Chinese Academy of Sciences; Suzhou 215123 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Shanni Hong
- Key Laboratory of Nano-Bio Interface; Division of Nanobiomedicine; Suzhou Institute of Nano-Tech and Nano-Bionics; Chinese Academy of Sciences; Suzhou 215123 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Xiaoqiang Shen
- Key Laboratory of Nano-Bio Interface; Division of Nanobiomedicine; Suzhou Institute of Nano-Tech and Nano-Bionics; Chinese Academy of Sciences; Suzhou 215123 China
- School of Chemistry and Molecular Engineering; Zhengzhou University; Zhengzhou 450001 China
| | - Lu Zhou
- Key Laboratory of Nano-Bio Interface; Division of Nanobiomedicine; Suzhou Institute of Nano-Tech and Nano-Bionics; Chinese Academy of Sciences; Suzhou 215123 China
| | - Jine Wang
- Key Laboratory of Nano-Bio Interface; Division of Nanobiomedicine; Suzhou Institute of Nano-Tech and Nano-Bionics; Chinese Academy of Sciences; Suzhou 215123 China
| | - Jianye Zhang
- School of Chemistry and Molecular Engineering; Zhengzhou University; Zhengzhou 450001 China
| | - Renjun Pei
- 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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16
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Guo Y, Xu L, Hong S, Sun Q, Yao W, Pei R. Label-free DNA-based biosensors using structure-selective light-up dyes. Analyst 2016; 141:6481-6489. [DOI: 10.1039/c6an01958g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Label-free biosensors (LFBs) have demonstrated great potential in cost-effective applications. This review collected the latest reported works which employed structure-selective nucleic acid dyes for the development of DNA-based LFBs.
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Affiliation(s)
- Yahui Guo
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
| | - Lijun Xu
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
| | - Shanni Hong
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
| | - Qingqing Sun
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
| | - Weirong Yao
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
| | - Renjun Pei
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
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