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Wang FP, Guan Y, Liu JW, Cheng H, Hu R. A functional nucleic acid-based fluorescence sensing platform based on DNA supersandwich nanowires and cation exchange reaction. Analyst 2023; 148:5033-5040. [PMID: 37667620 DOI: 10.1039/d3an01122d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Accurate and sensitive analysis of p53 DNA is important for early diagnosis of cancer. In this work, a fluorescence sensing system based on DNA supersandwich nanowires and cation exchange (CX)-triggered multiplex signal amplification was constructed for the detection of p53 DNA. In the presence of p53 DNA, the DNA self-assembles to form a DNA supersandwich nanowire that generates long double-stranded DNA. Subsequently, the cation exchange (CX) reaction between ZnS and Ag+ was utilized to release free Zn2+. With the participation of Zn2+, DNAzyme catalyzes the hydrolysis of numerous catalytic molecular beacons, resulting in a greatly enhanced fluorescence signal due to the cycling of DNAzyme. The fluorescence values increased in proportion to the concentrations of p53 DNA in the range of 10 pM to 200 nM, and a detection limit (LOD) of 2.34 pM (S/N = 3) was obtained. This method provides an effective strategy for the quantitative detection of p53 DNA.
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Affiliation(s)
- Fu-Peng Wang
- College of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming, 650500, P. R. China.
| | - Yan Guan
- College of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming, 650500, P. R. China.
| | - Jia-Wen Liu
- College of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming, 650500, P. R. China.
| | - Huan Cheng
- College of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming, 650500, P. R. China.
| | - Rong Hu
- College of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming, 650500, P. R. China.
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2
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Cheraghi S, Shalali F, Taher MA. Kojic acid exploring as an essential food additive in real sample by a nanostructure sensor amplified with ionic liquid. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2022. [DOI: 10.1007/s11694-022-01738-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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3
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4
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Pan J, Bao D, Bao E, Chen J. A hairpin probe-mediated DNA circuit for the detection of the mecA gene of Staphylococcus aureus based on exonuclease III and DNAzyme-mediated signal amplification. Analyst 2021; 146:3673-3678. [PMID: 33954316 DOI: 10.1039/d1an00028d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A simple, highly sensitive biosensor for S. aureus detection is becoming increasingly important in human health and safety. In this work, a hairpin probe-mediated DNA circuit for the detection of the mecA gene of S. aureus was reported cascading Exo III-assisted cycling signal amplification and the DNAzyme-mediated cleavage reaction. In the presence of the target mecA gene, the recognition and hybridization between HP1 and mecA can trigger Exo III and DNAzyme-mediated signal amplification and further release numerous ATMND, resulting in an enhanced fluorescence response, which serves as a response signal for the fluorescence detection of mecA gene. This biosensor enables the sensitive and specific detection of the mecA gene, showing a linear response ranging from 1 fM to 1 nM with a detection limit of 0.5 fM. Moreover, this fluorescence assay has been applied for the analysis of clinical samples with satisfactory recovery. Importantly, this universal platform can be further extended for the analysis of other targets by alternating the corresponding recognition unit, which holds much promise in point-of-care testing for bacterial analysis.
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Affiliation(s)
- Jiafeng Pan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China and National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.
| | - Dongqin Bao
- Shuyang Hospital Affiliated to Xuzhou Medical University, Suqian 223800, China
| | - Enhu Bao
- Shuyang Hospital Affiliated to Xuzhou Medical University, Suqian 223800, China
| | - Junhua Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.
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5
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Jiang K, Wu Y, Chen J, Shi M, Meng HM, Li Z. Molecular recognition triggered aptazyme cascade for ultrasensitive detection of exosomes in clinical serum samples. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2020.11.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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6
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Liu LS, Wang F, Ge Y, Lo PK. Recent Developments in Aptasensors for Diagnostic Applications. ACS APPLIED MATERIALS & INTERFACES 2021; 13:9329-9358. [PMID: 33155468 DOI: 10.1021/acsami.0c14788] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Aptamers are exciting smart molecular probes for specific recognition of disease biomarkers. A number of strategies have been developed to convert target-aptamer binding into physically detectable signals. Since the aptamer sequence was first discovered, a large variety of aptamer-based biosensors have been developed, with considerable attention paid to their potential applications in clinical diagnostics. So far, a variety of techniques in combination with a wide range of functional nanomaterials have been used for the design of aptasensors to further improve the sensitivity and detection limit of target determination. In this paper, the advantages of aptamers over traditional antibodies as the molecular recognition components in biosensors for high-throughput screening target molecules are highlighted. Aptamer-target pairing configurations are predominantly single- or dual-site binding; the design of recognition modes of each aptamer-target pairing configuration is described. Furthermore, signal transduction strategies including optical, electrical, mechanical, and mass-sensitive modes are clearly explained together with examples. Finally, we summarize the recent progress in the development of aptamer-based biosensors for clinical diagnosis, including detection of cancer and disease biomarkers and in vivo molecular imaging. We then conclude with a discussion on the advanced development and challenges of aptasensors.
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Affiliation(s)
- Ling Sum Liu
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Fei Wang
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Yonghe Ge
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Pik Kwan Lo
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China
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7
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Yadav DK, Ganesan V, Gupta R, Yadav M, Rastogi PK. Sensitive determination of kojic acid in tomato sauces using Ni–Fe layered double hydroxide synthesized through Fe-MIL-88 metal-organic framework templated route. J CHEM SCI 2020. [DOI: 10.1007/s12039-020-01777-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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8
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Khoshbin Z, Housaindokht MR, Izadyar M, Bozorgmehr MR, Verdian A. Temperature and molecular crowding effects on the sensitivity of T30695 aptamer toward Pb2+ion: a joint molecular dynamics simulation and experimental study. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1751842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Zahra Khoshbin
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Mohammad Izadyar
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Asma Verdian
- Department of Food Safety and Quality Control, Research Institute of Food Science and Technology (RIFST), Mashhad, Iran
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9
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Economical Approach for Determination of Kojic Acid by Nanostructured Ionic Liquid-Based Carbon Paste Sensor. BIONANOSCIENCE 2020. [DOI: 10.1007/s12668-020-00723-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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10
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Kong RM, Ma L, Han X, Ma C, Qu F, Xia L. Hg 2+-mediated stabilization of G-triplex based molecular beacon for label-free fluorescence detection of Hg 2+, reduced glutathione, and glutathione reductase activity. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 228:117855. [PMID: 31784222 DOI: 10.1016/j.saa.2019.117855] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 11/21/2019] [Accepted: 11/23/2019] [Indexed: 06/10/2023]
Abstract
G-triplexes have been reported recently with the similar function to G-quadruplex that can combine with thioflavin T (ThT) and emit strong fluorescence but easier to be controlled and excited. In this work, we report an Hg2+-mediated stabilization of G-triplex based functional molecular beacon (G3TMB) sensing system for the label-free detection of Hg2+, reduced glutathione (GSH), and glutathione reductase (GR) activity. In the presence of Hg2+, the extended G-triplex sequence containing the "T" bases can form a stable hairpin structure due to the strong interactions of "T-Hg2+-T", resulting in the locking of G-tracts in the stem of the G3TMB effectively. However, the hairpin structure of the G3TMB can be opened by the introduction of GSH through the stronger "GSH-Hg2+" interaction. Therefore, by employing the fact that GR can catalyze the reduction of oxidized glutathione (GSSG) into GSH, this concept can be applied to fluorescence "off-on" detection of GR activity, with a linear range of 0.02-30 mU/mL and detection limit of 0.01 mU/mL. This work may expand a new perspective of G-triplex based functional molecular beacon as the label-free fluorescent probes in the detection of small biomolecule and enzyme activity.
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Affiliation(s)
- Rong-Mei Kong
- College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong 273165, PR China.
| | - Lin Ma
- College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong 273165, PR China
| | - Xue Han
- College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong 273165, PR China
| | - Chunran Ma
- College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong 273165, PR China
| | - Fengli Qu
- College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong 273165, PR China
| | - Lian Xia
- College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong 273165, PR China
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11
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Deng S, Zhou B, Li W, Li H, Zhang F, Ming J. Label-free fluorescence DNA walker for protein analysis based on terminal protection and dual enzyme assisted cleavage induced G-quadruplex/berberine conformation. Analyst 2020; 145:46-51. [DOI: 10.1039/c9an01853k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Development of a simple, fast, cost-efficient and sensitive approach for accurate protein analysis is of high significance due to its potential application in disease diagnosis and biomedicine research.
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Affiliation(s)
- Shue Deng
- College of Pharmacy
- Weifang Medical University
- Weifang 261053
- China
| | - Baolong Zhou
- College of Pharmacy
- Weifang Medical University
- Weifang 261053
- China
| | - Wenjing Li
- College of Pharmacy
- Weifang Medical University
- Weifang 261053
- China
| | - Hui Li
- College of Pharmacy
- Weifang Medical University
- Weifang 261053
- China
| | - Fenglian Zhang
- College of Pharmacy
- Weifang Medical University
- Weifang 261053
- China
| | - Jingjing Ming
- College of Pharmacy
- Weifang Medical University
- Weifang 261053
- China
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12
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Mao X, Li Q, Zuo X, Fan C. Catalytic Nucleic Acids for Bioanalysis. ACS APPLIED BIO MATERIALS 2019; 3:2674-2685. [PMID: 35025402 DOI: 10.1021/acsabm.9b00928] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Xiuhai Mao
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Chunhai Fan
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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13
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Du S, Li Y, Chai Z, Shi W, He J. Functionalization of 8-17 DNAzymes modulates catalytic efficiency and divalent metal ion preference. Bioorg Chem 2019; 94:103401. [PMID: 31711763 DOI: 10.1016/j.bioorg.2019.103401] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/17/2019] [Accepted: 10/24/2019] [Indexed: 11/26/2022]
Abstract
8-17 and 17E DNAzyme are being explored as biosensors for metal ions and RNA motifs of interest, more sensitive and efficient DNAzymes are required to meet the practical applications. Their similarity in the catalytic cores and differences in catalytic efficiency and metal ion dependence initiated great interest about the contribution of the catalytic residues. Functionalization of four adenine residues in the catalytic cores of 8-17 DNAzyme and 17E was conducted with amino, guanidinium, and imidazolyl groups. In the bulge loops of 8-17 and 17E, N6-(3-aminopropyl)-2'-deoxyadenosine (residue 1) at A15 led to new DNAzymes 8-17DZ-A15-1 and 17E-A15-1, with much more efficient cleavage ability in the Ca2+-mediated reaction and the greater preference for Ca2+ over Mg2+ than 8-17 DNAzyme and 17E, respectively, especially with a concentration-dependent increase of the selectivity, which is different from most DNAzymes with the similar dependence on both Mg2+ and Ca2+. With this kind of post-selection modification on 8-17 DNAzymes, for the first time, the catalytic efficiency and metal ion selectivity could be positively modulated. It is also helpful for the catalyic mechanistic studies of these DNAzymes, especially, the role of the unconserved A15 should be emphasized.
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Affiliation(s)
- Shanshan Du
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Yang Li
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Zhilong Chai
- School of Pharmaceutical Sciences, Guizhou University, Guizhou 550025, China
| | - Weiguo Shi
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China.
| | - Junlin He
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China.
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14
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Khoshbin Z, Housaindokht MR, Izadyar M, Bozorgmehr MR, Verdian A. The investigation of the G-quadruplex aptamer selectivity to Pb 2+ ion: a joint molecular dynamics simulation and density functional theory study. J Biomol Struct Dyn 2019; 38:3659-3675. [PMID: 31496379 DOI: 10.1080/07391102.2019.1664933] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The aptamers with the ability to form a G-quadruplex structure can be stable in the presence of some ions. Hence, study of the interactions between such aptamers and ions can be beneficial to determine the highest selective aptamer toward an ion. In this article, molecular dynamics (MD) simulations and quantum mechanics (QM) calculations have been applied to investigate the selectivity of the T30695 aptamer toward Pb2+ in comparison with some ions. The Free Energy Landscape (FEL) analysis indicates that Pb2+ has remained inside the aptamer during the MD simulation, while the other ions have left it. The Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) binding energies prove that the conformational stability of the aptamer is the highest in the presence of Pb2+. According to the compaction parameters, the greatest compressed ion-aptamer complex, and hence, the highest ion-aptamer interaction have been induced in the presence of Pb2+. The contact maps clarify the closer contacts between the nucleotides of the aptamer in the presence of Pb2+. The density functional theory (DFT) results show that Pb2+ forms the most stable complex with the aptamer, which is consistent with the MD results. The QM calculations reveal that the N-H bonds and the O…H distances are the longest and the shortest, respectively, in the presence of Pb2+. The obtained results verify that the strongest hydrogen bonds (HBs), and hence, the most compressed aptamer structure are induced by Pb2+. Besides, atoms in molecules (AIM) and natural bond orbital (NBO) analyses confirm the results.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zahra Khoshbin
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Mohammad Izadyar
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Asma Verdian
- Department of Food Safety and Quality Control, Research Institute of Food Science and Technology (RIFST), Mashhad, Iran
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15
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Yang Y, Zhong S, Wang K, Huang J. Gold nanoparticle based fluorescent oligonucleotide probes for imaging and therapy in living systems. Analyst 2019; 144:1052-1072. [DOI: 10.1039/c8an02070a] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Gold nanoparticles (AuNPs) with unique physical and chemical properties have become an integral part of research in nanoscience.
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Affiliation(s)
- Yanjing Yang
- College of Chemistry and Chemical Engineering
- Central South University
- Changsha
- PR China
- State Key Laboratory of Chemo/Biosensing and Chemometrics
| | - Shian Zhong
- College of Chemistry and Chemical Engineering
- Central South University
- Changsha
- PR China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
- Changsha 410082
| | - Jin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
- Changsha 410082
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Yang K, Wang H, Ma N, Zeng M, Luo H, He D. Programmable Target-Initiated DNAzyme Walker Walking along a Spatially Isolated and Highly Hybridizable Substrate Track on a Nanoparticle Surface. ACS APPLIED MATERIALS & INTERFACES 2018; 10:44546-44553. [PMID: 30489066 DOI: 10.1021/acsami.8b16408] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Synthetic DNA machines that operate on the nanoscale three-dimensional (3D) track have attracted rapidly increasing interest because of their potential in biocomputing, drug delivery, and biosensing applications. Current nanoscale 3D DNA tracks are typically created by self-assembling thiolated oligonucleotides at gold nanoparticle (AuNP) surfaces via the strong Au-S chemistry. However, it remains challenging to accurately control the conformation and orientation of the 3D DNA track on AuNP surfaces and finely adjust the hybridization ability of the 3D track. Herein, we describe for the first time a polyadenine (polyA)-based, spatially isolated 3D DNA track, on which a target-initiated DNAzyme walker moves by a burnt-bridge mechanism with improved efficiency and processivity. PolyA serves as an anchoring block for preferential binding with the AuNP surface, and the appended substrate block adopts an upright conformation that favors the hybridization and subsequent DNAzyme-mediated cleavage. The operation of this target-initiated DNAzyme walker was monitored in real time and at a single-particle level. We tested the cleavage efficiency of 3D substrates with various polyA block lengths, which displayed that the DNAzyme activity was remarkably improved as compared with a thiol-based 3D track. We also explored bioanalytical applications of this DNAzyme nanomachine by movement-triggered cascade signal amplification.
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Affiliation(s)
- Ke Yang
- Hunan Key Laboratory Cultivation Base of the Research and Development of Novel Pharmaceutical Preparations, Department of Human Anatomy, Histology and Embryology , Changsha Medical University , Changsha 410219 , China
| | - Huizhen Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , China
| | - Ning Ma
- Hunan Key Laboratory Cultivation Base of the Research and Development of Novel Pharmaceutical Preparations, Department of Human Anatomy, Histology and Embryology , Changsha Medical University , Changsha 410219 , China
| | - Ming Zeng
- Hunan Key Laboratory Cultivation Base of the Research and Development of Novel Pharmaceutical Preparations, Department of Human Anatomy, Histology and Embryology , Changsha Medical University , Changsha 410219 , China
| | - Huaiqing Luo
- Hunan Key Laboratory Cultivation Base of the Research and Development of Novel Pharmaceutical Preparations, Department of Human Anatomy, Histology and Embryology , Changsha Medical University , Changsha 410219 , China
| | - Dinggeng He
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences , Hunan Normal University , Changsha 410081 , China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , China
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China
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17
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Target-switched triplex nanotweezer and synergic fluorophore translocation for highly selective melamine assay. Mikrochim Acta 2018; 186:42. [PMID: 30569196 DOI: 10.1007/s00604-018-3134-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/29/2018] [Indexed: 10/27/2022]
Abstract
This paper describes a triplex DNA nanotweezer to specifically capture melamine (MEL). The triplex-forming oligonucleotide (TFO) arm can be switched from the open state to the closed state once MEL binds to the abasic site (AP site) in duplex via the bifacial hydrogen bonding with thymines. Following this nanotweezer operation, the AP site-bound fluorophore is translocated to the terminal triplet to subsequently light up the nanotweezer. The TFO arm is found to be pivotal for permitting the AP site binding. The synergic processes of target competition and fluorophore translocation support a high selectivity for the MEL assay even against the inherent adenosine and the MEL hydrolysis products. Chelerythrine is employed as the fluorescent probe. The detection limit of MEL was estimated to be about 140 nM assuming a signal-to-noise ratio of 3. It was applied to the determination of MEL in spiked milk samples without any separation procedure. Conceivably, this method opens a new avenue towards highly selective triplex-based sensors by making use of other commercially available DNA modifications for recognizing other analytes. Graphical abstract Schematic presentation of a triplex nanotweezer with an open-to-close conversion upon the abasic site binding of melamine. The assay is based on a synergic fluorophore translocation. The corresponding duplex otherwise shows no binding with melamine. Chelerythrine (CHE) with a yellow-green emission peaking at 544 nm is employed as the fluorescent probe.
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18
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Quesada-González D, Jairo GA, Blake RC, Blake DA, Merkoçi A. Uranium (VI) detection in groundwater using a gold nanoparticle/paper-based lateral flow device. Sci Rep 2018; 8:16157. [PMID: 30385866 PMCID: PMC6212437 DOI: 10.1038/s41598-018-34610-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 10/16/2018] [Indexed: 12/12/2022] Open
Abstract
The contamination in groundwater due to the presence of uranium is nowadays a subject of concern due to the severe health problems associated with renal failure, genotoxicity and cancer. The standard methods to detect uranium require time-consuming processes and expensive non-portable equipment, so these measurements are rarely performed in-field, which increases the time until water samples are analysed. Furthermore, the few portable methods available do not allow quantitative analysis and the detection limit is often not low enough to reach the recommendations for drinking water (30 ppb or 126 nM of uranium). For the first time, we propose a portable, fast, inexpensive and sensitive paper-based biosensor able to detect in situ U(VI) in water samples: U(VI) selective gold nanoparticle-based lateral flow strips. Antibody-coated gold nanoparticles are used as labels in the proposed lateral flow system because of their biocompatibility; in addition, these nanoparticles provide high sensitivity due to their intense plasmonic effect. The antibody used in the assay recognizes soluble U(VI) complexed to the chelator, 2,9-dicarboxyl-1,10-phenanthroline (DCP). Because of the small size of the U(VI)-DCP complex, this assay employs a competitive format that reaches a limit of detection of 36.38 nM, lower than the action level (126 nM) established by the World Health Organization and the U.S. Environmental Protection Agency for drinking waters.
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Affiliation(s)
- Daniel Quesada-González
- Nanobioelectronics & Biosensors Group, Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193, Barcelona, Spain
| | - Grace A Jairo
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, Louisiana, 70112, United States
| | - Robert C Blake
- Division of Basic Pharmaceutical Sciences, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana, 70125, United States
| | - Diane A Blake
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, Louisiana, 70112, United States
| | - Arben Merkoçi
- Nanobioelectronics & Biosensors Group, Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193, Barcelona, Spain. .,ICREA, Institució Catalana de Recerca i Estudis Avançats, Pg. Lluís Companys 23, 08010, Barcelona, Spain.
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19
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A "Turn-On" Fluorescence Copper Biosensor Based on DNA Cleavage-Dependent Graphene Oxide-dsDNA-CdTe Quantum Dots Complex. SENSORS 2018; 18:s18082605. [PMID: 30096861 PMCID: PMC6111893 DOI: 10.3390/s18082605] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 07/27/2018] [Accepted: 08/03/2018] [Indexed: 11/29/2022]
Abstract
A novel “turn-on” fluorescent copper biosensor is developed successfully based on the graphene oxide (GO)-dsDNA-CdTe quantum dots (QDs) complex via chemical crosslink method. The optical and structure properties of GO-dsDNA-CdTe QDs complex are studied by fluorescence (FL) spectra and transmission electron microscopy (TEM) in detail. It is demonstrated that the fluorescence quenching of CdTe QDs is a process of fluorescence resonance energy transfer (FRET) due to the essential surface and quenching properties of two-dimensional GO. Copper ions induce the catalytic reaction of DNA chain and irreversibly break at the cleavage site, which will cause the G-quadruplex formation, moreover further result in the CdTe QDs separated from GO and restored its fluorescence. Therefore, a significant recovery effect on the fluorescence of the GO-dsDNA-CdTe QDs complex is observed in the presence of copper ions. The fluorescence responses are concentration-dependent and can be well described by a linear equation. Compared with other metal ions, the sensor performs good selectivity for copper ions.
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20
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Zhu L, Liu Q, Yang B, Ju H, Lei J. Pixel Counting of Fluorescence Spots Triggered by DNA Walkers for Ultrasensitive Quantification of Nucleic Acid. Anal Chem 2018; 90:6357-6361. [DOI: 10.1021/acs.analchem.8b01146] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Longyi Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Qihui Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Bangyu Yang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Jianping Lei
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
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21
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Zhang L, Yuan Y, Zhang Y, Liu Z, Xiao W, Nie J, Li J. Equipment-Free Quantitative Aptamer-Based Colorimetric Assay Based on Target-Mediated Viscosity Change. ACS OMEGA 2018; 3:1451-1457. [PMID: 30023804 PMCID: PMC6044812 DOI: 10.1021/acsomega.7b01814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 01/24/2018] [Indexed: 06/08/2023]
Abstract
In this paper, we describe an aptamer-based colorimetric assay (ABCA), which integrates enzyme-loaded microparticles for signal amplification with distance measurement for equipment-free quantitative readout. The distance measurement readout is on the basis of target-induced selective reduction in viscosity of reaction solution. Its utility is well demonstrated with inexpensive, sensitive, and selective detection of adenosine (model analyte) in buffer samples and real samples of human serum and urine with the naked eye. This ABCA method just requires operators to simply count the number of colored distance-relevant marked bars on the calibrated glass microsyringes (testing containers) to provide quantitative results. It thus holds great promise for wide applications particularly in limited-resource settings.
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22
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Rossetti M, Porchetta A. Allosterically regulated DNA-based switches: From design to bioanalytical applications. Anal Chim Acta 2018; 1012:30-41. [PMID: 29475471 DOI: 10.1016/j.aca.2017.12.046] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 12/10/2017] [Accepted: 12/28/2017] [Indexed: 02/07/2023]
Abstract
DNA-based switches are structure-switching biomolecules widely employed in different bioanalytical applications. Of particular interest are DNA-based switches whose activity is regulated through the use of allostery. Allostery is a naturally occurring mechanism in which ligand binding induces the modulation and fine control of a connected biomolecule function as a consequence of changes in concentration of the effector. Through this general mechanism, many different allosteric DNA-based switches able to respond in a highly controlled way at the presence of a specific molecular effector have been engineered. Here, we discuss how to design allosterically regulated DNA-based switches and their applications in the field of molecular sensing, diagnostic and drug release.
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Affiliation(s)
- Marianna Rossetti
- Chemistry Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Alessandro Porchetta
- Chemistry Department, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy.
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23
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Li X, Yang J, Xie J, Jiang B, Yuan R, Xiang Y. Cascaded signal amplification via target-triggered formation of aptazyme for sensitive electrochemical detection of ATP. Biosens Bioelectron 2017; 102:296-300. [PMID: 29156404 DOI: 10.1016/j.bios.2017.11.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 10/08/2017] [Accepted: 11/01/2017] [Indexed: 11/29/2022]
Abstract
The construction of reliable sensors for adenosine triphosphate (ATP) detection gains increasing interest because of its important roles in various enzymatic activities and biological processes. Based on a cascaded, significant signal amplification approach by the integration of the aptazymes and catalytic hairpin assembly (CHA), we have developed a sensitive electrochemical sensor for the detection of ATP. The target ATP leads to the conformational change of the aptazyme sequences and their association with the hairpin substrates to form active aptazymes, in which the hairpin substrates are cyclically cleaved by the metal ion cofactors in buffer to release the enzymatic sequences that can also bind the hairpin substrates to generate active DNAzymes. The catalytic cleavage of the hairpin substrates in the aptazymes/DNAzymes thus results in the generation of a large number of intermediate sequences. Subsequently, these intermediate sequences trigger catalytic capture of many methylene blue-tagged signal sequences on the electrode surface through CHA, producing significantly amplified current response for sensitive detection of ATP at 0.6nM. Besides, the developed sensor can discriminate ATP from analogous interference molecules and be applied to human serum samples, making the sensor a useful addition to the arena for sensitive detection of small molecules.
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Affiliation(s)
- Xia Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Jianmei Yang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Jiaqing Xie
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, PR China
| | - Bingying Jiang
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, PR China.
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yun Xiang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
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24
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Cui L, Lu M, Li Y, Tang B, Zhang CY. A reusable ratiometric electrochemical biosensor on the basis of the binding of methylene blue to DNA with alternating AT base sequence for sensitive detection of adenosine. Biosens Bioelectron 2017; 102:87-93. [PMID: 29127900 DOI: 10.1016/j.bios.2017.11.025] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/02/2017] [Accepted: 11/05/2017] [Indexed: 12/13/2022]
Abstract
We develop a reusable ratiometric electrochemical biosensor on the basis of the binding of methylene blue (MB) to DNA with alternating AT base sequence for sensitive detection of adenosine. We design a strand 1 with MB-modified thymine (T) base in the proximal 3' termini as the capture probe for its immobilization on the gold electrode and a 3' termini ferrocene (Fc)-modified aptamer for the recognition of adenosine. The hybridization of strand 1 with the aptamer leads to the formation of a double-stranded DNA (dsDNA) and consequently the away of MB from the electrode surface and the close of Fc to the electrode surface, generating a small value of IMB/IFc (IMB and IFc are the peak currents of MB and Fc, respectively). In the presence of adenosine, its binding with the aptamer induces the release of Fc from the electrode surface and the close of MB to the electrode surface, generating a large value of IMB/IFc. As a result, adenosine may be accurately quantified by the measurement of ratiometric signal (IMB/IFc). This ratiometric electrochemical biosensor can be simply fabricated and exhibits high sensitivity with a limit of detection of as low as 90.8pM and a large dynamic range from 0.1nM to 100μM. Moreover, this biosensor demonstrates good performance with excellent selectivity, regeneration capability, high reliability and good reproducibility, and may become a universal platform for the detection of various biomolecules which can be recognized by aptamers, holding great potential for further applications in biomedical research and clinical diagnosis.
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Affiliation(s)
- Lin Cui
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, PR China
| | - Mengfei Lu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, PR China
| | - Ying Li
- School of Medicine, Health Science Center,Shenzhen University, Shenzhen 518060, PR China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, PR China.
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, PR China.
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25
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Smith AL, Kolpashchikov DM. Divide and Control: Comparison of Split and Switch Hybridization Sensors. ChemistrySelect 2017; 2:5427-5431. [PMID: 29372178 PMCID: PMC5777618 DOI: 10.1002/slct.201701179] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Hybridization probes have been intensively used for nucleic acid analysis in medicine, forensics and fundamental research. Instantaneous hybridization probes (IHPs) enable signalling immediately after binding to a targeted DNA or RNA sequences without the need to isolate the probe-target complex (e. g. by gel electrophoresis). The two most common strategies for IHP design are conformational switches and split approach. A conformational switch changes its conformation and produces signal upon hybridization to a target. Split approach uses two (or more) strands that independently or semi independently bind the target and produce an output signal only if all components associate. Here, we compared the performance of split vs switch designs for deoxyribozyme (Dz) hybridization probes under optimal conditions for each of them. The split design was represented by binary Dz (BiDz) probes; while catalytic molecular beacon (CMB) probes represented the switch design. It was found that BiDz were significantly more selective than CMBs in recognition of single base substitution. CMBs produced high background signal when operated at 55°C. An important advantage of BiDz over CMB is more straightforward design and simplicity of assay optimization.
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Affiliation(s)
- Alexandra L Smith
- Chemistry Department, University of Central Florida, 4000 N. Central Florida Ave, Orlando, FL 32826
| | - Dmitry M Kolpashchikov
- Chemistry Department, Burnett School of Biomedical Sciences, National Center for Forensic Science, University of Central Florida, 4000 N. Central Florida Ave, Orlando, FL 32826
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26
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Xu X, Wei H, Jiang W. A target triggered proximity combination-based fluorescence sensing strategy for adenosine detection. Analyst 2017; 142:2247-2252. [PMID: 28536711 DOI: 10.1039/c7an00654c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Adenosine is a potent physiological and pharmacological regulator, and its abnormal level is closely related to disease development. The sensitive and specific detection of adenosine is crucial for health evaluation and disease diagnosis. In this work, a target triggered proximity combination-based fluorescence sensing strategy is developed for the sensitive and specific detection of adenosine. A difunctional probe showing target recognition and signal amplification is designed, by integration of DNA linker-connected split aptamer fragments with a fragment-elongated polymerase/nicking template. The presence of adenosine would glue the split aptamers, which triggers the two distal aptamer fragments to combine with each other into proximity. The approaching aptamer fragment ends then initiate the strand displacement amplification (SDA) reaction, generating numerous DNA primers. The DNA primers further hybridize with a padlock probe and initiate the rolling circle amplification (RCA) reaction, producing numerous G-quadruplex sequences. The G-quadruplex sequences finally bind with Thioflavin T to obtain enhanced fluorescence signals. The method exhibits a linear correlation within the adenosine concentration range from 5.0 × 10-7 M to 2.0 × 10-5 M (R = 0.999) with a detection limit of 8.4 × 10-8 M, and a good selectivity to distinguish adenosine from its analogues. The recoveries of adenosine in human serum are from 91% to 94%, demonstrating that the system works well in biological fluids. The proposed sensing strategy is anticipated to hold promise in biochemical research, clinical diagnosis and disease treatment.
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Affiliation(s)
- Xiaowen Xu
- Key Laboratory for Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, 250100 Jinan, P.R. China.
| | - Haiping Wei
- Key Laboratory for Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, 250100 Jinan, P.R. China.
| | - Wei Jiang
- Key Laboratory for Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, 250100 Jinan, P.R. China.
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27
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Using the Rubik's Cube to directly produce paper analytical devices for quantitative point-of-care aptamer-based assays. Biosens Bioelectron 2017; 96:194-200. [PMID: 28499195 DOI: 10.1016/j.bios.2017.05.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 04/15/2017] [Accepted: 05/05/2017] [Indexed: 12/25/2022]
Abstract
In this article, we describe a facile method named as Rubik's Cube stamping (RCS) for equipment-free fabrication of microfluidic paper-based analytical devices (μPADs). RCS is inspired by the worldwide ubiquitous RC toy and requires no specialized electric equipment other than a classical six-faced RC that is assembled with home-made small iron components. It can pattern various rosin microstructures in paper simply by either using different functional faces of the modified RC or applying its internal pivot mechanism to adjust the components' patterning forms on one functional face. Such a versatile stamping method is quite simple and inexpensive, and thus holds potential for producing rosin-patterned μPADs by untrained users in resource-limited environments such as small laboratories and private clinics, or even at home and in the field. Moreover, a set of one-channel devices are fabricated to design a point-of-care aptamer-based assay with near sample-in-answer-out capability that integrates enzymatic reactions for robust yet efficient signal amplification and a personal glucometer for portable, user-friendly, rapid and quantitative readout. Its utility is well demonstrated with the sensitive and specific detection of adenosine as a model target in buffer samples and undiluted human urine within several minutes. With the advantages of low cost, simplicity, portability, rapidity, and aptamer variety, this general point-of-care assay system reported here may find broad applications including home healthcare, field-based environmental monitoring or food analysis and emergency situations.
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28
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Chen X, Chen S, Hu T, Ma Q. Fluorescent aptasensor for adenosine based on the use of quaternary CuInZnS quantum dots and gold nanoparticles. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2128-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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29
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Hu Y, Lin F, Wu T, Zhou Y, Li Q, Shao Y, Xu Z. DNA Duplex Engineering for Enantioselective Fluorescent Sensor. Anal Chem 2017; 89:2181-2185. [DOI: 10.1021/acs.analchem.6b04709] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Yuehua Hu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Fan Lin
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Tao Wu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Yufeng Zhou
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Qiusha Li
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Yong Shao
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Zhiai Xu
- School
of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
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30
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Cox AJ, Bengtson HN, Gerasimova YV, Rohde KH, Kolpashchikov DM. DNA Antenna Tile-Associated Deoxyribozyme Sensor with Improved Sensitivity. Chembiochem 2016; 17:2038-2041. [PMID: 27620365 DOI: 10.1002/cbic.201600438] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Indexed: 12/17/2022]
Abstract
Some natural enzymes increase the rate of diffusion-limited reactions by facilitating substrate flow to their active sites. Inspired by this natural phenomenon, we developed a strategy for efficient substrate delivery to a deoxyribozyme (DZ) catalytic sensor. This resulted in a three- to fourfold increase in sensitivity and up to a ninefold improvement in the detection limit. The reported strategy can be used to enhance catalytic efficiency of diffusion-limited enzymes and to improve sensitivity of enzyme-based biosensors.
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Affiliation(s)
- Amanda J Cox
- Chemistry Department, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL, 32816-2366, USA.,Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd., Orlando, FL, 32827, USA
| | - Hillary N Bengtson
- Chemistry Department, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL, 32816-2366, USA.,Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd., Orlando, FL, 32827, USA
| | - Yulia V Gerasimova
- Chemistry Department, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL, 32816-2366, USA
| | - Kyle H Rohde
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd., Orlando, FL, 32827, USA
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL, 32816-2366, USA. .,Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd., Orlando, FL, 32827, USA. .,National Center for Forensic Science, University of Central Florida, 12354 Research Pkwy. Suite 225, Orlando, FL, 32826, USA.
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31
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Zhang W, Feng Q, Chang D, Tram K, Li Y. In vitro selection of RNA-cleaving DNAzymes for bacterial detection. Methods 2016; 106:66-75. [DOI: 10.1016/j.ymeth.2016.03.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/22/2016] [Accepted: 03/23/2016] [Indexed: 12/23/2022] Open
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32
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Binding induced colocalization activated hybridization chain reaction on the surface of magnetic nanobead for sensitive detection of adenosine. Biosens Bioelectron 2016; 86:966-970. [PMID: 27498322 DOI: 10.1016/j.bios.2016.07.108] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 07/26/2016] [Accepted: 07/29/2016] [Indexed: 11/22/2022]
Abstract
Herein, a sensitive and enzyme-free assay for adenosine detection has been developed on the basis of binding induced colocalization activated hybridization chain reaction (HCR) strategy on the surface of magnetic nanobead. First, the recognition probe was fabricated and divided into two parts: the Apt-1 that composed a part of adenosine aptamer and toehold domain, and the Apt-2 that consisted of another part of adenosine aptamer and branch migration domain. The Apt-1 was immobilized on a streptavidin-magnetic nanobead (streptavidin-MNBs) that played the roles of enrichment and separation. Then the recognition event of adenosine could bring the two parts of aptamer together and induce the colocalization of toehold domain and branch migration domain, which could serve as an integrated initiator to trigger the HCR, producing a long nicked double-stranded polymer. Finally, the intercalating dye SYBR Green I was inserted into the polymer, generating an enhanced fluorescence signal. In this strategy, the initiator was divided into two parts and could be suppressed effectively in the absence of adenosine. Utilizing the separated function, the spontaneous hybridization of H1 and H2 could be avoided, and a low background could be acquired. Moreover, through the double amplification of HCR and multimolecules binding of SYBR Green I, highly sensitive and enzyme-free detection were achieved. The detection limit for adenosine detection was 2.0×10(-7)mol/L, which was comparable or superior to the previous aptasensors. Importantly, adenosine analysis in human urines has been performed, and this strategy could significantly distinguish the adenosine content in normal human urines and cancer patient urines, suggesting that this proposed assay will become a reliable and sensitive adenosine detection method in early clinical diagnosis and medical research.
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Song L, Zhang Y, Li J, Gao Q, Qi H, Zhang C. Non-Covalent Fluorescent Labeling of Hairpin DNA Probe Coupled with Hybridization Chain Reaction for Sensitive DNA Detection. APPLIED SPECTROSCOPY 2016; 70:688-694. [PMID: 26879193 DOI: 10.1177/0003702816631305] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 08/17/2015] [Indexed: 06/05/2023]
Abstract
An enzyme-free signal amplification-based assay for DNA detection was developed using fluorescent hairpin DNA probes coupled with hybridization chain reaction (HCR). The hairpin DNAs were designed to contain abasic sites in the stem moiety. Non-covalent labeling of the hairpin DNAs was achieved when a fluorescent ligand was bound to the abasic sites through hydrogen bonding with the orphan cytosine present on the complementary strand, accompanied by quench of ligand fluorescence. As a result, the resultant probes, the complex formed between the hairpin DNA and ligand, showed almost no fluorescence. Upon hybridization with target DNA, the probe underwent a dehybridization of the stem moiety containing an abasic site. The release of ligand from the abasic site to the solution resulted in an effective fluorescent enhancement, which can be used as a signal. Compared with a sensing system without HCR, a 20-fold increase in the sensitivity was achieved using the sensing system with HCR. The fluorescent intensity of the sensing system increased with the increase in target DNA concentration from 0.5 nM to 100 nM. A single mismatched target ss-DNA could be effectively discriminated from complementary target DNA. Genotyping of a G/C single-nucleotide polymorphism of polymerase chain reaction (PCR) products was successfully demonstrated with the sensing system. Therefore, integrating HCR strategy with non-covalent labeling of fluorescent hairpin DNA probes provides a sensitive and cost-effective DNA assay.
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Affiliation(s)
- Luna Song
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, China
| | - Yonghua Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, China
| | - Junling Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, China
| | - Qiang Gao
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, China
| | - Honglan Qi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, China
| | - Chengxiao Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, China
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34
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Wang Y, Sun Q, Zhu L, Zhang J, Wang F, Lu L, Yu H, Xu Z, Zhang W. Triplex molecular beacons for sensitive recognition of melamine based on abasic-site-containing DNA and fluorescent silver nanoclusters. Chem Commun (Camb) 2016; 51:7958-61. [PMID: 25865656 DOI: 10.1039/c5cc01660f] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A melamine aptamer derived from an abasic-site-containing triplex molecular beacon (tMB) was designed and developed for sensitive recognition of melamine by integrating tMBs and fluorescent silver nanoclusters (Ag NCs).
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Affiliation(s)
- Ya Wang
- Department of Chemistry, East China Normal University, Shanghai 200241, P. R. China
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35
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Nagaya Y, Kitamura Y, Nakashima R, Shibata A, Ikeda M, Kitade Y. Practical and Reliable Synthesis of 1,2-Dideoxy-d-ribofuranose and its Application in RNAi Studies. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2016; 35:64-75. [PMID: 26822569 DOI: 10.1080/15257770.2015.1114128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
We developed a practical and reliable method for synthesizing an abasic deoxyribonucleoside, 1,2-dideoxy-d-ribofuranose (dR(H)) via elimination of nucleobase from thymidine. To synthesize oligonucleotides bearing dR(H) by the standard phosphoramidite solid-phase method, dR(H) was converted to the corresponding phosphoramidite derivative and linked to a solid support (controlled pore glass resin). Chemically modified small interfering RNAs (siRNAs) possessing dR(H) at their 3'-overhang regions were synthesized. Introducing dR(H) to the 3'-end of the antisense strand of siRNA reduced its knockdown effect.
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Affiliation(s)
- Yuki Nagaya
- a United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University , 1-1 Yanagido, Gifu , Japan
| | - Yoshiaki Kitamura
- b Department of Biomolecular Science , Graduate School of Engineering, Gifu University , 1-1 Yanagido, Gifu , Japan.,c Department of Chemistry and Biomolecular Science , Faculty of Engineering, Gifu University , 1-1 Yanagido, Gifu , Japan
| | - Remi Nakashima
- b Department of Biomolecular Science , Graduate School of Engineering, Gifu University , 1-1 Yanagido, Gifu , Japan
| | - Aya Shibata
- b Department of Biomolecular Science , Graduate School of Engineering, Gifu University , 1-1 Yanagido, Gifu , Japan.,c Department of Chemistry and Biomolecular Science , Faculty of Engineering, Gifu University , 1-1 Yanagido, Gifu , Japan
| | - Masato Ikeda
- a United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University , 1-1 Yanagido, Gifu , Japan.,b Department of Biomolecular Science , Graduate School of Engineering, Gifu University , 1-1 Yanagido, Gifu , Japan.,c Department of Chemistry and Biomolecular Science , Faculty of Engineering, Gifu University , 1-1 Yanagido, Gifu , Japan
| | - Yukio Kitade
- a United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University , 1-1 Yanagido, Gifu , Japan.,b Department of Biomolecular Science , Graduate School of Engineering, Gifu University , 1-1 Yanagido, Gifu , Japan.,c Department of Chemistry and Biomolecular Science , Faculty of Engineering, Gifu University , 1-1 Yanagido, Gifu , Japan
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Wang Y, Hu Y, Wu T, Zhang L, Liu H, Zhou X, Shao Y. Recognition of DNA abasic site nanocavity by fluorophore-switched probe: Suitable for all sequence environments. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 153:645-650. [PMID: 26454091 DOI: 10.1016/j.saa.2015.09.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Revised: 07/26/2015] [Accepted: 09/29/2015] [Indexed: 06/05/2023]
Abstract
Removal of a damaged base in DNA produces an abasic site (AP site) nanocavity. If left un-repaired in vivo by the specific enzyme, this nanocavity will result in nucleotide mutation in the following DNA replication. Therefore, selective recognition of AP site nanocavity by small molecules is important for identification of such DNA damage and development of genetic drugs. In this work, we investigate the fluorescence behavior of isoquinoline alkaloids including palmatine (PAL), berberine (BER), epiberberine (EPI), jatrorrhizine (JAT), coptisine (COP), coralyne (COR), worenine (WOR), berberrubine (BEU), sanguinarine (SAN), chelerythrine (CHE), and nitidine (NIT) upon binding with the AP nanocavity. PAL is screened out as the most efficient fluorophore-switched probe to recognize the AP nanocavity over the fully matched DNA. Its fluorescence enhancement occurs for all of the AP nanocavity sequence environments, which has not been achieved by the previously used probes. The bridged π conjugation effect should partially contribute to the AP nanocavity-specific fluorescence, as opposed to the solvent effect. Due to the strong binding with the AP nanocavity, PAL will find wide applications in the DNA damage recognition and sensor development.
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Affiliation(s)
- Ying Wang
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China
| | - Yuehua Hu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China
| | - Tao Wu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China
| | - Lihua Zhang
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China
| | - Hua Liu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China
| | - Xiaoshun Zhou
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China
| | - Yong Shao
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
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37
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Sato Y, Sato T, Sato T, Nishizawa S, Teramae N. The effect of LNA nucleobases as enhancers for the binding of amiloride to an abasic site in DNA/DNA and DNA/RNA duplexes. Org Biomol Chem 2015; 12:7250-6. [PMID: 25101634 DOI: 10.1039/c4ob00977k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We report on a significant effect of locked nucleic acid (LNA) nucleobases on the binding of amiloride for abasic site (AP)-containing DNA duplexes. Fluorescence titration experiments showed that the binding affinity of amiloride for the target thymine (T) opposite an AP site significantly improves for the DNA duplexes possessing LNA nucleobases that flank the AP site, compared to the corresponding normal DNA duplexes. In particular, LNA flanking nucleobases on both 5'- and 3'-sides of the AP site are found to be effective for the enhancement of the binding affinity. From thermodynamic characterization of the amiloride binding, the loss in the binding entropy is remarkably reduced for the LNA-containing DNA duplexes, which is indeed responsible for the enhanced affinity of amiloride. Moreover, such an effect of LNA nucleobases was also observed for amiloride binding to DNA/RNA hybrid duplexes.
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Affiliation(s)
- Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
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38
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Label-free fluorescence dual-amplified detection of adenosine based on exonuclease III-assisted DNA cycling and hybridization chain reaction. Biosens Bioelectron 2015; 70:15-20. [PMID: 25775969 DOI: 10.1016/j.bios.2015.03.014] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 03/04/2015] [Accepted: 03/07/2015] [Indexed: 01/03/2023]
Abstract
In this work, we constructed a label-free and dual-amplified fluorescence aptasensor for sensitive analysis of adenosine based on exonuclease III (Exo III)-assisted DNA cycling and hybridization chain reaction (HCR). Firstly, we fabricated a trifunctional probe that consisting of the catalytic strand, the aptamer sequence and a streptavidin-magnetic nanobead (streptavidin-MNB). The streptavidin-MNB played a role of enrichment and separation to achieve a low background. The aptamer sequence was employed as a recognition element to bind the target adenosine, leading to the releasing of the catalytic stand. Then, the catalytic strand induced the Exo III-assisted DNA cycling reaction and produced a large amount of DNA fragments, which got a primary amplification. Subsequently, the DNA fragments acted as trigger strands to initiate HCR, forming nicked double helices with multiple G-quadruplex structures, which achieved a secondary amplification. Finally, the G-quadruplex structures bonded with the N-nethyl mesopor-phyrin IX (NMM) and yielded an enhanced fluorescence signal, realizing the label-free detection. In the proposed strategy, a small amount of adenosine can be converted to a large amount of DNA triggers, leading to a significant amplification for the target. This method exhibited a high sensitivity toward adenosine with a detection limit of 4.2×10(-7) mol L(-1), which was about 10 times lower than that of the reported label-free strategies. Moreover, this assay can significantly distinguish the content of adenosine in urine samples of cancer patients and normal human, indicating that our method will offer a new strategy for reliable quantification of adenosine in medical research and early clinical diagnosis.
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39
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Avidin–biotin capped mesoporous silica nanoparticles as an ion-responsive release system to determine lead(II). Anal Biochem 2015; 471:17-22. [DOI: 10.1016/j.ab.2014.10.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 10/27/2014] [Accepted: 10/28/2014] [Indexed: 11/18/2022]
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Tao J, Song P, Sato Y, Nishizawa S, Teramae N, Tong A, Xiang Y. A label-free and sensitive fluorescent method for the detection of uracil-DNA glycosylase activity. Chem Commun (Camb) 2015; 51:929-32. [DOI: 10.1039/c4cc06170e] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A label-free fluorescent method has been developed for sensitive detection of uracil-DNA glycosylase activity as well as UDG inhibitors.
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Affiliation(s)
- Jing Tao
- Department of Chemistry
- Beijing Key Laboratory for Microanalytical Methods and Instrumentation
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)
- Tsinghua University
- Beijing 100084
| | - Panshu Song
- National Institute of Metrology
- Beijing 100029
- China
| | - Yusuke Sato
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Seiichi Nishizawa
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Norio Teramae
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Aijun Tong
- Department of Chemistry
- Beijing Key Laboratory for Microanalytical Methods and Instrumentation
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)
- Tsinghua University
- Beijing 100084
| | - Yu Xiang
- Department of Chemistry
- Beijing Key Laboratory for Microanalytical Methods and Instrumentation
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)
- Tsinghua University
- Beijing 100084
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41
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Wang Y, Zhang J, Zhu L, Lu L, Feng C, Wang F, Xu Z, Zhang W. Activation of Mg2+-dependent DNAzymes based on AP site-containing triplex for specific melamine recognition. Analyst 2015; 140:7508-12. [DOI: 10.1039/c5an01515d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A novel strategy for melamine recognition based on melamine binding-triggered triplex formation and DNAzyme activity regulation was developed.
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Affiliation(s)
- Ya Wang
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai 200241
- P.R. China
| | - Junying Zhang
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai 200241
- P.R. China
| | - Linling Zhu
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai 200241
- P.R. China
| | - Linlin Lu
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai 200241
- P.R. China
| | - Chongchong Feng
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai 200241
- P.R. China
| | - Fengyang Wang
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai 200241
- P.R. China
| | - Zhiai Xu
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai 200241
- P.R. China
| | - Wen Zhang
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai 200241
- P.R. China
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42
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He S, Qu L, Shen Z, Tan Y, Zeng M, Liu F, Jiang Y, Li Y. Highly specific recognition of breast tumors by an RNA-cleaving fluorogenic DNAzyme probe. Anal Chem 2014; 87:569-77. [PMID: 25479319 DOI: 10.1021/ac5031557] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Breast cancer is one of the most commonly diagnosed cancers among females worldwide. Early detection of breast cancer is of vital importance to the reduction of the mortality rate. However, the lack of specific biomarkers that can effectively identify breast cancer cells limits the ability for early diagnosis of breast cancer. RNA-cleaving fluorogenic DNAzymes (RFDs), which can be produced through the systematic evolution of ligands by exponential enrichment (SELEX) process, are catalytic DNA molecules capable of generating a fluorescent signal when the appropriate target is bound. In this study, we carried out a SELEX experiment to select for RFDs that are active in the cell lysate of MDA-MB-231, a model breast cancer cell line. We obtained a RFD probe, named AAI2-5, that can detect MDA-MB-231 at a concentration of cell lysate proteins as low as 0.5 μg/mL (which is equivalent to ∼5000 cell/mL). AAI2-5 is capable of distinguishing MDA-MB-231 cells from normal cells as well as other types of tumor cells, including other subtypes of breast cancer cells. Moreover, AAI2-5 responded positively to more than 90% of malignant breast tumors. This report is the first study to explore the RFD system for the detection of cancer cells. The results suggest that RFD can be potentially applied for the diagnosis and treatment of breast cancer in the future.
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Affiliation(s)
- Shengnan He
- Department of Chemistry, Tsinghua University , Beijing, 100084, China
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43
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Hung SY, Shih YC, Tseng WL. Tween 20-stabilized gold nanoparticles combined with adenosine triphosphate-BODIPY conjugates for the fluorescence detection of adenosine with more than 1000-fold selectivity. Anal Chim Acta 2014; 857:64-70. [PMID: 25604821 DOI: 10.1016/j.aca.2014.11.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 11/26/2014] [Accepted: 11/30/2014] [Indexed: 01/27/2023]
Abstract
This study describes the development of a simple, enzyme-free, label-free, sensitive, and selective system for detecting adenosine based on the use of Tween 20-stabilized gold nanoparticles (Tween 20-AuNPs) as an efficient fluorescence quencher for boron dipyrromethene-conjugated adenosine 5'-triphosphate (BODIPY-ATP) and as a recognition element for adenosine. BODIPY-ATP can interact with Tween 20-AuNPs through the coordination between the adenine group of BODIPY-ATP and Au atoms on the NP surface, thereby causing the fluorescence quenching of BODIPY-ATP through the nanometal surface energy transfer (NSET) effect. When adenosine attaches to the NP surface, the attached adenosine exhibits additional electrostatic attraction to BODIPY-ATP. As a result, the presence of adenosine enhances the efficiency of AuNPs in fluorescence quenching of BODIPY-ATP. The AuNP-induced fluorescence quenching of BODIPY-ATP progressively increased with an increase in the concentration of adenosine; the detection limit at a signal-to-noise ratio of 3 for adenosine was determined to be 60nM. The selectivity of the proposed system was more than 1000-fold for adenosine over any adenosine analogs and other nucleotides. The proposed system combined with a phenylboronic acid-containing column was successfully applied to the determination of adenosine in urine.
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Affiliation(s)
- Szu-Ying Hung
- Department of Chemistry, National Sun Yat-sen University, Taiwan
| | - Ya-Chen Shih
- Department of Chemistry, National Sun Yat-sen University, Taiwan
| | - Wei-Lung Tseng
- Department of Chemistry, National Sun Yat-sen University, Taiwan; School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Taiwan; Center for Nanoscience and Nanotechnology, National Sun Yat-sen University, Taiwan; Center for Stem Cell Research, Kaohsiung Medical University, Taiwan.
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44
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Li S, Gao Z, Shao N. Non-covalent conjugation of CdTe QDs with lysozyme binding DNA for fluorescent sensing of lysozyme in complex biological sample. Talanta 2014; 129:86-92. [DOI: 10.1016/j.talanta.2014.04.062] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Revised: 04/15/2014] [Accepted: 04/21/2014] [Indexed: 12/13/2022]
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45
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Nieh CC, Tseng WL. Thymine-based molecular beacon for sensing adenosine based on the inhibition of S-adenosylhomocysteine hydrolase activity. Biosens Bioelectron 2014; 61:404-9. [DOI: 10.1016/j.bios.2014.05.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/12/2014] [Accepted: 05/13/2014] [Indexed: 01/23/2023]
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46
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Bone SM, Hasick NJ, Lima NE, Erskine SM, Mokany E, Todd AV. DNA-only cascade: a universal tool for signal amplification, enhancing the detection of target analytes. Anal Chem 2014; 86:9106-13. [PMID: 25157928 DOI: 10.1021/ac501811r] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Diagnostic tests performed in the field or at the site of patient care would benefit from using a combination of inexpensive, stable chemical reagents and simple instrumentation. Here, we have developed a universal "DNA-only Cascade" (DoC) to quantitatively detect target analytes with increased speed. The DoC utilizes quasi-circular structures consisting of temporarily inactivated deoxyribozymes (DNAzymes). The catalytic activity of the DNAzymes is restored in a universal manner in response to a broad range of environmental and biological targets. The present study demonstrates DNAzyme activation in the presence of metal ions (Pb(2+)), small molecules (deoxyadenosine triphosphate) and nucleic acids homologous to genes from Meningitis-causing bacteria. Furthermore, DoC efficiently discriminates nucleic acid targets differing by a single nucleotide. When detection of analytes is orchestrated by functional nucleic acids, the inclusion of DoC reagents substantially decreases time for detection and allows analyte quantification. The detection of nucleic acids using DoC was further characterized for its capability to be multiplexed and retain its functionality following long-term exposure to ambient temperatures and in a background of complex medium (human serum).
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Affiliation(s)
- Simon M Bone
- The University of New South Wales , Kensington, New South Wales 2052, Australia
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47
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Liu Z, Jia X, Bian P, Ma Z. A simple and novel system for colorimetric detection of cobalt ions. Analyst 2014; 139:585-8. [PMID: 24326358 DOI: 10.1039/c3an01845h] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A simple and novel method for the colorimetric detection of Co(2+) was developed based on controlling the oxidation level of methylene blue (MB). After a complex was formed between MB, 2-aminothiophenol (ATP) and copper nitrate (MB-ATP-Cu(2+)), the sensing of Co(2+) showed high selectivity. The mechanism of sensing has also been discussed.
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Affiliation(s)
- Zhimin Liu
- Department of Chemistry, Capital Normal University, Beijing, China.
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48
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Han YH, Tian CB, Du SW. An unusual chiral 3D inorganic connectivity featuring a {Pb₁₈} wheel: rapid and highly selective and sensitive sensing of Co(II). Dalton Trans 2014; 43:11461-4. [PMID: 24898276 DOI: 10.1039/c4dt00905c] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A pair of enantiomorphic frameworks featuring rare chiral 3D inorganic connectivity and a {Pb18} wheel, has been obtained via spontaneous resolution. They exhibit rapid and highly selective and sensitive sensing of Co(2+) ions.
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Affiliation(s)
- Yun-Hu Han
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, P. R. China.
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49
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Qiang W, Liu H, Li W, Chen X, Xu D. Label-free detection of adenosine based on fluorescence resonance energy transfer between fluorescent silica nanoparticles and unmodified gold nanoparticles. Anal Chim Acta 2014; 828:92-8. [DOI: 10.1016/j.aca.2014.04.043] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 04/10/2014] [Accepted: 04/19/2014] [Indexed: 12/20/2022]
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50
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Feng C, Dai S, Wang L. Optical aptasensors for quantitative detection of small biomolecules: a review. Biosens Bioelectron 2014; 59:64-74. [PMID: 24690563 DOI: 10.1016/j.bios.2014.03.014] [Citation(s) in RCA: 186] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/27/2014] [Accepted: 03/06/2014] [Indexed: 01/16/2023]
Abstract
Aptasensors are aptamer-based biosensors with excellent recognition capability towards a wide range of targets. Specially, there have been ever-growing interests in the development of aptasensors for the detection of small molecules. This phenomenon is contributed to two reasons. On one hand, small biomolecules play an important role in living organisms with many kinds of biological function, such as antiarrhythmic effect and vasodilator activity of adenosine. On the other hand, the concentration of small molecules can be an indicator for disease diagnosis, for example, the concentration of ATP is closely associated with cell injury and cell viability. As a potential analysis tool in the construction of aptasensors, optical analysis has attracted much more interest of researchers due to its high sensitivity, quick response and simple operation. Besides, it promises the promotion of aptasensors in performance toward a new level. Review the development of optical aptasensors for small biomolecules will give readers an overall understanding of its progress and provide some theoretical guidelines for its future development. Hence, we give a mini-review on the advance of optical aptasensors for small biomolecules. This review focuses on recent achievements in the design of various optical aptasensors for small biomolecules, containing fluorescence aptasensors, colorimetric aptasensors, chemiluminescence aptasensors and other optical aptasensors.
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Affiliation(s)
- Chunjing Feng
- Key Laboratory of Natural Products Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 250012 Jinan, PR China
| | - Shuang Dai
- Key Laboratory of Natural Products Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 250012 Jinan, PR China
| | - Lei Wang
- Key Laboratory of Natural Products Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 250012 Jinan, PR China.
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