1
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Wang Z, Pan T, Shen M, Liao J, Tian Y. Cross-conjugated polymers as fluorescent probes for intracellular potassium ion detection. SENSORS AND ACTUATORS B: CHEMICAL 2023; 390:134008. [DOI: 10.1016/j.snb.2023.134008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
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2
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Li T, Zhang Y, Sun X, Zhang Y, Wang Y, Nie Z. Dual dye-labeled G-quadruplex aptasensor for detection of thallium(I) using ratiometric fluorescence resonance energy transfer. Talanta 2021; 233:122508. [PMID: 34215123 DOI: 10.1016/j.talanta.2021.122508] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/03/2021] [Accepted: 05/06/2021] [Indexed: 11/29/2022]
Abstract
A fluorescent probe was developed for ratiometric detection of thallium ions in mineral water samples by modifying a G-rich aptamer (PS2.M - 7) with a fluorescence donor (Cyanine-3, Cy3) and a quencher (Cyanine-5, Cy5). The probe had a random coil structure that changed into a G-quadruplex structure upon binding with Tl+. This change in structure decreased the distance between the donor and acceptor moieties, which resulted in fluorescence resonance energy transfer between Cy3 and Cy5. Under optimized conditions, the limit of detection and linear concentration range for Tl+ were 30.1 μM (3σ) and 10 μM-10 mM (R2 = 0.9981), respectively. This simple and cost-effective fluorescence sensor provided satisfactory results for detection of thallium ions in spiked mineral water samples.
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Affiliation(s)
- Tongtong Li
- State Key Laboratory of Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China; School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China.
| | - Yan Zhang
- State Key Laboratory of Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China; School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China.
| | - Xiaohong Sun
- State Key Laboratory of Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China.
| | - Yanjin Zhang
- State Key Laboratory of Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China.
| | - Yongan Wang
- State Key Laboratory of Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China.
| | - Zhiyong Nie
- State Key Laboratory of Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China.
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3
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Abstract
Aminoglycosides (AGs) are broad-spectrum antibiotics used in both human infection and animal medicine. The overuse of AGs causes undesirable residues in food, leading to serious health problems due to food chain accumulation. In recent years, various methods have been developed to determine AGs in food. Among these methods, fluorescent (FL), colorimetric and chemiluminescent (CL) optical methods possess advantages such as their simple instrumentation, low cost, simple operation, feasibility of realizing visualization, and smartphone imaging. This mini-review summarizes optical assays for the detection of AGs in food developed in recent years. The detection principles for different categories are discussed. Then, the amplification techniques for the ultrasensitive detection of AGs are introduced. We also discuss multiplex methods for the simultaneous detection of AGs. Finally, the challenges and future prospects are discussed in the Conclusions and Perspectives section.
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4
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Cui MR, Chen LX, Li XL, Xu JJ, Chen HY. NIR Remote-Controlled "Lock-Unlock" Nanosystem for Imaging Potassium Ions in Living Cells. Anal Chem 2020; 92:4558-4565. [PMID: 32066238 DOI: 10.1021/acs.analchem.9b05820] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Despite great achievements in sensitive and selective detection of important biomolecules in living cells, it is still challenging to develop smart and controllable sensing nanodevices for cellular studies that can be activated at desired time in target sites. To address this issue, we have constructed a remote-controlled "lock-unlock" nanosystem for visual analysis of endogenous potassium ions (K+), which employed a dual-stranded aptamer precursor (DSAP) as recognition molecules, SiO2 based gold nanoshells (AuNS) as nanocarriers, and near-infrared ray (NIR) as the remotely applied stimulus. With the well-designed and activatable DSAP-AuNS, the deficiencies of traditional aptamer-based sensors have been successfully overcome, and the undesired response during transport has been avoided, especially in complex physiological microenvironments. While triggered by NIR, the increased local temperature of AuNS induced the dehybridiztion of DSAP, realized the "lock-unlock" switch of the DSAP-AuNS nanosystem, activated the binding capability of aptamer, and then monitored intracellular K+ via the change of fluorescence signal. This DSAP-AuNS nanosystem not only allows us to visualize endogenous ions in living cells at a desired time but also paves the way for fabricating temporal controllable nanodevices for cellular studies.
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Affiliation(s)
- Mei-Rong Cui
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
| | - Li-Xian Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
| | - Xiang-Ling Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China.,College of Life Science and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, P.R. China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
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5
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Ma G, Yu Z, Zhou W, Li Y, Fan L, Li X. Investigation of Na+ and K+ Competitively Binding with a G-Quadruplex and Discovery of a Stable K+–Na+-Quadruplex. J Phys Chem B 2019; 123:5405-5411. [DOI: 10.1021/acs.jpcb.9b02823] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ge Ma
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ze Yu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Wei Zhou
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Yunchao Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Louzhen Fan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Xiaohong Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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Świtalska A, Dembska A, Fedoruk-Wyszomirska A, Juskowiak B. Cholesterol-Bearing Fluorescent G-Quadruplex Potassium Probes for Anchoring at the Langmuir Monolayer and Cell Membrane. SENSORS (BASEL, SWITZERLAND) 2018; 18:E2201. [PMID: 29987195 PMCID: PMC6069133 DOI: 10.3390/s18072201] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 06/29/2018] [Accepted: 07/02/2018] [Indexed: 12/31/2022]
Abstract
The purpose of the present work was to design, synthesize and spectrally characterize cholesterol-anchored fluorescent oligonucleotide probes (Ch(F-TBA-T), Ch(py-TBA-py)), based on G-quadruplexes, which were able to incorporate into a lipid structure (Langmuir monolayer, living cell membrane). The probes, based on the thrombin-binding aptamer (TBA) sequence, were labeled with fluorescent dyes which enabled simultaneous monitoring of the formation of G-quadruplex structures and visualization of probe incorporation into the cellular membrane. The combinations of fluorophores used included fluorescence resonance energy transfer (FRET) and excimer emission approaches. The structural changes of the probes upon binding with K⁺ or Na⁺ ions were monitored with fluorescence techniques. These systems showed a very high binding preference for K⁺ over Na⁺ ions. The use of confocal fluorescence microscopy indicated successful anchoring of the cholesterol-bearing fluorescent probes to the living cell membrane. These structurally simple cholesterol-based fluorescent probes have good potential for opening up new and exciting opportunities in the field of biosensors; e.g., in vivo detection of K⁺ ions.
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Affiliation(s)
- Angelika Świtalska
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
| | - Anna Dembska
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
| | | | - Bernard Juskowiak
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
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7
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Naderi M, Hosseini M, Ganjali MR. Naked-eye detection of potassium ions in a novel gold nanoparticle aggregation-based aptasensor. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 195:75-83. [PMID: 29414585 DOI: 10.1016/j.saa.2018.01.051] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/10/2018] [Accepted: 01/16/2018] [Indexed: 05/27/2023]
Abstract
In this work, we studied the feasibility of interaction among gold nanoparticles (AuNPs) and a cationic dye in an aptasensor system for the detection of potassium ions. The presence and absence of potassium in the solution was distinguishable by different colors (between orange and green) appeared after reaction. Cationic dye (Y5GL) acts as a new aggregator for AuNP-based sensors which changes the aggregated AuNP solution color from blue-purple to green. In the presence of K+ ions, the aptamer dissociated from the surface of the AuNP so that free AuNPs and cationic dye make the solution green. The aptasensor showed that the analytical linear range was from 10 nM to 50 mM and the detection limit was 4.4 nM. Also, we examined the practicality of this method on a simple paper based platform. The linear range of the colorimetric paper sensor covered of K+ concentration from 10 μM to 40 mM and the detection limit of 6.2 μM was obtained. The selectivity of AuNP aggregation-based sensor improved by the use of cationic dye. Rapidity, simplicity, high sensitivity and excellent selectivity made this assay suitable for practical determination of K+ in real urine samples.
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Affiliation(s)
- Mahboube Naderi
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Morteza Hosseini
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran; Department of Pharmaceutical Biomaterials and Medical Biomaterials Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.
| | - Mohammad Reza Ganjali
- Center of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, Tehran, Iran; Biosensor Research Center, Endocrinology & Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
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8
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Analysis of Cation-Dependent DNA (G3T1)4 Shape Change Using Fluorescence Correlation Spectroscopy. J Fluoresc 2017; 27:2037-2043. [DOI: 10.1007/s10895-017-2142-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 07/18/2017] [Indexed: 10/19/2022]
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9
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The G-BHQ synergistic effect: Improved double quenching molecular beacons based on guanine and Black Hole Quencher for sensitive simultaneous detection of two DNAs. Talanta 2017; 174:289-294. [PMID: 28738581 DOI: 10.1016/j.talanta.2017.06.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 05/31/2017] [Accepted: 06/07/2017] [Indexed: 11/21/2022]
Abstract
We designed two double quenching molecular beacons (MBs) with simple structure based on guanine (G base) and Black Hole Quencher (BHQ), and developed a new analytical method for sensitive simultaneous detection of two DNAs by synchronous fluorescence analysis. In this analytical method, carboxyl fluorescein (FAM) and tetramethyl-6-carboxyrhodamine (TAMRA) were respectively selected as fluorophore of two MBs, Black Hole Quencher 1 (BHQ-1) and Black Hole Quencher 2 (BHQ-2) were respectively selected as organic quencher, and three continuous nucleotides with G base were connected to organic quencher (BHQ-1 and BHQ-2). In the presence of target DNAs, the two MBs hybridize with the corresponding target DNAs, the fluorophores are separated from organic quenchers and G bases, leading to recovery of fluorescence of FAM and TAMRA. Under a certain conditions, the fluorescence intensities of FAM and TAMRA all exhibited good linear dependence on their concentration of target DNAs (T1 and T2) in the range from 4 × 10-10 to 4 × 10-8molL-1 (M). The detection limit (3σ, n = 13) of T1 was 3 × 10-10M and that of T2 was 2×10-10M, respectively. Compared with the existing analysis methods for multiplex DNA with MBs, this proposed method based on double quenching MBs is not only low fluorescence background, short analytical time and low detection cost, but also easy synthesis and good stability of MB probes.
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10
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Ding Y, Li X, Guo Y, Duan W, Ling J, Zha L, Yan J, Zou Y, Cai J. Estimation of postmortem interval by vitreous potassium evaluation with a novel fluorescence aptasensor. Sci Rep 2017; 7:1868. [PMID: 28500353 PMCID: PMC5431803 DOI: 10.1038/s41598-017-02027-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 04/04/2017] [Indexed: 01/17/2023] Open
Abstract
Estimation of postmortem interval (PMI) is a central role in medico-legal identification. Analysis of vitreous potassium ions (K+) concentration is frequently used by forensic workers to estimate PMI. This paper describes interdisciplinary research to introduce fluorescence sensing techniques into forensic medicine. On the basis of silver nanoclusters (AgNCs) probe stabilized by DNA, a simple and highly sensitive fluorescence aptasensor has been proposed to selectively detect K+ ions. The linear range for K+ ions was found to be 0.1 nM-1 mM, with limit of detection of 0.06 nM. Moreover, 63 vitreous humour cases within 36 h after death were further studied to verify the utility of K+ ions in estimating the PMI. By the fluorescence aptasensor method, a new formula was built to determine the postmortem interval based on K+ ions concentration: PMI(h) = −0.55 + 1.66 × CK+(r = 0.791). And the real significance of this research was demonstrated by additional 6 cases with known PMIs. In comparison with the conventional method, the presented aptasensor strategy is cost-effective and easy in measuring vitreous K+, which may be potentially a better way for estimation of PMI in medico-legal practice.
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Affiliation(s)
- Yanjun Ding
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, P.R. China
| | - Xingmei Li
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, P.R. China.,Department of Pathophysiology, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, P.R. China
| | - Yadong Guo
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, P.R. China
| | - Weicheng Duan
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, P.R. China
| | - Jiang Ling
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, P.R. China.,Department of Pathophysiology, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, P.R. China
| | - Lagabaiyla Zha
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, P.R. China
| | - Jie Yan
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, P.R. China
| | - Ying Zou
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, P.R. China
| | - Jifeng Cai
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, P.R. China.
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11
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Xiong M, Zhu H, Rong Q, Yang C, Qiu L, Zhang XB, Tan W. A membrane-anchored fluorescent probe for detecting K(+) in the cell microenvironment. Chem Commun (Camb) 2017; 52:4679-82. [PMID: 26952866 DOI: 10.1039/c6cc00192k] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cell-surface fluorescent probes are effective tools in cell biology and engineering. Here, we for the first time report a diacyllipid-aptamer conjugate-based fluorescent probe which could anchor on cell membrane for real-time tracking of potassium ions in the cell microenvironment.
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Affiliation(s)
- Mengyi Xiong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China.
| | - Huijie Zhu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China.
| | - Qiming Rong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China.
| | - Chan Yang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China.
| | - Liping Qiu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China.
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China.
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, P. R. China.
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12
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Swiatkowska A, Kosman J, Juskowiak B. FRET study of G-quadruplex forming fluorescent oligonucleotide probes at the lipid monolayer interface. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 152:614-621. [PMID: 25698056 DOI: 10.1016/j.saa.2015.01.102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 01/08/2015] [Accepted: 01/30/2015] [Indexed: 06/04/2023]
Abstract
Spectral properties and G-quadruplex folding ability of fluorescent oligonucleotide probes at the cationic dioctadecyldimethylammonium bromide (DODAB) monolayer interface are reported. Two oligonucleotides, a 19-mer bearing thrombin binding aptamer sequence and a 21-mer with human telomeric sequence, were end-labeled with fluorescent groups (FAM and TAMRA) to give FRET probes F19T and F21T, respectively. The probes exhibited abilities to fold into a quadruplex structure and to bind metal cations (Na(+) and K(+)). Fluorescence spectra of G-quadruplex FRET probes at the monolayer interface are reported for the first time. Investigations included film balance measurements (π-A isotherms) and fluorescence spectra recording using a fiber optic accessory interfaced with a spectrofluorimeter. The effect of the presence of DODAB monolayer, metal cations and the surface pressure of monolayer on spectral behavior of FRET probes were examined. Adsorption of probe at the cationic monolayer interface resulted in the FRET signal enhancement even in the absence of metal cations. Variation in the monolayer surface pressure exerted rather modest effect on the spectral properties of probes. The fluorescence energy transfer efficiency of monolayer adsorbed probes increased significantly in the presence of sodium or potassium ion in subphase, which indicated that the probes retained their cation binding properties when adsorbed at the monolayer interface.
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Affiliation(s)
- Angelika Swiatkowska
- Adam Mickiewicz University, Faculty of Chemistry, Umultowska 89b, 61-614 Poznan, Poland
| | - Joanna Kosman
- Adam Mickiewicz University, Faculty of Chemistry, Umultowska 89b, 61-614 Poznan, Poland
| | - Bernard Juskowiak
- Adam Mickiewicz University, Faculty of Chemistry, Umultowska 89b, 61-614 Poznan, Poland.
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13
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Zhang S, Zhang R, Ma B, Qiu J, Li J, Sang Y, Liu W, Liu H. Specific detection of potassium ion in serum by a modified G-quadruplex method. RSC Adv 2016. [DOI: 10.1039/c6ra04046b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A modified dual-labelled G-quadruplex method is successfully designed to rapidly detect K+ in complex matrix of real serum.
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Affiliation(s)
- Shan Zhang
- State Key Laboratory of Crystal Materials
- Shandong University
- Jinan
- China
| | - Ruibin Zhang
- Blood Purification Center
- Jinan Central Hospital
- Jinan
- China
| | - Baojin Ma
- State Key Laboratory of Crystal Materials
- Shandong University
- Jinan
- China
| | - Jichuan Qiu
- State Key Laboratory of Crystal Materials
- Shandong University
- Jinan
- China
| | - Jianhua Li
- State Key Laboratory of Crystal Materials
- Shandong University
- Jinan
- China
| | - Yuanhua Sang
- State Key Laboratory of Crystal Materials
- Shandong University
- Jinan
- China
| | - Wei Liu
- State Key Laboratory of Crystal Materials
- Shandong University
- Jinan
- China
| | - Hong Liu
- State Key Laboratory of Crystal Materials
- Shandong University
- Jinan
- China
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14
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Olejko L, Cywinski PJ, Bald I. Ionenselektive Guanin-Quadruplex-Faltung auf DNA-Origami- Strukturen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201409278] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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15
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Lee HL, Dhenadhayalan N, Lin KC. Metal ion induced fluorescence resonance energy transfer between crown ether functionalized quantum dots and rhodamine B: selectivity of K+ ion. RSC Adv 2015. [DOI: 10.1039/c4ra10925b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A ratiometric fluorescent metal ion sensor based on the mechanism of fluorescence resonance energy transfer between 15-crown-5-ether capped CdSe/ZnS quantum dots and 15-crown-5-ether attached rhodamine B.
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Affiliation(s)
- Hsin-Lung Lee
- Department of Chemistry
- National Taiwan University
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 106
| | - Namasivayam Dhenadhayalan
- Department of Chemistry
- National Taiwan University
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 106
| | - King-Chuen Lin
- Department of Chemistry
- National Taiwan University
- Institute of Atomic and Molecular Sciences
- Academia Sinica
- Taipei 106
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16
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Lin JH, Tseng WL. Ultrasensitive detection of target analyte-induced aggregation of gold nanoparticles using laser-induced nanoparticle Rayleigh scattering. Talanta 2015; 132:44-51. [DOI: 10.1016/j.talanta.2014.08.055] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 08/19/2014] [Accepted: 08/20/2014] [Indexed: 01/09/2023]
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17
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Effect of Cholesterol Anchoring Group on the Properties of G-Quadruplex-Based FRET Probes for Potassium Ion. CHEMOSENSORS 2014. [DOI: 10.3390/chemosensors2040267] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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18
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Olejko L, Cywinski PJ, Bald I. Ion-Selective Formation of a Guanine Quadruplex on DNA Origami Structures. Angew Chem Int Ed Engl 2014; 54:673-7. [DOI: 10.1002/anie.201409278] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Indexed: 01/14/2023]
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19
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Verdian-Doghaei A, Housaindokht MR, Abnous K. A fluorescent aptasensor for potassium ion detection-based triple-helix molecular switch. Anal Biochem 2014; 466:72-5. [PMID: 25173515 DOI: 10.1016/j.ab.2014.08.014] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 08/12/2014] [Accepted: 08/15/2014] [Indexed: 12/21/2022]
Abstract
Here, a biosensor based on a quadruplex-forming aptamer for the determination of potassium ion (K(+)) is presented. The aptamer was used as a molecular recognition element; it was adjacent to two arm fragments and a dual-labeled oligonucleotide serving as a signal transduction probe (STP) that is complementary of the arm fragment sequence. In the presence of K(+), the aptamer was displaced from the STP, which was accompanied by decreased signal. The quenching percentage of fluorescence intensity was proportional to the concentration of K(+) in the range of 0.05 to 1.4mM. A detection limit of 0.014 mM was achieved. Furthermore, other metal ions, such as Na(+), Li(+), NH4(+), Mg(2+), and Ca(2+), caused no notable interference on the detection of K(+).
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Affiliation(s)
- A Verdian-Doghaei
- Biophysical Chemistry Laboratory, Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - M R Housaindokht
- Biophysical Chemistry Laboratory, Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Kh Abnous
- Pharmaceutical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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Pfeiffer C, Rehbock C, Hühn D, Carrillo-Carrion C, de Aberasturi DJ, Merk V, Barcikowski S, Parak WJ. Interaction of colloidal nanoparticles with their local environment: the (ionic) nanoenvironment around nanoparticles is different from bulk and determines the physico-chemical properties of the nanoparticles. J R Soc Interface 2014; 11:20130931. [PMID: 24759541 PMCID: PMC4032524 DOI: 10.1098/rsif.2013.0931] [Citation(s) in RCA: 203] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 11/27/2013] [Indexed: 12/22/2022] Open
Abstract
The physico-chemical properties of colloidal nanoparticles (NPs) are influenced by their local environment, as, in turn, the local environment influences the physico-chemical properties of the NPs. In other words, the local environment around NPs has a profound impact on the NPs, and it is different from bulk due to interaction with the NP surface. So far, this important effect has not been addressed in a comprehensive way in the literature. The vicinity of NPs can be sensitively influenced by local ions and ligands, with effects already occurring at extremely low concentrations. NPs in the Hückel regime are more sensitive to fluctuations in the ionic environment, because of a larger Debye length. The local ion concentration hereby affects the colloidal stability of the NPs, as it is different from bulk owing to Debye Hückel screening caused by the charge of the NPs. This can have subtle effects, now caused by the environment to the performance of the NP, such as for example a buffering effect caused by surface reaction on ultrapure ligand-free nanogold, a size quenching effect in the presence of specific ions and a significant impact on fluorophore-labelled NPs acting as ion sensors. Thus, the aim of this review is to clarify and give an unifying view of the complex interplay between the NP's surface with their nanoenvironment.
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Affiliation(s)
| | - Christoph Rehbock
- Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Essen, Germany
| | - Dominik Hühn
- Fachbereich Physik, Philipps Universität Marburg, Marburg, Germany
| | | | | | - Vivian Merk
- Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Essen, Germany
| | - Stephan Barcikowski
- Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Essen, Germany
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21
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Lee J, Park J, Lee HH, Kim HI, Kim WJ. DNA-templated silver nanoclusters as label-free, sensitive detection probes for potassium ions and nitric oxide. J Mater Chem B 2014; 2:2616-2621. [DOI: 10.1039/c3tb21446j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Wu TC, Vasudev M, Dutta M, Stroscio MA. Raman and surface-enhanced Raman scattering (SERS) studies of the thrombin-binding aptamer. IEEE Trans Nanobioscience 2013; 12:93-7. [PMID: 23694695 DOI: 10.1109/tnb.2013.2242484] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Surface-enhanced Raman scattering is used to study the Raman spectra and peak shifts the thrombin-binding aptamer (TBA) on substrates having two different geometries; one with a single stranded sequence and one with double stranded sequence. The Raman signals of the deoxyribonucleic acids on both substrates are enhanced and specific peaks of bases are identified. These results are highly reproducible and have promising applications in low cost nucleic acid detection.
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Affiliation(s)
- Tsai-Chin Wu
- Bioengineering Department, University of Illinois, Chicago, IL 60607, USA.
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Radom F, Jurek PM, Mazurek MP, Otlewski J, Jeleń F. Aptamers: molecules of great potential. Biotechnol Adv 2013; 31:1260-74. [PMID: 23632375 DOI: 10.1016/j.biotechadv.2013.04.007] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 03/27/2013] [Accepted: 04/19/2013] [Indexed: 01/08/2023]
Abstract
Aptamers emerged over 20 years ago as a class of nucleic acids able to recognize specific targets. Today, aptamer-related studies constitute a large and important field of biotechnology. Functional oligonucleotides have proved to be a versatile tool in biomedical research due to the ease of synthesis, a wide range of potentially recognized molecular targets and the simplicity of selection. Similarly to antibodies, aptamers can be used to detect or isolate specific molecules, as well as to act as targeting and therapeutic agents. In this review we present different approaches to aptamer application in nanobiotechnology, diagnostics and medicine.
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Affiliation(s)
- Filip Radom
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Tamka 2, 50-137 Wroclaw, Poland
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Akter F, Mie M, Kobatake E. Aptamer-based protein detection using a bioluminescent fusion protein. Analyst 2013; 137:5297-301. [PMID: 23013644 DOI: 10.1039/c2an35596e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An aptamer-based sandwich-type immunoassay is presented to detect human thrombin using a bioluminescent fusion protein, SSB-fLuc. Escherichia coli single-stranded DNA binding protein (SSB) is used as a linker between the aptamer and firefly luciferase (fLuc). For proof-of-principle, thrombin was used as the test analyte and thrombin aptamer as the sensing probe. In this fusion protein, both the SSB and the fLuc parts retained their biological activities after expression and purification. The SSB fragment of the fusion protein also had the thrombin aptamer binding ability either alone or in combination with thrombin as a triplex, which was confirmed by gel mobility shift assay using native polyacrylamide gels. The fusion protein can be used to detect thrombin in the nanomolar range. The present study thus demonstrates an aptamer-based bioluminescent assay that is simple and cost effective, and at the same time eliminates the need for labeling of either analytes or aptamers. This biomolecular detection scheme can be extended to the detection of a wide range of analytes.
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Affiliation(s)
- Farhima Akter
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
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25
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Zhou Z, Zhu J, Zhang L, Du Y, Dong S, Wang E. G-quadruplex-Based Fluorescent Assay of S1 Nuclease Activity and K+. Anal Chem 2013; 85:2431-5. [DOI: 10.1021/ac303440d] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Zhixue Zhou
- State Key Laboratory of
Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy
of Sciences, Changchun, Jilin 130022, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - Jinbo Zhu
- State Key Laboratory of
Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy
of Sciences, Changchun, Jilin 130022, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - Libing Zhang
- State Key Laboratory of
Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy
of Sciences, Changchun, Jilin 130022, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - Yan Du
- State Key Laboratory of
Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy
of Sciences, Changchun, Jilin 130022, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - Shaojun Dong
- State Key Laboratory of
Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy
of Sciences, Changchun, Jilin 130022, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - Erkang Wang
- State Key Laboratory of
Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy
of Sciences, Changchun, Jilin 130022, P. R. China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, P. R. China
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26
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Samanta S, Anderson K, Moran S, Hawke D, Gorenstein D, Fornage M. Characterization of a human 12/15-lipoxygenase promoter variant associated with atherosclerosis identifies vimentin as a promoter binding protein. PLoS One 2012; 7:e42417. [PMID: 22879973 PMCID: PMC3413658 DOI: 10.1371/journal.pone.0042417] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 07/04/2012] [Indexed: 11/18/2022] Open
Abstract
Background Sequence variation in the human 12/15 lipoxygenase (ALOX15) has been associated with atherosclerotic disease. We functionally characterized an ALOX15 promoter polymorphism, rs2255888, previously associated with carotid plaque burden. Methodology/Principal Findings We demonstrate specific in vitro and in vivo binding of the cytoskeletal protein, vimentin, to the ALOX15 promoter. We show that the two promoter haplotypes carrying alternate alleles at rs2255888 exhibit significant differences in promoter activity by luciferase reporter assay in two cell lines. Differences in in-vitro vimentin-binding to and formation of DNA secondary structures in the polymorphic promoter sequence are also detected by electrophoretic mobility shift assay and biophysical analysis, respectively. We show regulation of ALOX15 protein by vimentin. Conclusions/Significance This study suggests that vimentin binds the ALOX15 promoter and regulates its promoter activity and protein expression. Sequence variation that results in changes in DNA conformation and vimentin binding to the promoter may be relevant to ALOX15 gene regulation.
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Affiliation(s)
- Susmita Samanta
- Research Center for Human Genetics, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas, United States of America.
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27
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Buranachai C, Thavarungkul P, Kanatharana P. A novel reconfigurable optical biosensor based on DNA aptamers and a DNA molecular beacon. J Fluoresc 2012; 22:1617-25. [PMID: 22811040 DOI: 10.1007/s10895-012-1105-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 06/27/2012] [Indexed: 11/30/2022]
Abstract
In order to alter a typical molecular aptamer beacon (MAB) to detect a different analyte there is currently a need to change the whole sensor unit including the expensive labeling fluorophores. In this work a DNA-based reconfigurable molecular aptamer beacon was developed. It is composed of two parts: a variable part and a constant part. The variable part comprises an aptamer strand and its complementary strand while the constant part is an oligonucleotide doubly labeled with a Förster Resonance Energy Transfer (FRET) pair and the two parts become joined via DNA hybridization. The sensor exists in two conformations: a folded (high FRET) and an unfolded (low FRET) in the absence and presence of the aptamer-target binding respectively. This sensor can be reconfigured by washing away the aptamer and the complementary strand using proper complementary strands, called washers. As a proof of the principle, a sensor that bound the enzyme thrombin, an analyte with a strong binding, was first constructed and then reconfigured to bind adenosine, selected as an analyte with a weak binding. We believe that the design is of universal use applicable to many types of aptamers.
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Affiliation(s)
- Chittanon Buranachai
- Trace Analysis and Biosensor Research Center, Department of Physics, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand.
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28
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Ma C, Zeng F, Wu G, Wu S. A nanoparticle-supported fluorescence resonance energy transfer system formed via layer-by-layer approach as a ratiometric sensor for mercury ions in water. Anal Chim Acta 2012; 734:69-78. [DOI: 10.1016/j.aca.2012.05.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 04/27/2012] [Accepted: 05/15/2012] [Indexed: 10/28/2022]
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29
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Ohtsuka K, Sato S, Sato Y, Sota K, Ohzawa S, Matsuda T, Takemoto K, Takamune N, Juskowiak B, Nagai T, Takenaka S. Fluorescence imaging of potassium ions in living cells using a fluorescent probe based on a thrombin binding aptamer-peptide conjugate. Chem Commun (Camb) 2012; 48:4740-2. [PMID: 22475983 DOI: 10.1039/c2cc30536d] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
When a biotinylated FRET probe based on a peptide-thrombin binding aptamer conjugate was introduced together with streptavidin and biotinylated nuclear export signal peptide into HeLa cells, the resulting ternary complex enabled visualization of K(+) concentration changes in the cell.
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Affiliation(s)
- Keiichi Ohtsuka
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu Institute of Technology, Fukuoka 804-8550, Japan
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30
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Duan N, Wu S, Zhu C, Ma X, Wang Z, Yu Y, Jiang Y. Dual-color upconversion fluorescence and aptamer-functionalized magnetic nanoparticles-based bioassay for the simultaneous detection of Salmonella Typhimurium and Staphylococcus aureus. Anal Chim Acta 2012; 723:1-6. [PMID: 22444566 DOI: 10.1016/j.aca.2012.02.011] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2011] [Revised: 02/01/2012] [Accepted: 02/06/2012] [Indexed: 10/14/2022]
Abstract
A sensitive luminescent bioassay for the simultaneous detection of Salmonella Typhimurium and Staphylococcus aureus was developed using aptamer-conjugated magnetic nanoparticles (MNPs) for both recognition and concentration elements and using upconversion nanoparticles (UCNPs) as highly sensitive dual-color labels. The bioassay system was fabricated by immobilizing aptamer 1 and aptamer 2 onto the surface of MNPs, which were employed to capture and concentrate S. Typhimurium and S. aureus. NaY(0.78)F(4):Yb(0.2),Tm(0.02) UCNPs modified aptamer 1 and NaY(0.28)F(4):Yb(0.70),Er(0.02) UCNPs modified aptamer 2 further were bond onto the captured bacteria surface to form sandwich-type complexes. Under optimal conditions, the correlation between the concentration of S. Typhimurium and the luminescent signal was found to be linear within the range of 10(1)-10(5) cfu mL(-1) (R(2)=0.9964), and the signal was in the range of 10(1)-10(5) cfu mL(-1) (R(2)=0.9936) for S. aureus. The limits of detection of the developed method were found to be 5 and 8 cfu mL(-1) for S. Typhimurium and S. aureus, respectively. The ability of the bioassay to detect S. Typhimurium and S. aureus in real water samples was also investigated, and the results were compared to the experimental results from the plate-counting methods. Improved by the magnetic separation and concentration effect of MNPs, the high sensitivity of UCNPs, and the different emission lines of Yb/Er- and Yb/Tm-doped NaYF(4) UCNPs excited by a 980 nm laser, the present method performs with both high sensitivity and selectivity for the two different types of bacteria.
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Affiliation(s)
- Nuo Duan
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
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31
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Kiy MM, Zaki A, Menhaj AB, Samadi A, Liu J. Dissecting the effect of anions on Hg2+ detection using a FRET based DNA probe. Analyst 2012; 137:3535-40. [DOI: 10.1039/c2an35314h] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Yuanboonlim W, Siripornnoppakhun W, Niamnont N, Rashatasakhon P, Vilaivan T, Sukwattanasinitt M. Phenylene-ethynylene trication as an efficient fluorescent signal transducer in an aptasensor for potassium ion. Biosens Bioelectron 2011; 33:17-22. [PMID: 22244670 DOI: 10.1016/j.bios.2011.11.049] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 11/25/2011] [Accepted: 11/29/2011] [Indexed: 01/31/2023]
Abstract
A tricationic phenylene-ethynylene (N(3+)) fluorophore is investigated as a fluorescent transducer in homogeneous aptasensing system for potassium ion (K(+)) assay in aqueous media. The enhancement of the fluorescent signal of N(3+) by three K(+) aptamers consisting of 12, 15, and 21 nucleotides are observed and used for the determination of N(3+)-aptamer binding affinities. The binding affinities increase with the length of the aptameric oligonucleotides and are proven to be important to the sensitivity and selectivity of the aptasensors. The enhanced fluorescent signal of each N(3+)-aptamer solution is selectively quenched by K(+) due to the ability of K(+) in stabilizing the G-quadruplex structure of the aptamer. Among three aptamers, the 15-base aptamer provides optimal sensitivity and selectivity over other ions such as Li(+), Na(+), NH(4)(+), Mg(2+), Ca(2+) and Sr(2+). The sensing system shows the detection limit of 1 μM of K(+) in clean buffered solution and 30 μM of K(+) in the solution containing 4800-fold excess of Na(+), with wide linear dynamic ranges of micro- to millimolar concentration. This label-free fluorescence aptasensor is conveniently and effectively applicable for analysis of K(+) in urine samples.
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Affiliation(s)
- Wannapa Yuanboonlim
- Center for Petroleum, Petrochemicals and Advanced Materials, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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Kiy MM, Jacobi ZE, Liu J. Metal-induced specific and nonspecific oligonucleotide folding studied by FRET and related biophysical and bioanalytical implications. Chemistry 2011; 18:1202-8. [PMID: 22180064 DOI: 10.1002/chem.201102515] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2011] [Indexed: 01/12/2023]
Abstract
Metal induced nucleic acid folding has been extensively studied with ribozymes, DNAzymes, tRNA and riboswitches. These RNA/DNA molecules usually have a high content of double-stranded regions to support a rigid scaffold. On the other hand, such rigid structural features are not available for many in vitro selected or rationally designed DNA aptamers; they adopt flexible random coil structures in the absence of target molecules. Upon target binding, these aptamers adaptively fold into a compact structure with a reduced end-to-end distance, making fluorescence resonance energy transfer (FRET) a popular signaling mechanism. However, nonspecific folding induced by mono- or divalent metal ions can also reduce the end-to-end distance and thus lead to false positive results. In this study we used a FRET pair labeled Hg(II) binding DNA and monitored metal-induced folding in the presence of various cations. While nonspecific electrostatically mediated folding can be very significant, at each tested salt condition, Hg(II) induced folding was still observed with a similar sensitivity. We also studied the biophysical meaning of the acceptor/donor fluorescence ratio that allowed us to explain the experimental observations. Potential solutions for this ionic strength problem have been discussed. For example, probes designed to signal the formation of double-stranded DNA showed a lower dependency on ionic strength.
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Affiliation(s)
- Mehmet Murat Kiy
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
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34
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Liu Y, Li B, Cheng D, Duan X. Simple and sensitive fluorescence sensor for detection of potassium ion in the presence of high concentration of sodium ion using berberine–G-quadruplex complex as sensing element. Microchem J 2011. [DOI: 10.1016/j.microc.2011.07.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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35
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Gray RD, Chaires JB. Analysis of multidimensional G-quadruplex melting curves. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2011; Chapter 17:Unit17.4. [PMID: 21638271 PMCID: PMC3398426 DOI: 10.1002/0471142700.nc1704s45] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Multidimensional "3D" melting curves for G-quadruplexes are obtained by recording whole spectra (absorbance, CD, fluorescence) as a function of temperature, rather than the common approach of recording the spectral response to temperature at a single wavelength. 3D melting curves are richer in information, and can be used to enumerate the number of significant species and intermediate states required to properly analyze the thermal denaturation reaction to obtain thermodynamic information. This unit describes the application of the method of singular value decomposition to the analysis of 3D melting data obtained for G-quadruplex structures, and how the results of such an analysis can be used to provide a more complete characterization of the mechanism of quadruplex unfolding.
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Affiliation(s)
- Robert D Gray
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, USA
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36
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Ma C, Huang H, Zhao C. An aptamer-based and pyrene-labeled fluorescent biosensor for homogeneous detection of potassium ions. ANAL SCI 2011; 26:1261-4. [PMID: 21157094 DOI: 10.2116/analsci.26.1261] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A simple and homogeneous method based on aptamer and pyrene moieties for the detection of K(+) was developed. The aptamer was labeled by pyrene moiety at 3' end as the molecular recognition element. In the presence of K(+), the complementary oligonucleotide labeled by pyrene moiety at 5' end was displaced from the aptamer, which was accompanied by a dramatic decrease of the excimer fluorescence of pyrene. However, the excimer fluorescence remains in the absence of the target. With optimum conditions, relative changes of the pyrene excimer fluorescence intensity were proportional to the concentrations of K(+) in the range of 6.3 × 10(-4) to 1.0 × 10(-2) M with a detection limit of 5.0 × 10(-4) M. Importantly, in the presence of Na(+), NH(4)(+), Mg(2+) and Ca(2+) cations of biological fluids, this method was able to detect K(+) with high selectivity. In a word, the assay seems to have great potential applications, especially in biological fluids due to its simplicity, specificity and homogeneous detection.
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Affiliation(s)
- Cuiping Ma
- Key Laboratory of Eco-chemical Engineering, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, P. R. China.
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37
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Juskowiak B. Nucleic acid-based fluorescent probes and their analytical potential. Anal Bioanal Chem 2011; 399:3157-76. [PMID: 21046088 PMCID: PMC3044240 DOI: 10.1007/s00216-010-4304-5] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 10/04/2010] [Accepted: 10/05/2010] [Indexed: 12/21/2022]
Abstract
It is well known that nucleic acids play an essential role in living organisms because they store and transmit genetic information and use that information to direct the synthesis of proteins. However, less is known about the ability of nucleic acids to bind specific ligands and the application of oligonucleotides as molecular probes or biosensors. Oligonucleotide probes are single-stranded nucleic acid fragments that can be tailored to have high specificity and affinity for different targets including nucleic acids, proteins, small molecules, and ions. One can divide oligonucleotide-based probes into two main categories: hybridization probes that are based on the formation of complementary base-pairs, and aptamer probes that exploit selective recognition of nonnucleic acid analytes and may be compared with immunosensors. Design and construction of hybridization and aptamer probes are similar. Typically, oligonucleotide (DNA, RNA) with predefined base sequence and length is modified by covalent attachment of reporter groups (one or more fluorophores in fluorescence-based probes). The fluorescent labels act as transducers that transform biorecognition (hybridization, ligand binding) into a fluorescence signal. Fluorescent labels have several advantages, for example high sensitivity and multiple transduction approaches (fluorescence quenching or enhancement, fluorescence anisotropy, fluorescence lifetime, fluorescence resonance energy transfer (FRET), and excimer-monomer light switching). These multiple signaling options combined with the design flexibility of the recognition element (DNA, RNA, PNA, LNA) and various labeling strategies contribute to development of numerous selective and sensitive bioassays. This review covers fundamentals of the design and engineering of oligonucleotide probes, describes typical construction approaches, and discusses examples of probes used both in hybridization studies and in aptamer-based assays.
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Affiliation(s)
- Bernard Juskowiak
- Faculty of Chemistry, A. Mickiewicz University, Grunwaldzka 6, 60-780 Poznan, Poland.
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38
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TAKENAKA S, JUSKOWIAK B. Fluorescence Detection of Potassium Ion Using the G-Quadruplex Structure. ANAL SCI 2011; 27:1167-72. [DOI: 10.2116/analsci.27.1167] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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39
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Qin H, Ren J, Wang J, Luedtke NW, Wang E. G-Quadruplex-Modulated Fluorescence Detection of Potassium in the Presence of a 3500-Fold Excess of Sodium Ions. Anal Chem 2010; 82:8356-60. [DOI: 10.1021/ac101894b] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Haixia Qin
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China and Graduate School of the Chinese Academy of Sciences, Beijing, 100039, China, and Institute of Organic Chemistry, University of Zürich, Winterthurerstrasse 190, Zurich, CH-8057, Switzerland
| | - Jiangtao Ren
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China and Graduate School of the Chinese Academy of Sciences, Beijing, 100039, China, and Institute of Organic Chemistry, University of Zürich, Winterthurerstrasse 190, Zurich, CH-8057, Switzerland
| | - Jiahai Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China and Graduate School of the Chinese Academy of Sciences, Beijing, 100039, China, and Institute of Organic Chemistry, University of Zürich, Winterthurerstrasse 190, Zurich, CH-8057, Switzerland
| | - Nathan W. Luedtke
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China and Graduate School of the Chinese Academy of Sciences, Beijing, 100039, China, and Institute of Organic Chemistry, University of Zürich, Winterthurerstrasse 190, Zurich, CH-8057, Switzerland
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China and Graduate School of the Chinese Academy of Sciences, Beijing, 100039, China, and Institute of Organic Chemistry, University of Zürich, Winterthurerstrasse 190, Zurich, CH-8057, Switzerland
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Dembska A, Juskowiak B. The fluorescence properties and lifetime study of G-quadruplexes single- and double-labeled with pyrene. J Fluoresc 2010; 20:1029-35. [PMID: 20358281 DOI: 10.1007/s10895-010-0653-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Accepted: 03/24/2010] [Indexed: 10/19/2022]
Abstract
We report steady state fluorescence and lifetime emission studies of d(GGTTGGTGTGGTTGG) (TBA) and d(GGGTTAGGGTTAGGGTTAGGG) (Htelom) oligonucleotides labeled with pyrene through a 3-aminopropyl linker. Such G-rich sequences are able to self-assemble into G-quadruplexes, especially in the presence of specific cations like potassium. A comparative studies with single- and double-labeled G-quadruplexes were carried out. For each probe we have measured fluorescence decays for emission wavelength of 390 and 480 nm in the varying concentration of potassium ion. We have calculated average lifetimes <τ> for every system as well as the fractional distribution α(i) of emitting species.
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Affiliation(s)
- Anna Dembska
- Department of Chemistry, A.Mickiewicz University, Grunwaldzka 6, 60-780, Poznan, Poland
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41
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Shi C, Gu H, Ma C. An aptamer-based fluorescent biosensor for potassium ion detection using a pyrene-labeled molecular beacon. Anal Biochem 2010; 400:99-102. [PMID: 20056100 DOI: 10.1016/j.ab.2009.12.034] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2009] [Revised: 12/16/2009] [Accepted: 12/18/2009] [Indexed: 11/28/2022]
Abstract
A novel and sensitive biosensor based on aptamer and pyrene-labeled fluorescent probes for the determination of K+ was developed. The aptamer was used as a molecular recognition element and a partially complementary oligonucleotide with the aptamer was labeled by pyrene moieties at both ends to transduce the binding event of K+ with aptamer. In the presence of K+, the complementary oligonucleotides were displaced from aptamers, which was accompanied by excimer fluorescence of pyrenes because the self-hairpin structure of the complementary oligonucleotide brought pyrene moieties into close proximity. However, it gave only monomer emission in the absence of K+. Under optimum conditions, the relative fluorescence intensity of pyrene was proportional to the concentration of K+ in the range of 6.0 x 10(-4) to 2.0 x 10(-2) M. A detection limit of 4.0 x 10(-4) M was achieved. Moreover, this method was able to detect K+ with high selectivity in the presence of Na+, NH4+, Mg2+, and Ca2+ ions of biological fluids. In brief, the assay may have great potential applications, especially in a biological environment because of its simplicity, sensitivity, and specificity.
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Affiliation(s)
- Chao Shi
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing 210009, People's Republic of China
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42
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Yang X, Liu D, Lu P, Zhang Y, Yu C. Nucleic acid G-quadruplex based label-free fluorescence turn-on potassium selective sensing. Analyst 2010; 135:2074-8. [DOI: 10.1039/c0an00106f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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43
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Kong DM, Guo JH, Yang W, Ma YE, Shen HX. Crystal violet-G-quadruplex complexes as fluorescent sensors for homogeneous detection of potassium ion. Biosens Bioelectron 2009; 25:88-93. [PMID: 19559594 DOI: 10.1016/j.bios.2009.06.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2009] [Revised: 06/01/2009] [Accepted: 06/02/2009] [Indexed: 12/18/2022]
Abstract
A novel K(+) detection method was reported using a label-free G-quadruplex-forming oligonucleotide and a triphenylmethane fluorescent dye crystal violet (CV). This method is based on the fluorescence difference of some CV/G-quadruplex complexes in the presence of K(+) or Na(+), and the fluorescence change with the variation of K(+) concentration. According to the nature of the fluorescence change of CV as a function of ionic conditions, two K(+) detection modes can be developed. One is a fluorescence-decreasing mode, in which T(3)TT(3) (5'-GGGTTTGGGTGGGTTTGGG) is used, and the fluorescence of CV decreases with an increased concentration of K(+). The other is a fluorescence-increasing mode, in which Hum21 (5'-GGGTTAGGGTTAGGGTTAGGG) is used, and the fluorescence of CV increases with an increased concentration of K(+). Compared with some published K(+) detection methods, this method has some important characteristics, such as lower cost of the test, higher concentrations of Na(+) that can be tolerated, adjustable linear detection range and longer excitation and emission wavelengths. Preliminary results demonstrated that the method might be used in biological systems, for example in urine.
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Affiliation(s)
- De-Ming Kong
- Key Laboratory of Functional Polymer Materials (Nankai University), Ministry of Education, Nankai University, Tianjin 300071, PR China.
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Affiliation(s)
- Juewen Liu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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45
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Franceschin M. G‐Quadruplex DNA Structures and Organic Chemistry: More Than One Connection. European J Org Chem 2009. [DOI: 10.1002/ejoc.200801196] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Marco Franceschin
- Dipartimento di Chimica, Sapienza – Università di Roma, Piazzale A. Moro 5, 00185 Roma, Italy, Fax: +39‐06‐4991‐3841
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46
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Chen B, Liang J, Tian X, Liu X. G-quadruplex structure: a target for anticancer therapy and a probe for detection of potassium. BIOCHEMISTRY (MOSCOW) 2008; 73:853-61. [PMID: 18774931 DOI: 10.1134/s0006297908080026] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
G-Quadruplexes are four-stranded DNA structures that play important regulatory roles in the maintenance of telomere length by inhibiting telomerase activity. Telomeres are specialized functional DNA-protein structures consisting of a variable number of tandem G-rich repeats together with a group of specific proteins. Telomere losses during cell replication are compensated by telomerase, which adds telomeric repeats onto the chromosome ends in the presence of its substrate--the 3'-overhang. Recently, quadruplexes have been considered as a potential therapeutic target for human cancer because they can inhibit telomerase activity, and some quadruplex-interacting drugs can induce senescence and apoptosis of cancer cells. In addition, due to the potassium preference to the other cations, especially sodium ions, quadruplexes have been suggested for developing potassium detection probes with higher sensitivity and selectivity. This review will illustrate these two aspects to provide further understanding of G-quadruplex structures.
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Affiliation(s)
- Bo Chen
- Bioengineering Institute of Life Science Department, Zhejiang Sci-Tech University, Hangzhou, China
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Hayashida H, Paczesny J, Juskowiak B, Takenaka S. Interactions of sodium and potassium ions with oligonucleotides carrying human telomeric sequence and pyrene moieties at both termini. Bioorg Med Chem 2008; 16:9871-81. [PMID: 18851918 DOI: 10.1016/j.bmc.2008.08.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2008] [Revised: 08/09/2008] [Accepted: 08/14/2008] [Indexed: 10/21/2022]
Abstract
The organization of human telomeric DNA is of intense interest because of its role in aging, cancer research and bioanalytical applications. The Htelom sequence 5'-G(3)(T(2)AG(3))(3)-3' has been use to prepare two pyrene-modified fluorescence probes with three- and six-carbon linkers: Py-Htelom-Py(C3) and Py-Htelom-Py(C6), respectively. Results of the circular dichroism (CD), native PAGE, steady-state fluorescence, and anisotropy measurements of sodium and potassium quadruplex formation by these pyrene-modified conjugates are presented and discussed in order to clarify which conformation facilitates or renders the pyrene/pyrene or G-tetrad/pyrene stacking interaction. The CD spectra and native PAGE images suggested that conjugation of pyrene moieties has negligible effect on the folding properties of Htelom oligonucleotide. CD melting profiles and thermodynamic parameters revealed that both sodium and potassium quadruplexes are stabilized by the anchoring of pyrene tags with potassium ion being more effective than its sodium counterpart. Monomer emission of pyrene dominated in all investigated systems with fluorescence intensity being sensitive to the nature and concentration of cation and this phenomenon was attributed to the quenching processes and to the particular topologies of sodium and potassium quadruplexes. Strong quenching observed in the presence of KCl was attributed to the peculiarity of the potassium hybrid-type quadruplex, which enables effective stacking of pyrene moieties on the exposed guanine tetrads, thus facilitating static or electron transfer quenching. Plausibility of stacking interactions between pyrene and G-tetrad in a hybrid-type potassium quadruplex was further supported by the anisotropy measurements and molecular modeling results.
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Affiliation(s)
- Hirohisa Hayashida
- Department of Applied Chemistry, Faculty of Engineering, Kyushu Institute of Technology, Kitakyushu-shi 804-8550, Japan
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48
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Rapid determination of total hardness in water using fluorescent molecular aptamer beacon. Anal Chim Acta 2008; 610:105-11. [DOI: 10.1016/j.aca.2008.01.031] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2007] [Revised: 12/30/2007] [Accepted: 01/05/2008] [Indexed: 11/15/2022]
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49
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Centi S, Messina G, Tombelli S, Palchetti I, Mascini M. Different approaches for the detection of thrombin by an electrochemical aptamer-based assay coupled to magnetic beads. Biosens Bioelectron 2008; 23:1602-9. [PMID: 18313283 DOI: 10.1016/j.bios.2008.01.020] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Accepted: 01/18/2008] [Indexed: 11/17/2022]
Abstract
Different assay formats based on the coupling of magnetic beads with electrochemical transduction were compared here for the detection of thrombin by using a thrombin specific aptamer. By using the thrombin-binding aptamer, a direct and an indirect competitive assay for thrombin have been developed by immobilising the aptamer or the protein, respectively. Moreover, another strategy was based on the direct measurement of the enzymatic product of thrombin captured by the immobilised aptamer. All the assays were developed by coupling the electrochemical transduction with the innovative and advantageous use of magnetic beads. The assays based on the immobilisation of the protein were not successful since no binding was recorded between thrombin and its aptamer. With the direct competitive assay, when the aptamer was immobilised onto the magnetic beads, a detection limit of 430nM for thrombin was achieved. A lower detection limit for the protein (175nM) was instead obtained by detecting the product of the enzymatic reaction catalysed by thrombin. All these assays were finally compared with a sandwich assay which reached a detection limit of 0.45nM of thrombin demonstrating the best analytical performances. With this comparison the importance of a deep study on the different analytical approaches for thrombin detection to reach the performances of the best assay configuration has been demonstrated.
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Affiliation(s)
- S Centi
- Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
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50
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Huang CC, Chang HT. Aptamer-based fluorescence sensor for rapid detection of potassium ions in urine. Chem Commun (Camb) 2008:1461-3. [PMID: 18338056 DOI: 10.1039/b718752a] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We unveil a new homogeneous assay-using OliGreen and an ATP-binding aptamer-for the highly selective and sensitive detection of potassium ions.
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Affiliation(s)
- Chih-Ching Huang
- Department of Chemistry, National Taiwan University, Taipei, Taiwan.
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