101
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Yao W, Wang L, Wang H, Zhang X, Li L. An aptamer-based electrochemiluminescent biosensor for ATP detection. Biosens Bioelectron 2009; 24:3269-74. [PMID: 19443209 DOI: 10.1016/j.bios.2009.04.016] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2009] [Revised: 03/26/2009] [Accepted: 04/09/2009] [Indexed: 10/20/2022]
Abstract
An aptamer-based electrochemiluminescent (ECL-AB) biosensor for ATP detection with high sensitivity and specificity was developed. The biosensor was assembled based on several steps. First, a complementary DNA (cDNA) of the ATP-binding aptamer, which has six complementary bases at both its ends, was hybridized with the aptamer molecule to form a rigid, linear double-stranded DNA (ds-DNA). The ds-DNA was then labeled with a ruthenium complex at the 3' terminus of cDNA, followed by the immobilization of this ds-DNA onto Au electrode surface through the 5'-HS on the cDNA. In the presence of ATP, due to the ATP binding to the aptamer, the aptamer molecules dissociated from the ds-DNA complex, which resulted in the formation of stem-loop structure of the single-stranded cDNA and led to the increase of the ECL signal. The increased ECL intensity was found linearly to the logarithm of the concentration of ATP ranging from 0.05 nM to 10 nM with a detection limit of 0.02 nM. Different from other ECL-AB biosensors with aptamers as the probes, this sensing system proposed here is based on the utilization of the cDNA of aptamers as the probes for ECL sensing. Therefore, such sensing system could provide a promising label-free and more readily regenerated model for aptamer-based small-molecules detection.
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Affiliation(s)
- Wu Yao
- Anhui Key Laboratory of Chemo-Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, PR China
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102
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He JL, Wu ZS, Zhang SB, Shen GL, Yu RQ. Novel fluorescence enhancement IgE assay using a DNA aptamer. Analyst 2009; 134:1003-7. [PMID: 19381397 DOI: 10.1039/b812450g] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper, we demonstrate a fluorescence immunoglobulin E (IgE) assay probe based on a DNA aptamer. A Texas red-labeled short DNA strand (T-DNA) complementary with part of the IgE aptamer sequence was used to produce the fluorescence enhancement effected upon the binding of IgE to the aptamer. Another short DNA strand labeled with dabcyl quencher (Q-DNA) complementary with part of the aptamer sequence nearby the T-DNA location was used to lower the background fluorescence. The IgE can be detected in the concentration range from 9.2 x 10(-11) to 3.7 x 10(-8) mol L(-1) with a detection limit of 5.7 x 10(-11) mol L(-1).
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Affiliation(s)
- Jing-Lin He
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China.
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103
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Song Y, Zhao C, Ren J, Qu X. Rapid and ultra-sensitive detection of AMP using a fluorescent and magnetic nano-silica sandwich complex. Chem Commun (Camb) 2009:1975-7. [PMID: 19333462 DOI: 10.1039/b818415a] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We report here a novel AMP biosensor based on the aptamer-induced disassembly of fluorescent and magnetic nano-silica sandwich complexes with a direct detection limit of 0.1 microM.
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Affiliation(s)
- Yujun Song
- Division of Biological Inorganic Chemistry, State Key Laboratory of Rare Earth Resource Utilization, Graduate School of the Chinese Academy of Sciences, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
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104
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Wang K, Tang Z, Yang C, Kim Y, Fang X, Li W, Wu Y, Medley C, Cao Z, Li J, Colon P, Lin H, Tan W. Molekulartechnische DNA-Modifizierung: Molecular Beacons. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200800370] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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105
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Wang K, Tang Z, Yang CJ, Kim Y, Fang X, Li W, Wu Y, Medley CD, Cao Z, Li J, Colon P, Lin H, Tan W. Molecular engineering of DNA: molecular beacons. Angew Chem Int Ed Engl 2009; 48:856-70. [PMID: 19065690 PMCID: PMC2772660 DOI: 10.1002/anie.200800370] [Citation(s) in RCA: 492] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Molecular beacons (MBs) are specifically designed DNA hairpin structures that are widely used as fluorescent probes. Applications of MBs range from genetic screening, biosensor development, biochip construction, and the detection of single-nucleotide polymorphisms to mRNA monitoring in living cells. The inherent signal-transduction mechanism of MBs enables the analysis of target oligonucleotides without the separation of unbound probes. The MB stem-loop structure holds the fluorescence-donor and fluorescence-acceptor moieties in close proximity to one another, which results in resonant energy transfer. A spontaneous conformation change occurs upon hybridization to separate the two moieties and restore the fluorescence of the donor. Recent research has focused on the improvement of probe composition, intracellular gene quantitation, protein-DNA interaction studies, and protein recognition.
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Affiliation(s)
- Kemin Wang
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (P.R. China)
| | - Zhiwen Tang
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Chaoyong James Yang
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005 (P.R. China)
| | - Youngmi Kim
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Xiaohong Fang
- Institute of Chemistry, Chinese Academy of Sciences 2 Zhongguancun Beiyijie, Beijing 100190 (P.R. China)
| | - Wei Li
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (P.R. China)
| | - Yanrong Wu
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Colin D. Medley
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Zehui Cao
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Jun Li
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (P.R. China)
| | - Patrick Colon
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Hui Lin
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Weihong Tan
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (P.R. China)
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106
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Cho EJ, Lee JW, Ellington AD. Applications of aptamers as sensors. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2009; 2:241-64. [PMID: 20636061 DOI: 10.1146/annurev.anchem.1.031207.112851] [Citation(s) in RCA: 572] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Aptamers are ligand-binding nucleic acids whose affinities and selectivities can rival those of antibodies. They have been adapted to analytical applications not only as alternatives to antibodies, but as unique reagents in their own right. In particular, aptamers can be readily site-specifically modified during chemical or enzymatic synthesis to incorporate particular reporters, linkers, or other moieties. Also, aptamer secondary structures can be engineered to undergo analyte-dependent conformational changes, which, in concert with the ability to specifically place chemical agents, opens up a wealth of possible signal transduction schemas, irrespective of whether the detection modality is optical, electrochemical, or mass based. Finally, because aptamers are nucleic acids, they are readily adapted to sequence- (and hence signal-) amplification methods. However, application of aptamers without a basic knowledge of their biochemistry or technical requirements can cause serious analytical difficulties.
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Affiliation(s)
- Eun Jeong Cho
- The Institute for Drug and Diagnostic Development, University of Texas at Austin, Austin, Texas 78712, USA.
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107
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Pai S, Roberts A, Ellington AD. Aptamer amplification: divide and signal. ACTA ACUST UNITED AC 2008; 2:1333-46. [DOI: 10.1517/17530050802562016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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108
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A electrochemiluminescence aptasensor for detection of thrombin incorporating the capture aptamer labeled with gold nanoparticles immobilized onto the thio-silanized ITO electrode. Anal Chim Acta 2008. [DOI: 10.1016/j.aca.2008.08.041] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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109
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Abstract
This article provides an overview of principles and barriers relevant to intracellular drug and gene transport, accumulation and retention (collectively called as drug delivery) by means of nanovehicles (NV). The aim is to deliver a cargo to a particular intracellular site, if possible, to exert a local action. Some of the principles discussed in this article apply to noncolloidal drugs that are not permeable to the plasma membrane or to the blood-brain barrier. NV are defined as a wide range of nanosized particles leading to colloidal objects which are capable of entering cells and tissues and delivering a cargo intracelullarly. Different localization and targeting means are discussed. Limited discussion on pharmacokinetics and pharmacodynamics is also presented. NVs are contrasted to micro-delivery and current nanotechnologies which are already in commercial use. Newer developments in NV technologies are outlined and future applications are stressed. We also briefly review the existing modeling tools and approaches to quantitatively describe the behavior of targeted NV within the vascular and tumor compartments, an area of particular importance. While we list "elementary" phenomena related to different level of complexity of delivery to cancer, we also stress importance of multi-scale modeling and bottom-up systems biology approach.
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Affiliation(s)
- Ales Prokop
- Department of Chemical Engineering, 24th Avenue & Garland Avenues, 107 Olin Hall, Vanderbilt University, Nashville, Tennessee 37235, USA.
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110
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Hasegawa T, Hagihara M, Fukuda M, Nakano S, Fujieda N, Morii T. Context-dependent fluorescence detection of a phosphorylated tyrosine residue by a ribonucleopeptide. J Am Chem Soc 2008; 130:8804-12. [PMID: 18597435 DOI: 10.1021/ja801734f] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tools for selective recognition and sensing of specific phosphorylated tyrosine residues on the protein surface are essential for understanding signal transduction cascades in the cell. A stable complex of RNA and peptide, a ribonucleopeptide (RNP), provides effective approaches to tailor RNP receptors and fluorescent RNP sensors for small molecules. In vitro selection of an RNA-derived pool of RNP afforded RNP receptors specific for a phosphotyrosine residue within a defined amino-acid sequence Gly-Tyr-Ser-Arg. The RNP receptor for the specific phosphotyrosine residue was successfully converted to a fluorescent RNP sensor for sequence-specific recognition of a phosphorylated tyrosine by screening a pool of fluorescent phosphotyrosine-binding RNPs generated by a combination of the RNA subunits of phosphotyrosine-binding RNPs and various fluorophore-modified peptide subunits. The phosphotyrosine-binding RNP receptor and fluorescent RNP sensor constructed from the RNP receptor not only discriminated phosphotyrosine against tyrosine, phosphoserine, or phosphothreonine, but also showed specific recognition of amino acid residues surrounding the phosphotyrosine residue. A fluorescent RNP sensor for one of the tyrosine phosphorylation sites of p100 coactivator showed a binding affinity to the target site ~95-fold higher than the other tyrosine phosphorylation site. The fluorescent RNP sensor has an ability to function as a specific fluorescent sensor for the phosphorylated tyrosine residue within a defined amino-acid sequence in HeLa cell extracts.
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Affiliation(s)
- Tetsuya Hasegawa
- Institute of Advanced Energy, Institute of Sustainability Science, and Pioneering Research Unit for Next Generation, Kyoto University, Uji, Kyoto 611-0011, Japan
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111
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Phillips JA, Lopez-Colon D, Zhu Z, Xu Y, Tan W. Applications of aptamers in cancer cell biology. Anal Chim Acta 2008; 621:101-8. [PMID: 18573375 DOI: 10.1016/j.aca.2008.05.031] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Revised: 05/05/2008] [Accepted: 05/06/2008] [Indexed: 01/10/2023]
Abstract
Identifying cells associated with specific disease states is critically important for the early detection and diagnosis of cancer. To facilitate this task, molecular probes, which bind biomarkers that are either specifically or differentially expressed in diseased cells relative to healthy cells, provide a simple and effective method. This review focuses on the use of DNA aptamers as molecular probes for cancer cells. These aptamers are created by means of the cell-based Systematic Evolution of Ligands by EXponential enrichment (SELEX) process, which uses whole disease cells as targets. We describe at length the steps of the cell-SELEX process and discuss several applications for the aptamers, including profiling leukemia patient samples and discovering cell-surface cancer biomarkers. We conclude with a discussion of an aptamer-conjugated nanoparticle enrichment and detection scheme.
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Affiliation(s)
- Joseph A Phillips
- Center for Research at the Bio/Nano Interface, Department of Chemistry, Shands Cancer Center, University of Florida Genetics Institute, and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, USA
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112
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Real-time PCR detection of protein analytes with conformation-switching aptamers. Anal Biochem 2008; 380:164-73. [PMID: 18541130 DOI: 10.1016/j.ab.2008.05.018] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Revised: 05/12/2008] [Accepted: 05/13/2008] [Indexed: 11/23/2022]
Abstract
We have developed a novel method that uses conformation-switching aptamers for real-time PCR analysis of protein analytes. The aptamers have been designed so that they assume one secondary structure in the absence of a protein analyte and a different secondary structure in the presence of a protein such as thrombin or platelet-derived growth factor (PDGF). The protein-bound structure in turn assembles a ligation junction for the addition of a real-time PCR primer. Protein concentrations could be specifically detected into the picomolar range, even in the presence of cell lysates. The method has advantages relative to both immunoPCR (because no signal is produced by background binding) and the proximity ligation assay (PLA) (because only one epitope, rather than two epitopes, on a protein surface must be bound).
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113
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Cho M, Kim Y, Han SY, Min K, Rahman MA, Shim YB, Ban C. Detection for folding of the thrombin binding aptamer using label-free electrochemical methods. BMB Rep 2008; 41:126-31. [PMID: 18315948 DOI: 10.5483/bmbrep.2008.41.2.126] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The folding of aptamer immobilized on an Au electrode was successfully detected using label-free electrochemical methods. A thrombin binding DNA aptamer was used as a model system in the presence of various monovalent cations. Impedance spectra showed that the extent to which monovalent cations assist in folding of aptamer is ordered as K(+) > NH(4)(+) > Na(+) > Cs(+). Our XPS analysis also showed that K(+) and NH(4)(+) caused a conformational change of the aptamer in which it forms a stable complex with these monovalent ions. Impedance results for the interaction between aptamer and thrombin indicated that thrombin interacts more with folded aptamer than with unfolded aptamer. The EQCM technique provided a quantitative analysis of these results. In particular, the present impedance results showed that thrombin participates a folding of aptamer to some extent, and XPS analysis confirmed that thrombin stabilizes and induces the folding of aptamer.
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Affiliation(s)
- Minseon Cho
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Korea
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114
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Feng K, Kang Y, Zhao JJ, Liu YL, Jiang JH, Shen GL, Yu RQ. Electrochemical immunosensor with aptamer-based enzymatic amplification. Anal Biochem 2008; 378:38-42. [PMID: 18423388 DOI: 10.1016/j.ab.2008.03.047] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2008] [Revised: 03/21/2008] [Accepted: 03/28/2008] [Indexed: 10/22/2022]
Abstract
An electrochemical immunosensor is reported by using aptamer-based enzymatic amplification with immunoglobulin E (IgE) as the model analyte. In this method, the IgE antibody is covalently immobilized as the capture probe on the gold electrode via a self-assembled monolayer of cysteamine. After the target is captured, the biotinylated anti-IgE aptamer is used as the detection probe. The specific interaction of streptavidin-conjugated alkaline phosphatase to the surface-bound biotinylated detection probe mediates a catalytic reaction of ascorbic acid 2-phosphate substrate to produce a reducing agent ascorbic acid. Then silver ions in the solution can be reduced, leading to the deposition of metallic silver on the electrode surface. The amount of deposited silver, which is determined by the amount of IgE target bound on the electrode surface, can be quantified using the stripping voltammetry. The results obtained demonstrated that the electrochemical immunosensor possesses high specificity and a wide dynamic range with a low detection limit that possibly arises from the combination of the highly specific aptamer and the highly sensitive stripping determination of enzymatically deposited silver.
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Affiliation(s)
- Kejun Feng
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People's Republic of China
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115
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Degefa TH, Kwak J. Label-free aptasensor for platelet-derived growth factor (PDGF) protein. Anal Chim Acta 2008; 613:163-8. [PMID: 18395055 DOI: 10.1016/j.aca.2008.03.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2008] [Revised: 03/03/2008] [Accepted: 03/05/2008] [Indexed: 11/19/2022]
Abstract
A label-free aptasensor for platelet-derived growth factor (PDGF) protein is reported. The aptasensor uses mixed self-assembled monolayers (SAMs) composed of a thiol-modified PDGF binding aptamer and 6-mercaptohexanol (MCH) on a gold electrode. The SAMs were characterized by cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS), and differential pulse voltammetry (DPV) before and after binding of the protein using [Fe(CN)(6)](3-/4-), a redox marker ion as an indicator for the formation of a protein-aptamer complex. The CVs at the PDGF modified electrode showed significant differences, such as changes in the peak currents and peak-to-peak separation, before and after binding of the target protein. The EIS spectra, in the form of Nyquist plots, were analyzed with a Randles circuit while the electron transfer resistance R(ct) was used to monitor the binding of the target protein. The results showed that, without any modification to the aptamer, the target protein can be recognized effectively at the PDGF binding aptamer SAMs at the electrode surface. Control experiments using non-binding oligonucleotides assembled at the electrode surfaces also confirmed the results and showed that there was no formation of an aptamer-protein complex. The DPV signal at the aptamer functionalized electrode showed a linearly decreased marker ion peak current in a protein concentrations range of 1-40 nM. Thus, label-free detection of PDGF protein at an aptamer modified electrode has been demonstrated.
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Affiliation(s)
- Tesfaye Hailu Degefa
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea
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116
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A simple and direct electrochemical detection of interferon-gamma using its RNA and DNA aptamers. Biosens Bioelectron 2008; 23:1819-24. [PMID: 18406597 DOI: 10.1016/j.bios.2008.02.021] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2007] [Revised: 02/25/2008] [Accepted: 02/25/2008] [Indexed: 11/21/2022]
Abstract
Tuberculosis is the most frequent cause of infection-related death worldwide. We constructed a simple and direct electrochemical sensor to detect interferon (IFN)-gamma, a selective marker for tuberculosis pleurisy, using its RNA and DNA aptamers. IFN-gamma was detected by its 5'-thiol-modified aptamer probe immobilized on the gold electrode. Interaction between IFN-gamma and the aptamer was recorded using electrochemical impedance spectroscopy and quartz crystal microbalance (QCM) with high sensitivity. The RNA-aptamer-based sensor showed a low detection limit of 100 fM, and the DNA-aptamer-based sensor detected IFN-gamma to 1 pM in sodium phosphate buffer. With QCM analysis, the aptamer immobilized on the electrode and IFN-gamma bound to the aptamer probe was quantified. This QCM result shows that IFN-gamma exists in multimeric forms to interact with the aptamers, and the RNA aptamer prefers the high multimeric state of IFN-gamma. Such a preference may describe the low detection limit of the RNA aptamer shown by impedance analysis. In addition, IFN-gamma was detected to 10 pM by the DNA aptamer in fetal bovine serum, a mimicked biological system, which has similar components to pleural fluid.
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117
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Medley CD, Smith JE, Tang Z, Wu Y, Bamrungsap S, Tan W. Gold nanoparticle-based colorimetric assay for the direct detection of cancerous cells. Anal Chem 2008; 80:1067-72. [PMID: 18198894 DOI: 10.1021/ac702037y] [Citation(s) in RCA: 411] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Early and accurate detection of cancer often requires time-consuming techniques and expensive instrumentation. To address these limitations, we developed a colorimetric assay for the direct detection of diseased cells. The assay uses aptamer-conjugated gold nanoparticles to combine the selectivity and affinity of aptamers and the spectroscopic advantages of gold nanoparticles to allow for the sensitive detection of cancer cells. Samples with the target cells present exhibited a distinct color change while nontarget samples did not elicit any change in color. The assay also showed excellent sensitivity with both the naked eye and based on absorbance measurements. In addition, the assay was able to differentiate between different types of target and control cells based on the aptamer used in the assay indicating the wide applicability of the assay for diseased cell detection. On the basis of these qualities, aptamer-conjugated gold nanoparticles could become a powerful tool for point of care diagnostics.
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Affiliation(s)
- Colin D Medley
- Center for Research at the Bio/Nano Interface, Department of Chemistry and Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
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118
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Yigit MV, Mazumdar D, Kim HK, Lee JH, Odintsov B, Lu Y. Smart "turn-on" magnetic resonance contrast agents based on aptamer-functionalized superparamagnetic iron oxide nanoparticles. Chembiochem 2008; 8:1675-8. [PMID: 17696177 DOI: 10.1002/cbic.200700323] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mehmet Veysel Yigit
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 607 S. Mathews Avenue, Urbana, IL 61801, USA
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119
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Yigit MV, Mazumdar D, Lu Y. MRI detection of thrombin with aptamer functionalized superparamagnetic iron oxide nanoparticles. Bioconjug Chem 2008; 19:412-7. [PMID: 18173225 DOI: 10.1021/bc7003928] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Design of smart MRI contrast agent based on superparamagnetic iron oxide nanoparticles and aptamers has been described for the detection of human alpha-thrombin protein. The contrast agent is based on the assembly of the aptamer functionalized nanoparticles in the presence of thrombin. A detectable change in MRI signal is observed with 25 nM thrombin in human serum. Changes were neither observed with control analytes, streptavidin, or bovine serum albumin, nor with inactive aptamer functionalized nanoparticles.
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Affiliation(s)
- Mehmet Veysel Yigit
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA
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120
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Abstract
Real-time monitoring of DNA-protein interactions involving molecular beacon (MB) and molecular beacon aptamer (MBA) was discussed in this chapter. MBs are single-stranded oligonucleotide probes with a hairpin structure. MBs have been designed for oligonucleotide recognition and protein-DNA interaction studies. Real-time monitoring of enzymatic reactions, such as cleavage, ligation, and phosphorylation of single-stranded DNA by specific enzyme, has been studied using MBs. Meanwhile, a new generation of molecular probes, MBA, was designed by combining the excellent signal transduction properties of MBs with the specificity of aptamers for protein recognition. Two different aptamers, the one for thrombin and that for platelet-derived growth factor, have been successfully used to construct MBA probes. The interaction between the proteins and the MBA probes was investigated by fluorescence resonance energy transfer, fluorescence anisotropy, and time-resolved fluorescence. This chapter has reviewed our recent progress in this area.
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Affiliation(s)
- Jun Li
- Department of Chemistry, University of Florida, Gainesville, FL, USA
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121
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Parekh P, Martin J, Chen Y, Colon D, Wang H, Tan W. Using aptamers to study protein-protein interactions. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2008; 110:177-94. [PMID: 18677451 DOI: 10.1007/10_2008_104] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The emerging science of systems biology focuses on the systematic study of complex interactions in whole biological systems. A systemic, or integrative, methodology is employed as the chief means of discovering new properties and understanding the aggregate of processes that occur in a biological system. Accordingly, the Human Genome Project has provided a complete map of genes and resultant proteins corresponding to their function. Protein-protein interactions are important pieces of this biological tapestry, and understanding how they work cooperatively in a cell will result in a better understanding of the whole organism. To accomplish this objective, we report the use of DNA/RNA aptamers as a novel tool for the study and elucidation of protein-protein interactions, both in vivo and in vitro.
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Affiliation(s)
- Parag Parekh
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, FL 32611-7200, USA
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122
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Burrows SM, Pappas D. Measuring complexation by single-molecule fluorescence anisotropy. Analyst 2008; 133:870-3. [DOI: 10.1039/b800110c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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123
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Liao W, Cui XT. Reagentless aptamer based impedance biosensor for monitoring a neuro-inflammatory cytokine PDGF. Biosens Bioelectron 2007; 23:218-24. [PMID: 17512185 DOI: 10.1016/j.bios.2007.04.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2006] [Revised: 02/06/2007] [Accepted: 04/03/2007] [Indexed: 10/23/2022]
Abstract
Neural prostheses often suffer from undesired chronic inflammatory tissue response. This can lead to neuronal loss and formation of glial scar tissue, which would serve as a barrier to neural signal transduction. In situ monitoring of neuro-inflammatory cytokines may improve our understanding of device induced inflammatory responses. Furthermore, early detection of the onset and degree of inflammation and releasing drugs accordingly may lead to improved long term performance of such implanted devices. For this reason, biosensor applying aptamer as probe and non-faradic electrochemical impedance spectroscopy (NIS) as the detection method has been developed. Aptamers, certain kinds of DNA or RNA molecules which can bind variety of molecules at high specificity, have the overwhelming advantages over antibodies of low cost and ease of use. Platelet-derived growth factor BB (PDGF-BB), one of the important cytokines involved in neural inflammation, has been selected as our detection target. Binding of PDGF to its aptamer immobilized on the silicon electrode surface lead to a decrease in capacitance measured by NIS. A good linear relationship between the decrease of capacitance and the logarithm of protein concentration was obtained, which proves the feasibility of quantitative measurements. By sweeping the applied electrode potential of potentiostatic EIS, -0.1 V to +0.1 V was determined to be the optimal range for achieving best discrimination between specific target binding and non-specific protein adsorption on aptamer-modified silicon surface. Under such conditions, the specificity of the detection measured by the ratio of the positive to negative control is around 10:1 and the detection limit is approximately 1 microg/ml (40 nM). The online measurement result exhibited negligible response for non-specific adsorption but significant signal changes for the specific target. Since the non-faradic strategy does not require any reagent to be loaded when performing the test, together with the ability of online measurements, this biosensor design is promising for in vivo monitoring.
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Affiliation(s)
- Wei Liao
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA 15261, USA
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124
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Li YY, Zhang C, Li BS, Zhao LF, Li XB, Yang WJ, Xu SQ. Ultrasensitive densitometry detection of cytokines with nanoparticle-modified aptamers. Clin Chem 2007; 53:1061-6. [PMID: 17446332 DOI: 10.1373/clinchem.2006.082271] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND Aptamers mimic properties of antibodies and sometimes turn out to be even better than antibodies as reagents for assays. We describe the establishment of an ultrasensitive densitometry method for cytokine detection by nanoparticle (NP)-modified aptamers. METHODS The assay simultaneously uses a gold NP-modified aptamer and a biotin-modified aptamer to bind to the target protein, forming a sandwich complex. The absorbance signal generated by the aptamer-protein complex is amplified and detected with a microplate reader. RESULTS The assay for platelet-derived growth factor B-chain homodimer (PDGF-BB) was linear from 1 fmol/L to 100 pmol/L (R(2) = 0.9869). The analytical detection limit was 83 amol/L. The intraassay and interassay imprecision (CVs) was < or =7.5%. Serum concentrations of PDGF-BB determined with the gold NP-modified aptamer assay and with ELISA were not significantly different. CONCLUSIONS The gold NP-modified aptamer assay provides a fast, convenient method for cytokine detection and improves the detection range and the detection limit compared with ELISA.
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Affiliation(s)
- Yuan-Yuan Li
- MOE Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
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125
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Tombelli S, Minunni M, Mascini M. Aptamers-based assays for diagnostics, environmental and food analysis. ACTA ACUST UNITED AC 2007; 24:191-200. [PMID: 17434340 DOI: 10.1016/j.bioeng.2007.03.003] [Citation(s) in RCA: 174] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2007] [Revised: 03/12/2007] [Accepted: 03/13/2007] [Indexed: 10/23/2022]
Abstract
Aptamers are single stranded DNA or RNA ligands which can be selected for different targets starting from a huge library of molecules containing randomly created sequences. Aptamers have been selected to bind very different targets, from proteins to small organic dyes. In addition to the very important aspect of having an unlimited source of identical affinity recognition molecules available due to the selection process, aptamers can offer advantages over antibodies that make them very promising for analytical applications. The use of aptamers as therapeutic tools is nowadays well established. On the contrary, the analytical application of aptamers in diagnostic devices or in systems for environmental and food analysis, is still under investigation and the scientific community still need further research to demonstrate the advancements brought by this new kind of ligands. This review will focus on these latter applications with particular attention to the detection of food pathogens, terrorism threat agents, thrombin and cytokines.
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Affiliation(s)
- Sara Tombelli
- Dipartimento di Chimica, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
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126
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Li W, Wang K, Tan W, Ma C, Yang X. Aptamer-based analysis of angiogenin by fluorescence anisotropy. Analyst 2006; 132:107-13. [PMID: 17260069 DOI: 10.1039/b614138b] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Recognition and monitoring proteins in real time and in homogeneous solution has always been a difficult task. Here, we introduce a signal transduction strategy for quick protein recognition and real-time quantitative analysis in homogeneous solutions based on a high-affinity aptamer for protein angiogenin (Ang). The method takes advantage of the sensitive anisotropy signal change of fluorophore-labelled aptamer upon protein/aptamer binding. When the labelled aptamer is bound with its target protein Ang, the increased molecular weight causes the rotational motion of the fluorophore attached to the complex to become much slower. Therefore, increasing the amount of Ang results in a raised anisotropy value of the Ang/aptamer. By monitoring the anisotropy change, we are able to detect the binding events between the aptamer and Ang, and measure Ang concentration quantitatively in homogeneous solutions. This assay is highly selective, with a detection limit of 1 nM of Ang. The dissociation constant of the Ang/aptamer binding is determined in the nanomolar range and changes with increasing salt concentration. One can also use our assay to compare the binding affinities of different ligands for the target molecule. Ang in serum samples of malignant lung cancer was also detected. Efficient protein detection using aptamer-based fluorescence anisotropy measurements is expected to find wide applications in protein monitoring, cancer diagnosis, drug screening and other fields.
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Affiliation(s)
- Wei Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Engineering Center for Biomedicine, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
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127
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Kim YS, Jung HS, Matsuura T, Lee HY, Kawai T, Gu MB. Electrochemical detection of 17beta-estradiol using DNA aptamer immobilized gold electrode chip. Biosens Bioelectron 2006; 22:2525-31. [PMID: 17118645 DOI: 10.1016/j.bios.2006.10.004] [Citation(s) in RCA: 177] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2006] [Revised: 09/27/2006] [Accepted: 10/03/2006] [Indexed: 11/25/2022]
Abstract
An electrochemical detection method for chemical sensing has been developed using a DNA aptamer immobilized gold electrode chip. DNA aptamers specifically binding to 17beta-estradiol were selected by the SELEX (Systematic Evolution of Ligands by EXponential enrichment) process from a random ssDNA library, composed of approximately 7.2 x 10(14) DNA molecules. Gold electrode chips were employed to evaluate the electrochemical signals generated from interactions between the aptamers and the target molecules. The DNA aptamer immobilization on the gold electrode was based on the avidin-biotin interaction. The cyclic voltametry (CV) and square wave voltametry (SWV) values were measured to evaluate the chemical binding to aptamer. When 17beta-estradiol interacted with the DNA aptamer, the current decreased due to the interference of bound 17beta-estradiol with the electron flow produced by a redox reaction between ferrocyanide and ferricyanide. In the negative control experiments, the current decreased only mildly due to the presence of other chemicals.
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Affiliation(s)
- Yeon Seok Kim
- College of Life Sciences and Biotechnology, Korea University, Anam-dong, Seongbuk-gu, Seoul 136-701, Republic of Korea
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128
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Liu J, Lu Y. Fast colorimetric sensing of adenosine and cocaine based on a general sensor design involving aptamers and nanoparticles. Angew Chem Int Ed Engl 2006; 45:90-4. [PMID: 16292781 DOI: 10.1002/anie.200502589] [Citation(s) in RCA: 651] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Juewen Liu
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana--Champaign, Urbana, IL, 61801, USA
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129
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130
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Mallikaratchy P, Stahelin RV, Cao Z, Cho W, Tan W. Selection of DNA ligands for protein kinase C-delta. Chem Commun (Camb) 2006:3229-31. [PMID: 17028752 DOI: 10.1039/b604778e] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein kinase Cs are a family of serine and threonine kinases that mediate a wide variety of cellular signalling processes such as cell growth, differentiation, apoptosis and tumor development. We have selected high-affinity DNA aptamers for PKCdelta by capillary electrophoresis based SELEX (systematic evolution of ligands by exponential enrichment, CE-SELEX). We have demonstrated that fluorescently tagged PB9 aptamer can specifically recognize PKCdelta under in vitro conditions. The Kd of the aptamer-protein binding is 122 nM. These aptamers will enable us to apply fluorescently labelled probes to study the spatiotemporal dynamics and activation of individual endogenous PKC isoforms during various cell signalling processes.
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Affiliation(s)
- Prabodhika Mallikaratchy
- Center for Research at the Bio/nano Interface, Department of Chemistry, Shands Cancer Centre, University of Florida, Gainesville, FL 32611, USA
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131
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Zhou C, Jiang Y, Hou S, Ma B, Fang X, Li M. Detection of oncoprotein platelet-derived growth factor using a fluorescent signaling complex of an aptamer and TOTO. Anal Bioanal Chem 2006; 384:1175-80. [PMID: 16447044 DOI: 10.1007/s00216-005-0276-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2005] [Revised: 12/06/2005] [Accepted: 12/07/2005] [Indexed: 11/30/2022]
Abstract
There have recently been advances in the application of aptamers, a new class of nucleic acids that bind specifically with target proteins, as protein recognition probes for biomedical study. The development of a signaling aptamer with the capability of simple and rapid real-time detection of disease-related proteins has attracted increasing interest. We have recently reported a new protein-detection strategy using a signaling aptamer based on a DNA molecular light-switching complex, [Ru(phen)2(dppz)]2+. In this work we have used the commercially available DNA-intercalating dye, TOTO, to replace [Ru(phen)2(dppz)]2+ for detection of oncoprotein platelet-derived growth factor BB (PDGF-BB), a potential cancer marker. Taking advantage of the high affinity of the aptamer to PDGF-BB and the sensitive fluorescence change of the aptamer-TOTO signaling complex on protein binding, PDGF-BB was detected in physiological buffer with high selectivity and sensitivity. The detection limit was 0.1 nmol L(-1), which was better than that of other reported aptamer-based methods for PDGF-BB, including that using [Ru(phen)2(dppz)]2+. The method is very simple with no need for covalent labeling of the aptamer or probe synthesis. It facilitates wide application of the signaling mechanism to the analysis and study of cancer markers and other proteins.
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Affiliation(s)
- Cuisong Zhou
- College of Chemistry, Sichuan University, Chengdu 610064, People's Republic of China
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132
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Abstract
This chapter considers the use of aptamer-based biosensors (generally termed 'aptasensors') in various biomedical applications. A comparison of antibodies and aptamers is made with respect to their use in the development of biosensors. A brief introduction to biosensor design and theory is provided to illustrate the principles of the field. Various transduction approaches, viz. optical, fluorescence, acoustic wave and electrochemical, are discussed. Specific biomedical applications described include RNA folding, high-throughput screening of drugs, use as receptors for measuring biological concentrations, detection of platelet-derived growth factor, protein binding and detection of HIV-1 Tat protein.
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Affiliation(s)
- A K Deisingh
- Caribbean Industrial Research Institute, The University of the West Indies, St. Augustine, Trinidad and Tobago.
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133
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Liu J, Lu Y. Fast Colorimetric Sensing of Adenosine and Cocaine Based on a General Sensor Design Involving Aptamers and Nanoparticles. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200502589] [Citation(s) in RCA: 193] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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134
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Cho S, Kim JE, Lee BR, Kim JH, Kim BG. Bis-aptazyme sensors for hepatitis C virus replicase and helicase without blank signal. Nucleic Acids Res 2005; 33:e177. [PMID: 16314308 PMCID: PMC1292994 DOI: 10.1093/nar/gni174] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The fusion molecule (i.e. aptazyme) of aptamer and hammerhead ribozyme was developed as in situ sensor. Previously, the hammerhead ribozyme conjugated with aptamer through its stem II module showed a significant blank signal by self-cleavage. To reduce or remove its self-cleavage activity in the absence of target molecule, rational designs were attempted by reducing the binding affinity of the aptazyme to its RNA substrate, while maintaining the ribonuclease activity of the aptazyme. Interestingly, the bis-aptazymes which comprise the two aptamer-binding sites at both stem I and stem III of the hammerhead ribozyme showed very low blank signals, and their ratios of reaction rate constants, i.e. signal to noise ratios, were several tens to hundred times higher than those of the stem II-conjugated bis-aptazymes. The reduction in the blank signals seems to be caused by a higher dissociation constant between the main strand of the bis-aptazyme and its substrate arising from multi-point base-pairing of the bis-aptazymes. The bis-aptazymes for HCV replicase and helicase showed high selectivity against other proteins, and a linear relationship existed between their ribozyme activities and the target concentrations. In addition, a bis-aptazyme of dual functions was designed by inserting both aptamers for HCV replicase and helicase into the stem I and stem III of hammerhead ribozyme, respectively, and it also showed greater sensitivity and specificity for both proteins without blank signal.
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Affiliation(s)
- Suhyung Cho
- Interdisciplinary Program for Biochemical Engineering and Biotechnology, Seoul National UniversityShinlim-dong, Kwanak-Gu, Seoul 151-744, Korea
| | - Ji-Eun Kim
- School of Chemical and Biological Engineering, Seoul National UniversityShinlim-dong, Kwanak-Gu, Seoul 151-744, Korea
| | - Bo-Rahm Lee
- School of Chemical and Biological Engineering, Seoul National UniversityShinlim-dong, Kwanak-Gu, Seoul 151-744, Korea
| | - June-Hyung Kim
- School of Chemical and Biological Engineering, Seoul National UniversityShinlim-dong, Kwanak-Gu, Seoul 151-744, Korea
| | - Byung-Gee Kim
- Interdisciplinary Program for Biochemical Engineering and Biotechnology, Seoul National UniversityShinlim-dong, Kwanak-Gu, Seoul 151-744, Korea
- School of Chemical and Biological Engineering, Seoul National UniversityShinlim-dong, Kwanak-Gu, Seoul 151-744, Korea
- To whom correspondence should be addressed at Laboratory of Molecular Biotechnology and Biomaterials, School of Chemical and Biological Engineering, Seoul National University, Shinlim-dong, Kwanak-Gu, Seoul 151-744, Korea. Tel: +82 2 880 6774; Fax: +82 2 883 6020;
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135
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Yang CJ, Jockusch S, Vicens M, Turro NJ, Tan W. Light-switching excimer probes for rapid protein monitoring in complex biological fluids. Proc Natl Acad Sci U S A 2005; 102:17278-83. [PMID: 16301535 PMCID: PMC1297691 DOI: 10.1073/pnas.0508821102] [Citation(s) in RCA: 298] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Quantitative protein bioanalysis in complex biological fluids presents considerable challenges in biological studies and disease diagnosis. The major obstacles are the background signals from both the probe and the biological fluids where the proteins reside. We have molecularly engineered light-switching excimer aptamer probes for rapid and sensitive detection of a biomarker protein, platelet-derived growth factor (PDGF). Labeled with one pyrene at each end, the aptamer switches its fluorescence emission from approximately 400 nm (pyrene monomer) to 485 nm (pyrene excimer) upon PDGF binding. This fluorescence wavelength change from monomer to excimer emission is a result of aptamer conformation rearrangement induced by target binding. The excimer probe is able to effectively detect picomolar PDGF in homogeneous solutions. Because the excimer has a much longer fluorescence lifetime (approximately 40 ns) than that of the background (approximately 5 ns), time-resolved measurements were used to eliminate the biological background. We thus were able to detect PDGF in a cell sample quantitatively without any sample pretreatment. This molecular engineering strategy can be used to develop other aptamer probes for protein monitoring. Combined with lifetime-based measurements and molecular engineering, light-switching excimer aptamer probes hold great potential in protein analysis for biomedical studies.
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Affiliation(s)
- Chaoyong James Yang
- Center for Research at Bio/Nano Interface, Department of Chemistry, University of Florida Genetics Institute, Gainesville, FL 32611, USA
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136
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Wang J, Cao Z, Jiang Y, Zhou C, Fang X, Tan W. Molecular signaling aptamers for real-time fluorescence analysis of protein. IUBMB Life 2005; 57:123-8. [PMID: 16036574 DOI: 10.1080/15216540500090686] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Aptamers are a new class of nucleic acids that are selected in vitro for binding target molecules with high affinity and selectivity. They are promising protein-binding molecular probes that rival conventional antibodies for protein analysis. There have been recent advances in the development of molecular signaling aptamers that can transduce target protein binding to sensitive fluorescence signal changes. This facilitates the real time protein monitoring in homogenous solution as well as potentially in vivo. Different signaling strategies of using dual labeled aptamers based on fluorescence resonance energy transfer (FRET), one fluorophore labeled aptamers based on fluorescence anisotropy assay, or other label-free aptamers are reviewed.
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Affiliation(s)
- Jun Wang
- Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
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137
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Ikebukuro K, Kiyohara C, Sode K. Novel electrochemical sensor system for protein using the aptamers in sandwich manner. Biosens Bioelectron 2005; 20:2168-72. [PMID: 15741093 DOI: 10.1016/j.bios.2004.09.002] [Citation(s) in RCA: 224] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2004] [Revised: 09/02/2004] [Accepted: 09/03/2004] [Indexed: 11/29/2022]
Abstract
Novel electrochemical detection system for protein in sandwich manner using the aptamers was developed. Two different aptamers, which recognize different positions of thrombin, were chosen to construct sandwich type sensing system for protein, and one was immobilized onto the gold electrode for capturing thrombin onto the electrode and the other was used for detection. To obtain the signal, the aptamer for detection was labeled with pyrroquinoline quinone glucose dehydrogenase ((PQQ)GDH), and the electrical current, generated from glucose addition after the formation of the complex of thrombin, gold immobilized aptamer and the (PQQ)GDH labeled aptamer on the electrode, was measured. The increase of the electric current generated by (PQQ)GDH was observed in dependent manner of the concentration of thrombin added, and more than 10nM thrombin was detected selectively. The batch type protein sensing system was constructed using the two different aptamers sandwiching thrombin and it showed linear response to the increase of the thrombin concentration in the range of 40-100 nM.
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Affiliation(s)
- Kazunori Ikebukuro
- Department of Life Science and Biotechnology, Tokyo University of Agriculture and Technology, Nakamachi 2 24 16, Koganei, Tokyo 184 8588, Japan.
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138
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Unruh JR, Gokulrangan G, Lushington GH, Johnson CK, Wilson GS. Orientational dynamics and dye-DNA interactions in a dye-labeled DNA aptamer. Biophys J 2005; 88:3455-65. [PMID: 15731389 PMCID: PMC1305492 DOI: 10.1529/biophysj.104.054148] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report the picosecond and nanosecond timescale rotational dynamics of a dye-labeled DNA oligonucleotide or "aptamer" designed to bind specifically to immunoglobulin E. Rotational dynamics in combination with fluorescence lifetime measurements provide information about dye-DNA interactions. Comparison of Texas Red (TR), fluorescein, and tetramethylrhodamine (TAMRA)-labeled aptamers reveals surprising differences with significant implications for biophysical studies employing such conjugates. Time-resolved anisotropy studies demonstrate that the TR- and TAMRA-aptamer anisotropy decays are dominated by the overall rotation of the aptamer, whereas the fluorescein-aptamer anisotropy decay displays a subnanosecond rotational correlation time much shorter than that expected for the overall rotation of the aptamer. Docking and molecular dynamics simulations suggest that the low mobility of TR is a result of binding in the groove of the DNA helix. Additionally, associated anisotropy analysis of the TAMRA-aptamer reveals both quenched and unquenched states that experience significant coupling to the DNA motion. Therefore, quenching of TAMRA by guanosine must depend on the configuration of the dye bound to the DNA. The strong coupling of TR to the rotational dynamics of the DNA aptamer, together with the absence of quenching of its fluorescence by DNA, makes it a good probe of DNA orientational dynamics. The understanding of the nature of dye-DNA interactions provides the basis for the development of bioconjugates optimized for specific biophysical measurements and is important for the sensitivity of anisotropy-based DNA-protein interaction studies employing such conjugates.
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Affiliation(s)
- Jay R Unruh
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
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139
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Ikebukuro K, Kiyohara C, Sode K. Electrochemical Detection of Protein Using a Double Aptamer Sandwich. ANAL LETT 2004. [DOI: 10.1081/al-200035778] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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140
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Minunni M, Tombelli S, Gullotto A, Luzi E, Mascini M. Development of biosensors with aptamers as bio-recognition element: the case of HIV-1 Tat protein. Biosens Bioelectron 2004; 20:1149-56. [PMID: 15556361 DOI: 10.1016/j.bios.2004.03.037] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2003] [Revised: 03/02/2004] [Accepted: 03/04/2004] [Indexed: 10/26/2022]
Abstract
The in vitro selection of combinatorial libraries of RNA/DNA, has allowed the identification of specific nucleic acids (aptamers) which bind to a wide range of target molecules with high affinity and specificity. In this work, an RNA aptamer, specific for the protein trans-activator of transcription (Tat) of HIV-1, has been used as bio-recognition element to develop a biosensor (aptasensor). The biosensor was optimised using piezoelectric quartz-crystals as transducers and the aptamer was immobilised on the gold electrode of the crystal. The immobilisation procedure was based on the interaction between the biotinylated aptamer and streptavidin previously deposited on the electrode. The main analytical characteristics of the biosensor, such as sensitivity, selectivity and reproducibility, have been studied in details. An optimised regeneration procedure allowed the multiple use of the aptamer-coated crystal. The aptasensor has been compared with the corresponding immunosensor, based on the specific monoclonal anti-Tat antibody. The antibody was immobilised on a layer of carboxylated dextran previously deposited on the gold electrode. The results demonstrated that the use of a biosensor with a specific aptamer as bio-recognition element could be an interesting approach in the detection of proteins, which has been here examined considering a model system.
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Affiliation(s)
- M Minunni
- Università degli Studi di Firenze, Dipartimento di Chimica, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
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141
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Huang H, Wang K, Tan W, An D, Yang X, Huang S, Zhai Q, Zhou L, Jin Y. Design of a Modular-Based Fluorescent Conjugated Polymer for Selective Sensing. Angew Chem Int Ed Engl 2004. [DOI: 10.1002/ange.200460371] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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142
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Huang H, Wang K, Tan W, An D, Yang X, Huang S, Zhai Q, Zhou L, Jin Y. Design of a Modular-Based Fluorescent Conjugated Polymer for Selective Sensing. Angew Chem Int Ed Engl 2004; 43:5635-8. [PMID: 15495203 DOI: 10.1002/anie.200460371] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hongmei Huang
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
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143
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Drake TJ, Tan W. Molecular beacon DNA probes and their bioanalytical applications. APPLIED SPECTROSCOPY 2004; 58:269A-280A. [PMID: 15479516 DOI: 10.1366/0003702041959406] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Affiliation(s)
- Timothy J Drake
- Center for Research at the Bio/Nano Interface, Department of Chemistry and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, USA
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144
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Deocaris CC, Kaul SC, Taira K, Wadhwa R. Emerging Technologies: Trendy RNA Tools for Aging Research. J Gerontol A Biol Sci Med Sci 2004; 59:771-83. [PMID: 15345725 DOI: 10.1093/gerona/59.8.b771] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Aging is an inevitable biological phenomenon. Attempts to understand its mechanisms and, consequently, to therapeutically decelerate or even reverse the process are limited by its daunting complexity. Rapid and robust functional genomic tools suited to a wide array of experimental model systems are needed to dissect the interplay of individual genes during aging. In this article, we review principles that transcend the view of RNA, from a molecule merely mediating the flow of genetic information, into a unique molecular tool. In the form of catalytic molecular scissors (ribozymes), antibody-like antagonists (aptamers) and gene silencers (interfering RNAs, RNAi) can be effectively used to dissect biofunctions conserved throughout the evolution. In this review, application of recent RNA tools in aging research is discussed.
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Affiliation(s)
- Custer C Deocaris
- Gene Function Research Center, National Institute of Advanced Industrial Science & Technology (AIST), 1-1-1 Higashi, Tsukuba Science City 305-8562, Japan
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145
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Abstract
This review will consider the role of biosensors towards the detection of infectious bacteria, although non-infectious ones will be considered where necessary. Recently, there has been a heightened interest in developing rapid and reliable methods of detection. This is especially true for detection of organisms involved in bioterrorism, food poisoning, and clinical problems such as antibiotic resistance. Biosensors can assist in achieving these goals, and sensors using several of the different types of transduction modes are discussed: electrochemical, high frequency (surface acoustic wave), and optical. The paper concludes with a discussion of three areas that may make a great impact in the next few years: integrated (lab-on-a-chip) systems, molecular beacons, and aptamers.
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Affiliation(s)
- Anil K Deisingh
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada.
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146
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Flinders J, DeFina SC, Brackett DM, Baugh C, Wilson C, Dieckmann T. Recognition of Planar and Nonplanar Ligands in the Malachite Green-RNA Aptamer Complex. Chembiochem 2003; 5:62-72. [PMID: 14695514 DOI: 10.1002/cbic.200300701] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Ribonucleic acids are an attractive drug target owing to their central role in many pathological processes. Notwithstanding this potential, RNA has only rarely been successfully targeted with novel drugs. The difficulty of targeting RNA is at least in part due to the unusual mode of binding found in most small-molecule-RNA complexes: the ligand binding pocket of the RNA is largely unstructured in the absence of ligand and forms a defined structure only with the ligand acting as scaffold for folding. Moreover, electrostatic interactions between RNA and ligand can also induce significant changes in the ligand structure due to the polyanionic nature of the RNA. Aptamers are ideal model systems to study these kinds of interactions owing to their small size and the ease with which they can be evolved to recognize a large variety of different ligands. Here we present the solution structure of an RNA aptamer that binds triphenyl dyes in complex with malachite green and compare it with a previously determined crystal structure of a complex formed with tetramethylrosamine. The structures illustrate how the same RNA binding pocket can adapt to accommodate both planar and nonplanar ligands. Binding studies with single- and double-substitution mutant aptamers are used to correlate three-dimensional structure with complex stability. The two RNA-ligand complex structures allow a discussion of structural changes that have been observed in the ligand in the context of the overall complex structure. Base pairing and stacking interactions within the RNA fold the phosphate backbone into a structure that results in an asymmetric charge distribution within the binding pocket that forces the ligand to adapt through a redistribution of the positive partial charge.
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Affiliation(s)
- Jeremy Flinders
- Department of Chemistry, University of California, Davis, CA 95616, USA
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147
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148
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Abstract
Protein-DNA binding assays have been used in a variety of fields from fundamental studies regarding the binding process itself, to serving as probes for the detection, quantification and separation of target analytes. These assays have been used for the study of protein-DNA complex stoichiometry, the detection of DNA damage, and real-time separation of free and bound complexes by electrophoretic mobility. Synthetic DNA oligonucleotides, known as aptamers, have been increasingly used for affinity binding assays to proteins, as well as for separation studies and as biosensors. Recent advances have been made in protein-DNA binding assays using capillary electrophoresis, laser-induced fluorescence, fluorescence polarization, molecular beacons, and affinity chromatography.
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Affiliation(s)
- Victor Pavski
- Environmental Health Sciences Program, Department of Public Health Sciences, University of Alberta, Alberta, Edmonton, Canada T6G 2G3
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149
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Kim YM, Choi KH, Jang YJ, Yu J, Jeong S. Specific modulation of the anti-DNA autoantibody-nucleic acids interaction by the high affinity RNA aptamer. Biochem Biophys Res Commun 2003; 300:516-23. [PMID: 12504114 DOI: 10.1016/s0006-291x(02)02858-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Anti-DNA autoantibodies are one of the frequently found autoantibodies in systemic lupus erythematosus patient sera. RNA aptamers for the monoclonal G6-9 anti-DNA autoantibody were selected from a random pool of RNA library. Binding affinity of the best aptamer is around 2nM, which is at least 100-fold higher than that of cognate DNA antigen to the autoantibody. Aptamer binds specifically to the G6-9 autoantibody but not to other similar autoantibodies. Minimal binding motif of the aptamer was mapped, providing a hint for a natural epitope of the autoantibody. DNA binding to the G6-9 autoantibody is shown to be efficiently inhibited by the aptamer. Such binding property of the RNA aptamer could be used not only as a modulator for the pathogenic anti-DNA autoantibody, but also as a useful biochemical reagent for elucidating a fine specificity of the autoantibody-nucleic acid interaction.
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Affiliation(s)
- Young-Mee Kim
- Department of Molecular Biology, College of Natural Sciences, Dankook University, Hannam-dong san 8, Yongsan-ku, Seoul 140-714, Republic of Korea
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150
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Abstract
One of the most pressing problems facing those attempting to understand the regulation of gene expression and translation is the necessity to monitor protein production in a variety of metabolic states. Thus far, there is no easy solution that will either identify or quantitate proteins in real time. Here we introduce a novel protein probe, molecular aptamer beacon (MAB), for real time protein recognition and quantitative analysis. The MAB combines the signal transduction mechanism of molecular beacons and the molecular recognition specificity of aptamers. An MAB based on a thrombin-binding aptamer was prepared as a model to demonstrate the feasibility. Significant fluorescent signal change was observed when MAB was bound to thrombin, which is attributed to a significant conformational change in MAB from a loose random coil to a compact unimolecular quadruplex. The MAB recognizes its target protein with high specificity and high sensitivity (112 picomolar thrombin concentration) in homogeneous solutions. Ratiometric imaging has been conducted with MAB labeled with two fluorophores, which makes it feasible for protein quantitation in living specimen. The unique properties of the MAB will enable the development of a class of protein probes for real time protein tracing in living specimen and for efficient biomedical diagnosis in homogeneous solutions.
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Affiliation(s)
- Jianwei J Li
- Department of Chemistry, McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
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