151
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Ozaki H, Nishihira A, Wakabayashi M, Kuwahara M, Sawai H. Biomolecular sensor based on fluorescence-labeled aptamer. Bioorg Med Chem Lett 2006; 16:4381-4. [PMID: 16757168 DOI: 10.1016/j.bmcl.2006.05.054] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2006] [Revised: 05/12/2006] [Accepted: 05/16/2006] [Indexed: 11/24/2022]
Abstract
Fluorescent DNA probes for L-argininamide were developed by a combination of DNA aptamers and fluorophore-quencher pairs. These molecules were synthesized by a combination of pre- and post-synthetic modification methods. The fluorescence-labeled aptamer could detect L-argininamide specifically. The binding affinities were defined by the binding affinity of the original aptamer to indicate that the end labeling of the aptamer did not influence the affinities.
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Affiliation(s)
- Hiroaki Ozaki
- Department of Chemistry, Faculty of Engineering, Gunma University, Kiryu, Japan.
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152
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Kamekawa N, Shimomura Y, Nakamura M, Yamana K. Pyrene-modified DNA Aptamer as a Fluorescent Biosensor with High Affinity and Specificity for ATP Sensing. CHEM LETT 2006. [DOI: 10.1246/cl.2006.660] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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153
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Bang GS, Cho S, Kim BG. A novel electrochemical detection method for aptamer biosensors. Biosens Bioelectron 2006; 21:863-70. [PMID: 16257654 DOI: 10.1016/j.bios.2005.02.002] [Citation(s) in RCA: 207] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2004] [Revised: 02/02/2005] [Accepted: 02/04/2005] [Indexed: 01/25/2023]
Abstract
A beacon aptamer-based biosensor for the detection of thrombin was developed using electrochemical transduction method. Gold surface was modified with a beacon aptamer covalently linked at 5'-terminus with a linker containing a primary aliphatic amine. Methylene blue (MB) was intercalated into the beacon sequence, and used as an electrochemical marker. When the beacon aptamer immobilized on gold surface encounters thrombin, the hairpin forming beacon aptamer is conformationally changed to release the intercalated MB, resulting a decrease in electrical current intensity in voltamogram. The peak signal of the MB is clearly decreased by the binding of thrombin onto the beacon aptamer. The linear range of the signal was observed between 0 and 50.8 nM of thrombin with 0.999 correlation factor. This method was able to linearly and selectively detect thrombin with a detection limit of 11 nM.
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Affiliation(s)
- Gyeong Sook Bang
- School of Chemical and Biological Engineering and Institute of Molecular Biology and Genetics, Seoul National University, Kwanak-ku, South Korea
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154
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Santangelo P, Nitin N, Bao G. Nanostructured Probes for RNA Detection in Living Cells. Ann Biomed Eng 2006; 34:39-50. [PMID: 16463087 DOI: 10.1007/s10439-005-9003-6] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2005] [Accepted: 09/30/2005] [Indexed: 01/29/2023]
Abstract
The ability to visualize in real-time the expression level and localization of specific RNAs in living cells can offer tremendous opportunities for biological and disease studies. Here we review the recent development of nanostructured oligonucleotide probes for living cell RNA detection, and discuss the biological and engineering issues and challenges of quantifying gene expression in vivo. In particular, we describe methods that use dual FRET (fluorescence resonance energy transfer) or single molecular beacons in combination with peptide-based or membrane-permeabilization-based delivery, to image the relative level, localization, and dynamics of RNA in live cells. Examples of detecting endogenous mRNAs, as well as imaging their subcellular localization and colocalization are given to illustrate the biological applications, and issues in molecular beacon design, probe delivery, and target accessibility are discussed. The nanostructured probes promise to open new and exciting opportunities in sensitive gene detection for a wide range of biological and medical applications.
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Affiliation(s)
- Philip Santangelo
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
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155
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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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156
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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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157
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Marras SAE, Tyagi S, Kramer FR. Real-time assays with molecular beacons and other fluorescent nucleic acid hybridization probes. Clin Chim Acta 2006; 363:48-60. [PMID: 16111667 DOI: 10.1016/j.cccn.2005.04.037] [Citation(s) in RCA: 178] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2005] [Revised: 04/22/2005] [Accepted: 04/27/2005] [Indexed: 10/25/2022]
Abstract
BACKGROUND A number of formats for nucleic acid hybridization have been developed to identify DNA and RNA sequences that are involved in cellular processes and that aid in the diagnosis of genetic and infectious diseases. METHODS The introduction of hybridization probes with interactive fluorophore pairs has enabled the development of homogeneous hybridization assays for the direct identification of nucleic acids. A change in the fluorescence of these probes indicates the presence of a target nucleic acid, and there is no need to separate unbound probes from hybridized probes. CONCLUSIONS The advantages of homogeneous hybridization assays are their speed and simplicity. In addition, homogeneous assays can be combined with nucleic acid amplification, enabling the detection of rare target nucleic acids. These assays can be followed in real time, providing quantitative determination of target nucleic acids over a broad range of concentrations.
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Affiliation(s)
- Salvatore A E Marras
- Department of Molecular Genetics, Public Health Research Institute, Newark, NJ 07103, USA
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158
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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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159
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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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160
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Proske D, Blank M, Buhmann R, Resch A. Aptamers--basic research, drug development, and clinical applications. Appl Microbiol Biotechnol 2005; 69:367-74. [PMID: 16283295 DOI: 10.1007/s00253-005-0193-5] [Citation(s) in RCA: 159] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Revised: 08/16/2005] [Accepted: 09/14/2005] [Indexed: 01/28/2023]
Abstract
Since its discovery in the early 1990s, aptamer technology has progressed tremendously. Automated selection procedures now allow rapid identification of DNA and RNA sequences that can target a broad range of extra- and intracellular proteins with nanomolar affinities and high specificities. The unique binding properties of nucleic acids, which are amenable to various modifications, make aptamers perfectly suitable for different areas of biotechnology. Moreover, the approval of an aptamer for vascular endothelial growth factor by the US Food and Drug Administration highlights the potential of aptamers for therapeutic applications. This review summarizes recent developments and demonstrates that aptamers are valuable tools for diagnostics, purification processes, target validation, drug discovery, and even therapeutic approaches.
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Affiliation(s)
- Daniela Proske
- NascaCell IP GmbH, 3. OG, Modul D Max-Lebsche-Platz, 3181377 Munich, Germany.
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161
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Tombelli S, Minunni M, Luzi E, Mascini M. Aptamer-based biosensors for the detection of HIV-1 Tat protein. Bioelectrochemistry 2005; 67:135-41. [PMID: 16027048 DOI: 10.1016/j.bioelechem.2004.04.011] [Citation(s) in RCA: 161] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2004] [Revised: 03/04/2004] [Accepted: 04/01/2004] [Indexed: 11/29/2022]
Abstract
Two biosensors have been constructed using an RNA aptamer as biorecognition element. The aptamer, specific for HIV-1 Tat protein, has been immobilised on the gold surface of piezoelectric quartz crystals or surface plasmon resonance (SPR) chips to develop a quartz crystal microbalance (QCM)-based and an SPR-based biosensor, respectively. Both the biosensors were modified with the same immobilisation chemistry based on the binding of a biotinylated aptamer on a layer of streptavidin. The binding between the immobilised aptamer and its specific protein has been evaluated with the two biosensors in terms of sensitivity, reproducibility and selectivity. A protein very similar to Tat, Rev protein, has been used as negative control. The two biosensors both were very reproducible in the immobilisation and the binding steps. The selectivity was high in both cases.
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Affiliation(s)
- S Tombelli
- Università degli Studi di Firenze, Dipartimento di Chimica Polo Scientifico di Sesto Fiorentino Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
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162
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Abstract
Aptamers are single-stranded DNA or RNA molecules with ligand-binding capabilities. Signaling aptamers refer to aptamers or modified aptamers with recordable signal generation ability. Fluorescence-signaling aptamers, in particular, are valuable molecular tools that can be used to establish important techniques or assays for the interrogation of identities and concentrations of proteins and metabolites. Since standard DNA and RNA aptamers themselves are not inherently fluorescent, modification methods are required for rationally converting non-fluorescent aptamers into fluorescent reporters or for selecting fluorescent aptamers directly from random-sequence DNA libraries by in vitro selection. This article will provide a brief review of various signaling aptamer design strategies as well as a detailed description of methods that can be used to generate, by both rational design and in vitro selection, a special class of signaling aptamers dubbed "structure-switching signaling aptamers." This class of signaling aptamers are designed to function by switching structures from a pre-formed, lowly fluorescent duplex assembly to a ligand-aptamer complex having a higher level of fluorescence.
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Affiliation(s)
- Razvan Nutiu
- Department of Biochemistry and Biological Sciences, McMaster University, Hamilton, Ont., Canada L8N 3Z5
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163
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Xiao Y, Lubin AA, Heeger AJ, Plaxco KW. Label-Free Electronic Detection of Thrombin in Blood Serum by Using an Aptamer-Based Sensor. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200500989] [Citation(s) in RCA: 161] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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164
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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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165
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Dick LW, McGown LB. Aptamer-enhanced laser desorption/ionization for affinity mass spectrometry. Anal Chem 2005; 76:3037-41. [PMID: 15167780 DOI: 10.1021/ac049860e] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The thrombin-binding DNA aptamer was used for affinity capture of thrombin in MALDI-TOF-MS. The aptamer was covalently attached to the surface of a glass slide that served as the MALDI surface. Results show that thrombin is retained at the aptamer-modified surface while nonspecific proteins, such as albumin, are removed by rinsing with buffer. Upon application of the low-pH MALDI matrix, the G-quartet structure of the aptamer unfolds, releasing the captured thrombin. Following TOF-MS analysis, residual matrix and protein can be washed from the surface, and buffer can be applied to refold the aptamers, allowing the surface to be reused. Selective capture of thrombin from mixtures of thrombin and albumin and of thrombin and prothrombin from human plasma was demonstrated. This simple approach to affinity capture, isolation, and detection holds potential for analysis, sensing, purification, and preconcentration of proteins in biological fluids.
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Affiliation(s)
- Lawrence W Dick
- Department of Chemistry, Duke University, Box 90346, Durham, North Carolina 27708, USA
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166
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Affiliation(s)
- Razvan Nutiu
- Department of Biochemistry and Department of Chemistry, McMaster University, Hamilton, ON, L8N 3Z5, Canada, Fax: (+1) 905‐522‐9033
| | - Yingfu Li
- Department of Biochemistry and Department of Chemistry, McMaster University, Hamilton, ON, L8N 3Z5, Canada, Fax: (+1) 905‐522‐9033
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167
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Warsinke A, Stöcklein W, Leupold E, Micheel E, Scheller FW. Electrochemical Immunosensors on the Route to Proteomic Chips. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/s1871-0069(05)01014-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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168
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Kandimalla VB, Ju H. New Horizons with A Multi Dimensional Tool for Applications in Analytical Chemistry—Aptamer. ANAL LETT 2004. [DOI: 10.1081/al-200028005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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169
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Tombelli S, Minunni M, Mascini M. Analytical applications of aptamers. Biosens Bioelectron 2004; 20:2424-34. [PMID: 15854817 DOI: 10.1016/j.bios.2004.11.006] [Citation(s) in RCA: 671] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2004] [Revised: 10/25/2004] [Accepted: 11/11/2004] [Indexed: 11/19/2022]
Abstract
So far, several bio-analytical methods have used nucleic acid probes to detect specific sequences in RNA or DNA targets through hybridisation. More recently, specific nucleic acids, aptamers, selected from random sequence pools, have been shown to bind non-nucleic acid targets, such as small molecules or proteins. The development of in vitro selection and amplification techniques has allowed the identification of specific aptamers, which bind to the target molecules with high affinity. Many small organic molecules with molecular weights from 100 to 10,000 Da have been shown to be good targets for selection. Moreover, aptamers can be selected against difficult target haptens, such as toxins or prions. The selected aptamers can bind to their targets with high affinity and even discriminate between closely related targets. Aptamers can thus be considered as a valid alternative to antibodies or other bio-mimetic receptors, for the development of biosensors and other analytical methods. The production of aptamers is commonly performed by the SELEX (systematic evolution of ligands by exponential enrichment) process, which, starting from large libraries of oligonucleotides, allows the isolation of large amounts of functional nucleic acids by an iterative process of in vitro selection and subsequent amplification through polymerase chain reaction. Aptamers are suitable for applications based on molecular recognition as analytical, diagnostic and therapeutic tools. In this review, the main analytical methods, which have been developed using aptamers, will be discussed together with an overview on the aptamer selection process.
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Affiliation(s)
- S Tombelli
- Università degli Studi di Firenze, Dipartimento di Chimica, Polo Scientifico, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
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170
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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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171
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Abstract
We report the first examples of modular aptameric sensors, which transduce recognition events into fluorescence changes through allosteric regulation of noncovalent interactions with a fluorophore. These sensors consist of: (a) a reporting domain, which signals the binding event of an analyte through binding to a fluorophore; (b) a recognition domain, which binds the analyte; and (c) a communication module, which serves as a conduit between recognition and signaling domains. We tested recognition regions specific for ATP, FMN, and theophylline in combinations with malachite green binding aptamer as a signaling domain. In each case, we were able to obtain a functional sensor capable of responding to an increase in analyte concentration with an increase in fluorescence. Similar constructs that consist only of natural RNA could be expressed in cells and used as sensors for intracellular imaging.
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Affiliation(s)
- Milan N Stojanovic
- Division of Experimental Therapeutics, Department of Medicine, Columbia University, New York, New York 10032, USA.
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172
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Nutiu R, Yu JMY, Li Y. Signaling Aptamers for Monitoring Enzymatic Activity and for Inhibitor Screening. Chembiochem 2004; 5:1139-44. [PMID: 15300841 DOI: 10.1002/cbic.200400026] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Razvan Nutiu
- Departments of Biochemistry and Chemistry, McMaster University, 1200 Main Street West, Hamilton, L8N 3Z5 Ontario, Canada
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173
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174
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Yamana K, Ohtani Y, Nakano H, Saito I. Bis-pyrene labeled DNA aptamer as an intelligent fluorescent biosensor. Bioorg Med Chem Lett 2004; 13:3429-31. [PMID: 14505642 DOI: 10.1016/s0960-894x(03)00799-6] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The site-directed incorporation of bis-pyrenyl fluorophore into anti-ATP DNA aptamer results in a creation of an intelligent fluorescent sensor with high signal intensity and specificity for detecting the target ligand in a homogeneous system.
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Affiliation(s)
- Kazushige Yamana
- Department of Applied Chemistry, Himeji Institute of Technology, 2167 Shosha, Himeji 671-2201, Japan.
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175
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Rajendran M, Ellington AD. In vitro selection of molecular beacons. Nucleic Acids Res 2003; 31:5700-13. [PMID: 14500834 PMCID: PMC206464 DOI: 10.1093/nar/gkg764] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2003] [Revised: 08/11/2003] [Accepted: 08/11/2003] [Indexed: 11/15/2022] Open
Abstract
While molecular beacons are primarily known as biosensors for the detection of nucleic acids, it has proven possible to adapt other nucleic acid binding species (aptamers) to function in a manner similar to molecular beacons, yielding fluorescent signals only in the presence of a cognate ligand. Unfortunately, engineering aptamer beacons requires a detailed knowledge of aptamer sequence and structure. In order to develop a general method for the direct selection of aptamer beacons we have first developed a selection method for molecular beacons. A pool of random sequence DNA molecules were immobilized via a capture oligonucleotide on an affinity column, and those variants that could be released from the column by a target oligonucleotide were amplified. After nine rounds of selection and amplification the elution characteristics of the population were greatly improved. A fluorescent reporter in the selected beacons was located adjacent to a DABCYL moiety in the capture oligonucleotide; addition of the target oligonucleotide led to release of the capture oligonucleotide and up to a 17-fold increase in fluorescence. Signaling was specific for the target oligonucleotide, and occurred via a novel mechanism, relative to designed molecular beacons. When the target oligonucleotide is bound it can form a stacked helical junction with an intramolecular hairpin in the selected beacon; formation of the intramolecular hairpin in turn leads to release of the capture oligonucleotide. The ability to select molecular beacons may prove useful for identifying available sites on complex targets, such as mRNAs, while the method for selection can be easily generalized to other, non-nucleic acid target classes.
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Affiliation(s)
- Manjula Rajendran
- Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
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176
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Fang X, Sen A, Vicens M, Tan W. Synthetic DNA aptamers to detect protein molecular variants in a high-throughput fluorescence quenching assay. Chembiochem 2003; 4:829-34. [PMID: 12964156 DOI: 10.1002/cbic.200300615] [Citation(s) in RCA: 148] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Real-time protein detection in homogeneous solutions is necessary in many biotechnology and biomedical studies. The recent development of molecular aptamers, combined with fluorescence techniques, may provide an easy and efficient approach to protein elucidation. This report describes the development of a fluorescence-based assay with synthetic DNA aptamers that can detect and distinguish molecular variants of proteins in biological samples in a high-throughput process. We used an aptamer with high affinity for the B chain of platelet-derived growth factor (PDGF), labeled it with a fluorophore and a quencher at the two termini, and measured fluorescence quenching by PDGF. The specific quenching can be used to detect PDGF at picomolar concentrations even in the presence of serum and other cell-derived proteins in cell culture media. This is the first successful application of a synthetic aptamer for the detection of tumor-related proteins directly from the tumor cells. We also show that three highly related molecular variants of PDGF (AA, AB, and BB dimers) can be distinguished from one another in this single-step assay, which can be readily adapted to a microtiter plate assay for high-throughput analysis. The use of fluorescence quenching as a measure of binding between the DNA probe and the target protein eliminates potential false signals that may arise in traditional fluorescence enhancement assays as a result of degradation of the DNA aptamer by contaminating nucleases in biological specimens. This assay is applicable to proteins that are not naturally DNA binding. The excellent specificity, ultrahigh sensitivity, and simplicity of this one-step assay addresses a growing need for high-throughput methods that detect changes in the expression of gene products and their variants in cell cultures and biological specimens.
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Affiliation(s)
- Xiaohong Fang
- Department of Chemistry and McKnight Brain Institute, Shands Cancer Center, College of Medicine, University of Florida, Gainesville, FL 32611, USA
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177
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Stojanović MN, Green EG, Semova S, Nikić DB, Landry DW. Cross-reactive arrays based on three-way junctions. J Am Chem Soc 2003; 125:6085-9. [PMID: 12785838 DOI: 10.1021/ja0289550] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report herein a novel system for the parallel processing of molecular recognition events utilizing arrays of oligonucleotide-based fluorescent sensors to characterize hydrophobic molecules in solution. The binding domains of the sensors were based on three-way junctions that utilize double helical stems as framework regions to reliably fold regardless of variations in or around the binding domain. A reporting domain was introduced by the specific substitution of a single phosphodiester group with a phosphorothioate, followed by selective functionalization with a fluorophore. The sensors were organized into cross-reactive arrays to yield characteristic fingerprints for samples containing hydrophobic molecules. The fingerprints can be used to characterize steroids in solution, including complex biologically important fluids. Arrays have the potential for clinical applications such as the detection of gross errors in steroidogenesis.
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Affiliation(s)
- Milan N Stojanović
- Division of Clinical Pharmacology and Experimental Therapeutics, Department of Medicine, Columbia University, New York, New York 10032, USA.
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178
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You KM, Lee SH, Im A, Lee SB. Aptamers as functional nucleic acids:In vitro selection and biotechnological applications. BIOTECHNOL BIOPROC E 2003. [DOI: 10.1007/bf02940259] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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179
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Wang DY, Lai BHY, Sen D. A general strategy for effector-mediated control of RNA-cleaving ribozymes and DNA enzymes. J Mol Biol 2002; 318:33-43. [PMID: 12054766 DOI: 10.1016/s0022-2836(02)00046-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A novel and general approach is described for generating versions of RNA-cleaving ribozymes (RNA enzymes) and DNAzymes (DNA enzymes), whose catalytic activity can be controlled by the binding of activator molecules. Variants of the RNA-cleaving 10-23 DNAzyme and 8-17 DNAzyme were created, whose catalysis was activated by up to approximately 35-fold by the binding of the effector adenosine. The design of such variants was possible even though the tertiary folding of the two DNAzymes is not known. Variants of the hammerhead ribozyme were constructed, to respond to the effectors ATP and flavin mononucleotide. Whereas in conventional allosteric ribozymes, effector-binding modulates the chemical step of catalysis, here, effectors exercise their effect upon the substrate-binding step, by stabilizing the enzyme-substrate complex. Because such an approach for controlling the activity of DNAzymes/ribozymes requires no prior knowledge of the enzyme's secondary or tertiary folding, this regulatory strategy should be generally applicable to any RNA-cleaving ribozyme or DNAzyme, natural or in vitro selected, provided substrate-recognition is achieved by Watson-Crick base-pairing.
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Affiliation(s)
- Dennis Y Wang
- Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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180
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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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181
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Affiliation(s)
- Amy Yan
- Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
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182
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Bruno JG, Ulvick SJ, Uzzell GL, Tabb JS, Valdes ER, Batt CA. Novel immuno-FRET assay method for Bacillus spores and Escherichia coli O157:H7. Biochem Biophys Res Commun 2001; 287:875-80. [PMID: 11573946 DOI: 10.1006/bbrc.2001.5669] [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: 11/22/2022]
Abstract
Novel immunofluorescence resonance energy transfer (immuno-FRET) assays for both Bacillus cereus spores and Escherichia coli O157:H7 are reported. Both assays involve the use of dual (QSY-7 and Oregon Green 514-antibody)-labeled spores or vegetative bacteria, such that Oregon Green 514-labeled antibodies are quenched by proximal QSY-7 molecules that are covalently bound to the dual (Oregon Green 514 and QSY-7)-labeled cells. Upon introduction of unlabeled bacteria or spores, in the respective assays, an increase in fluorescence is observed in proportion to the numbers of unlabeled cells. This is due to migration of Oregon Green 514-labeled antibody from the dual-labeled cells to the unlabeled target cells as verified by fluorescence microscopy. Optimization of the QSY-7 surface density led to a B. cereus spore detection sensitivity of approximately 1.0 x 10(5) to 2.5 x 10(5) spores per milliliter and 3.5 x 10(5) cells per milliliter for E. coli using a conventional cuvette-based spectrofluorometer.
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Affiliation(s)
- J G Bruno
- OmniSite BioDiagnostics, Incorporated, 101 West Sixth Street, Suite 200, Austin, TX 78701-2932, USA.
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183
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Yamamoto R, Katahira M, Nishikawa S, Baba T, Taira K, Kumar PK. A novel RNA motif that binds efficiently and specifically to the Ttat protein of HIV and inhibits the trans-activation by Tat of transcription in vitro and in vivo. Genes Cells 2000; 5:371-88. [PMID: 10886365 DOI: 10.1046/j.1365-2443.2000.00330.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND To find a novel RNA that would bind efficiently and specifically to Tat protein but not to other cellular factors, we used an in vitro selection method and isolated a novel aptamer RNATat, a 37-mer RNA oligomer, that binds efficiently to the Tat protein of HIV-1. In the present study, we analysed various properties of aptamer RNATat, including binding kinetics, identification of functional groups for Tat binding, and inhibition of Tat function. RESULTS The binding affinity of the isolated aptamer RNATat to Tat-1 was 133 times higher than that of authentic TAR-1 RNA. RNATat is composed of inverted repeats of two TAR-like motifs, and even though RNATat had two Tat-binding core elements, the interaction with Tat took place at a molar ratio of 1 : 1. Several functional groups of aptamer RNATat responsible for Tat binding were identified. The selected aptamer RNATat competed effectively for binding to Tat even in the presence of a large excess of TAR-1 or TAR-2 RNA in vitro, and specifically prevented Tat-dependent trans-activation both in vitro and in vivo. CONCLUSIONS Our results indicate that a novel aptamer, RNATat, retained strong affinity for Tat even in the presence of a large excess of HIV TAR. RNATat binds efficiently to Tat proteins or peptides derived from either HIV-1 or HIV-2. Unlike TAR RNA, RNATat affinity does not depend upon cellular proteins such as cyclin T1, thus RNATat has the potential for use as a molecular recognition element in biosensors.
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Affiliation(s)
- R Yamamoto
- National Institute of Bioscience and Human Technology, University of Tsukuba, Japan
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