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Ahn JY, Lee SW, Kang HS, Jo M, Lee DK, Laurell T, Kim S. Aptamer microarray mediated capture and mass spectrometry identification of biomarker in serum samples. J Proteome Res 2010; 9:5568-73. [PMID: 20806970 DOI: 10.1021/pr100300t] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Sensitive detection of molecular biomarkers in clinical samples is crucially important in disease diagnostics. This paper reports the development of an aptamer microarray platform combined with sol-gel technology to identify low-abundance targets in complex serum samples. Because of the nanoporous structure of the sol-gel, a high capacity to immobilize the affinity specific aptamers is accomplished which allows binding and detection of target molecules with high sensitivity. The captured protein is digested in situ and the obtained digest was analyzed by ESI-MS without any interference from the affinity probe. TBP (TATA Box Protein) and its specific aptamers were chosen as a model system. A proof of concept with protein concentrations ranging between nanomolar to micromolar is reported, showing a good linearity up to 400 nM when characterized in an aptamer sandwich assay. Moreover, as low as 0.001% of target protein present in total serum proteins could be identified without any pretreatment step using ESI MS/MS mass spectrometry. We believe this novel strategy could become an efficient method for aptamer-based biomarker detection linked directly to mass spectrometry readout.
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Affiliation(s)
- Ji-Young Ahn
- Department of Biomedical Engineering, Dongguk University, Joong-Gu, Seoul, 100-715, Korea
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Cheng G, Shen B, Zhang F, Wu J, Xu Y, He P, Fang Y. A new electrochemically active-inactive switching aptamer molecular beacon to detect thrombin directly in solution. Biosens Bioelectron 2010; 25:2265-9. [PMID: 20378327 DOI: 10.1016/j.bios.2010.03.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 03/03/2010] [Accepted: 03/03/2010] [Indexed: 11/30/2022]
Abstract
A new electrochemical aptamer molecular beacon (MB) was designed by the carminic acid (CA) covalently linking at the each end of a special single-stranded stem-loop shaped oligonucleotide and named as CAs-MB. CA is an electrochemically active molecule and two CA molecules at the ends of molecular beacon stem were closed enough to associate each other to be as CA dimer. The dimer was electrochemically inactive. It separated into two CA monomers and produced the electrochemical signal while CAs-MB combined with target. In this protocol, the detection strategy of CAs-MB for thrombin is based on electrochemical active-inactive switching between monomer and dimer forms of CA. In order to enhance the electrochemical signal, magnetic nanobeads (MNB) was applied by connecting CAs-MB with MNB through a duplex of DNA. With the magnetic enrichment, the detection limit for thrombin reached to 42.4 pM. The experiment results showed that this type of electrochemical active-inactive switching aptamer molecular beacon allowed the direct detection of target proteins in the solution with no requirement of removing uncombined CAs-MB. Besides, CAs-MB/MNB can be easily regenerated by using 2M NaCl solution to cleave the thrombin from the aptasensor.
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Affiliation(s)
- Guifang Cheng
- Department of Chemistry, East China Normal University, Shanghai 200062, China.
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Yadav R, Dwivedi S, Kumar S, Chaudhury A. Trends and Perspectives of Biosensors for Food and Environmental Virology. FOOD AND ENVIRONMENTAL VIROLOGY 2010; 2. [PMCID: PMC7090531 DOI: 10.1007/s12560-010-9034-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Food and environmental virology has become a very important and interesting area of research because of food safety and public health concerns. During the last few decades, increasing foodborne diseases and environmental generated illnesses are considered to be highly challenging issues. Biosensor technology holds great promise for the healthcare market, and the security sector. Similar to clinical diagnostic tools, biosensors are being developed for the rapid, reliable, yet inexpensive identification and enumeration of pathogenic viruses which are adulterating environment, food and feed commodities. In this modern era, bio-and nano-technologies play a pivotal role in virological diagnostics of food industry, environmental and veterinary samples. This review covers the recent advances and future prospects of nanotechnology-based bioanalytical microsystems for food and environmental virology.
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Affiliation(s)
- Rakesh Yadav
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, 125001 Haryana India
| | - Sadhana Dwivedi
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, 125001 Haryana India
| | - Sandeep Kumar
- Division of Biochemistry, Directorate of Rapeseed-Mustard Research, ICAR, Sewar, Bharatpur, 321303 Rajasthan India
| | - Ashok Chaudhury
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, 125001 Haryana India
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Ahn DG, Jeon IJ, Kim JD, Song MS, Han SR, Lee SW, Jung H, Oh JW. RNA aptamer-based sensitive detection of SARS coronavirus nucleocapsid protein. Analyst 2009; 134:1896-901. [PMID: 19684916 DOI: 10.1039/b906788d] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV) is the etiological agent of a newly emerged disease SARS. The SARS-CoV nucleocapsid (N) protein is one of the most abundant structural proteins and serves as a diagnostic marker for accurate and sensitive detection of the virus. Using a SELEX (systematic evolution of ligand by exponential enrichment) procedure and recombinant N protein, we selected a high-affinity RNA aptamer capable of binding to N protein with a dissociation constant of 1.65 nM. Electrophoretic mobility shift assays and RNA competition experiments showed that the selected aptamer recognized selectively the C-terminal region of N protein with high specificity. Using a chemiluminescence immunosorbent assay and a nanoarray aptamer chip with the selected aptamer as an antigen-capturing agent, we could sensitively detect N protein at a concentration as low as 2 pg/ml. These aptamer-antibody hybrid immunoassays may be useful for rapid, sensitive detection of SARS-CoV N protein.
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Affiliation(s)
- Dae-Gyun Ahn
- Department of Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea
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Torres-Chavolla E, Alocilja EC. Aptasensors for detection of microbial and viral pathogens. Biosens Bioelectron 2009; 24:3175-82. [PMID: 19117748 PMCID: PMC7125720 DOI: 10.1016/j.bios.2008.11.010] [Citation(s) in RCA: 209] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Revised: 11/14/2008] [Accepted: 11/17/2008] [Indexed: 12/01/2022]
Abstract
Aptamers are specific nucleic acid sequences that can bind to a wide range of non-nucleic acid targets with high affinity and specificity. These molecules are identified and selected through an in vitro process called SELEX (systematic evolution of ligands by exponential enrichment). Proteins are the most common targets in aptamer selection. In diagnostic and detection assays, aptamers represent an alternative to antibodies as recognition agents. Cellular detection is a promising area in aptamer research. One of its principal advantages is the ability to target and specifically differentiate microbial strains without having previous knowledge of the membrane molecules or structural changes present in that particular microorganism. The present review focuses on aptamers, SELEX procedures, and aptamer-based biosensors (aptasensors) for the detection of pathogenic microorganisms and viruses. Special emphasis is placed on nanoparticle-based platforms.
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Affiliation(s)
- Edith Torres-Chavolla
- Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI 48824, USA
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Ban JO, Oh JH, Hwang BY, Moon DC, Jeong HS, Lee S, Kim S, Lee H, Kim KB, Han SB, Hong JT. Inflexinol inhibits colon cancer cell growth through inhibition of nuclear factor-kappaB activity via direct interaction with p50. Mol Cancer Ther 2009; 8:1613-24. [PMID: 19509257 DOI: 10.1158/1535-7163.mct-08-0694] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Kaurane diterpene compounds have been known to be cytotoxic against several cancer cells through inhibition of nuclear factor-kappaB (NF-kappaB) activity. Here, we showed that inflexinol, a novel kaurane diterpene compound, inhibited the activity of NF-kappaB and its target gene expression as well as cancer cell growth through induction of apoptotic cell death in vitro and in vivo. These inhibitory effects on NF-kappaB activity and on cancer cell growth were suppressed by the reducing agents DTT and glutathione and were abrogated in the cells transfected with mutant p50 (C62S). Sol-gel biochip and surface plasmon resonance analysis showed that inflexinol binds to the p50 subunit of NF-kappaB. These results suggest that inflexinol inhibits colon cancer cell growth via induction of apoptotic cell death through inactivation of NF-kappaB by a direct modification of cysteine residue in the p50 subunit of NF-kappaB.
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Affiliation(s)
- Jung Ok Ban
- College of Pharmacy, Chungbuk National University, 48 Gaeshin-dong, Heungduk-gu, Cheonju, Korea
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Park SM, Ahn JY, Jo M, Lee DK, Lis JT, Craighead HG, Kim S. Selection and elution of aptamers using nanoporous sol-gel arrays with integrated microheaters. LAB ON A CHIP 2009; 9:1206-12. [PMID: 19370238 DOI: 10.1039/b814993c] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
RNA and DNA aptamers that bind to target molecules with high specificity and affinity have been a focus of diagnostics and therapeutic research. These aptamers are obtained by SELEX (Systematic Evolution of Ligands by EXponential enrichment) often requiring more than 10 successive cycles of selection and amplification, where each cycle normally takes 2 days per cycle of SELEX. Here, we have demonstrated the use of sol-gel arrays of proteins in a microfluidic system for efficient selection of RNA aptamers against multiple target molecules. The microfluidic chip incorporates five sol-gel binding droplets, within which specific target proteins are imbedded. The droplets are patterned on top of individually addressable electrical microheaters used for selective elution of aptamers bound to target proteins in the sol-gel droplets. We demonstrate that specific aptamers bind their respective protein targets and can be selectively eluted by micro-heating. Finally, our microfluidic SELEX system greatly improved selection efficiency, reducing the number of selection cycles needed to produce high affinity aptamers. The process is readily scalable to larger arrays of sol-gel-embedded proteins. To our knowledge, this is the first demonstration of a chip-based selection of aptamers using microfluidics, thereby allowing development of a high throughput and efficient SELEX procedures.
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Affiliation(s)
- Seung-Min Park
- Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
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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: 577] [Impact Index Per Article: 38.5] [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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Rich RL, Myszka DG. Survey of the year 2007 commercial optical biosensor literature. J Mol Recognit 2008; 21:355-400. [DOI: 10.1002/jmr.928] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Abstract
Systematic evolution of ligand by exponential enrichment (SELEX) is a new combinational chemical methodology for in vitro selection of specific aptamers. Aptamers are artificial oligonucleotide ligands with high affinity binding to target molecules. They are isolated from combinational libraries of synthetic oligonucleotide by an iterative process of affinity selection, recovery and amplification. Several properties of aptamers such as convenient affinity selection and high affinity and specificify make them widely used. Their affinity and specificity for a given protein are superior to antibodies and make it possible to isolate a matching ligand and adjust its bioactivity. This article reviews the development and potentially clinical application of aptamers targeting at hepatitis C virus.
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Nitsche A, Kurth A, Dunkhorst A, Pänke O, Sielaff H, Junge W, Muth D, Scheller F, Stöcklein W, Dahmen C, Pauli G, Kage A. One-step selection of Vaccinia virus-binding DNA aptamers by MonoLEX. BMC Biotechnol 2007; 7:48. [PMID: 17697378 PMCID: PMC1994675 DOI: 10.1186/1472-6750-7-48] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2007] [Accepted: 08/15/2007] [Indexed: 11/15/2022] Open
Abstract
Background As a new class of therapeutic and diagnostic reagents, more than fifteen years ago RNA and DNA aptamers were identified as binding molecules to numerous small compounds, proteins and rarely even to complete pathogen particles. Most aptamers were isolated from complex libraries of synthetic nucleic acids by a process termed SELEX based on several selection and amplification steps. Here we report the application of a new one-step selection method (MonoLEX) to acquire high-affinity DNA aptamers binding Vaccinia virus used as a model organism for complex target structures. Results The selection against complete Vaccinia virus particles resulted in a 64-base DNA aptamer specifically binding to orthopoxviruses as validated by dot blot analysis, Surface Plasmon Resonance, Fluorescence Correlation Spectroscopy and real-time PCR, following an aptamer blotting assay. The same oligonucleotide showed the ability to inhibit in vitro infection of Vaccinia virus and other orthopoxviruses in a concentration-dependent manner. Conclusion The MonoLEX method is a straightforward procedure as demonstrated here for the identification of a high-affinity DNA aptamer binding Vaccinia virus. MonoLEX comprises a single affinity chromatography step, followed by subsequent physical segmentation of the affinity resin and a single final PCR amplification step of bound aptamers. Therefore, this procedure improves the selection of high affinity aptamers by reducing the competition between aptamers of different affinities during the PCR step, indicating an advantage for the single-round MonoLEX method.
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Affiliation(s)
- Andreas Nitsche
- Centre for Biological Safety 1, Robert Koch-Institut, Nordufer 20, 13353 Berlin, Germany
| | - Andreas Kurth
- Centre for Biological Safety 1, Robert Koch-Institut, Nordufer 20, 13353 Berlin, Germany
| | - Anna Dunkhorst
- Centre for Biological Safety 1, Robert Koch-Institut, Nordufer 20, 13353 Berlin, Germany
| | - Oliver Pänke
- Department of Biology/Chemistry, Division of Biophysics, University of Osnabrueck, 49069 Osnabrueck, Germany
- Biosystems Technology, University of Applied Sciences Wildau, Bahnhofstr. 1, 15747 Wildau, Germany
| | - Hendrik Sielaff
- Department of Biology/Chemistry, Division of Biophysics, University of Osnabrueck, 49069 Osnabrueck, Germany
| | - Wolfgang Junge
- Department of Biology/Chemistry, Division of Biophysics, University of Osnabrueck, 49069 Osnabrueck, Germany
| | - Doreen Muth
- Centre for Biological Safety 1, Robert Koch-Institut, Nordufer 20, 13353 Berlin, Germany
| | - Frieder Scheller
- Institute of Biochemistry and Biology, Department of Analytical Biochemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Golm, Germany
| | - Walter Stöcklein
- Institute of Biochemistry and Biology, Department of Analytical Biochemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Golm, Germany
| | - Claudia Dahmen
- AptaRes AG, Im Biotechnologiepark TGZ I, 14943 Luckenwalde, Germany
| | - Georg Pauli
- Centre for Biological Safety 1, Robert Koch-Institut, Nordufer 20, 13353 Berlin, Germany
| | - Andreas Kage
- Institute of Laboratory Medicine and Pathobiochemistry, Charité Universitätsmedizin Berlin, Westend Haus 31, Spandauer Damm 130, 14050 Berlin, Germany
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