1
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Nurmi C, Gu J, Mathai A, Brennan J, Li Y. Making target sites in large structured RNAs accessible to RNA-cleaving DNAzymes through hybridization with synthetic DNA oligonucleotides. Nucleic Acids Res 2024; 52:11177-11187. [PMID: 39248110 PMCID: PMC11472044 DOI: 10.1093/nar/gkae778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 08/26/2024] [Indexed: 09/10/2024] Open
Abstract
The 10-23 DNAzyme is one of the most active DNA-based enzymes, and in theory, can be designed to target any purine-pyrimidine junction within an RNA sequence for cleavage. However, purine-pyrimidine junctions within a large, structured RNA (lsRNA) molecule of biological origin are not always accessible to 10-23, negating its general utility as an RNA-cutting molecular scissor. Herein, we report a generalizable strategy that allows 10-23 to access any purine-pyrimidine junction within an lsRNA. Using three large SARS-CoV-2 mRNA sequences of 566, 584 and 831 nucleotides in length as model systems, we show that the use of antisense DNA oligonucleotides (ASOs) that target the upstream and downstream regions flanking the cleavage site can restore the activity (kobs) of previously poorly active 10-23 DNAzyme systems by up to 2000-fold. We corroborated these findings mechanistically using in-line probing to demonstrate that ASOs reduced 10-23 DNAzyme target site structure within the lsRNA substrates. This approach represents a simple, efficient, cost-effective, and generalizable way to improve the accessibility of 10-23 to a chosen target site within an lsRNA molecule, especially where direct access to the genomic RNA target is necessary.
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MESH Headings
- DNA, Catalytic/chemistry
- DNA, Catalytic/metabolism
- SARS-CoV-2/genetics
- RNA, Viral/chemistry
- RNA, Viral/metabolism
- RNA, Viral/genetics
- Nucleic Acid Hybridization
- Oligonucleotides, Antisense/chemistry
- Nucleic Acid Conformation
- RNA Cleavage
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Messenger/chemistry
- COVID-19/virology
- RNA/chemistry
- RNA/metabolism
- DNA, Single-Stranded
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Affiliation(s)
- Connor Nurmi
- Department of Biochemistry and Biomedical Sciences, McMaster University, Ontario L8S 4L8, Canada
- Biointerfaces Institute, McMaster University, Ontario L8S 4L8, Canada
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Ontario L8S 4L8, Canada
| | - Amal Mathai
- Department of Biochemistry and Biomedical Sciences, McMaster University, Ontario L8S 4L8, Canada
- Biointerfaces Institute, McMaster University, Ontario L8S 4L8, Canada
| | - John D Brennan
- Department of Biochemistry and Biomedical Sciences, McMaster University, Ontario L8S 4L8, Canada
- Biointerfaces Institute, McMaster University, Ontario L8S 4L8, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, Ontario L8S 4L8, Canada
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2
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Hu P, Li M, Wei X, Yang B, Li Y, Li CY, Du J. Cooperative Toehold: A Mechanism To Activate DNA Strand Displacement and Construct Biosensors. Anal Chem 2018; 90:9751-9760. [PMID: 30040891 DOI: 10.1021/acs.analchem.8b01202] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Toehold-mediated DNA strand displacement has proven powerful in the construction of various DNA circuits, DNA machines, and biosensors. So far, many new toehold activation mechanisms have been developed to achieve programmed DNA strand displacement behaviors. However, almost all those toeholds are inflexible via either a covalently attached manner or a complementary hybridization strategy, which limit the versatility of DNA devices. To solve this problem, we developed a new toehold, named "cooperative toehold", to activate DNA strand displacement. On the basis of a base stacking mechanism, the cooperative toehold is comprised of two moieties with completely independent DNA sequences between each other. The cooperative toehold enabled one to continuously tune the rate of DNA strand displacement, as well as more sophisticated strand displacement reactions. The cooperative toehold has also been employed as a universal signal translator for biosensors to qualitatively determine RNA and ATP. Moreover, as a novel specific PCR monitoring system, cooperative toehold-mediated DNA strand displacement can detect the pUC18 plasmid in genomic DNA samples with an aM detection limit.
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Affiliation(s)
- Pan Hu
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry , Xiangtan University , Xiangtan , Hunan 410005 , P. R. China
| | - Mengmeng Li
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry , Xiangtan University , Xiangtan , Hunan 410005 , P. R. China
| | - Xijiao Wei
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry , Xiangtan University , Xiangtan , Hunan 410005 , P. R. China
| | - Bin Yang
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry , Xiangtan University , Xiangtan , Hunan 410005 , P. R. China
| | - Ye Li
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry , Xiangtan University , Xiangtan , Hunan 410005 , P. R. China
| | - Chun-Yan Li
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry , Xiangtan University , Xiangtan , Hunan 410005 , P. R. China
| | - Jun Du
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry , Xiangtan University , Xiangtan , Hunan 410005 , P. R. China
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3
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Wang Y, Sun Y, Lau C, Lu J. Duplex microRNAs assay based on target-triggered universal reporter hybridization. J Pharm Anal 2018; 8:265-270. [PMID: 30140491 PMCID: PMC6104290 DOI: 10.1016/j.jpha.2018.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/09/2018] [Accepted: 07/10/2018] [Indexed: 12/14/2022] Open
Abstract
In this paper, we designed and evaluated a duplex detection strategy for microRNAs (miRNAs) using universal probe-based target-triggered double hybridization and fluorescent microsphere-based assay system (xMAP array). In the absence of target miRNA, reporter DNA cannot hybridize stably with the immobilized capture DNA due to its low melting temperature. Only after adding target miRNA, can reporter probe hybridize with capture probe to form a stable three-component complex. This target-triggered stable hybridization makes this method possible for highly selective and sensitive detection of multiple miRNAs. We exemplified a quantitative detection of duplex miRNAs with a limit of detection of 40 pM. The xMAP array platform holds the potential of extending this approach to simultaneous detection of up to 100 miRNA targets. Considering the simplicity, rapidity and multiplexing, this work promised a potential detection of multiple miRNA biomarkers for early disease diagnosis and prognosis.
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Affiliation(s)
- Yinan Wang
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Yue Sun
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Choiwan Lau
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Jianzhong Lu
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
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4
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Uliana CV, Riccardi CS, Yamanaka H. Diagnostic tests for hepatitis C: Recent trends in electrochemical immunosensor and genosensor analysis. World J Gastroenterol 2014; 20:15476-15491. [PMID: 25400433 PMCID: PMC4229514 DOI: 10.3748/wjg.v20.i42.15476] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 02/19/2014] [Accepted: 06/13/2014] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C is a liver disease that is transmitted through contact with the blood of an infected person. An estimated 150 million individuals worldwide have been chronically infected with the hepatitis C virus (HCV). Hepatitis C shows significant genetic variation in the global population, due to the high rate of viral RNA mutation. There are six variants of the virus (HCV genotypes 1, 2, 3, 4, 5, and 6), with 15 recorded subtypes that vary in prevalence across different regions of the world. A variety of devices are used to diagnose hepatitis C, including HCV antibody test, HCV viral load test, HCV genotype test and liver biopsy. Rapid, inexpensive, sensitive, and robust analytical devices are therefore essential for effective diagnosis and monitoring of disease treatment. This review provides an overview of current electrochemical immunosensor and genosensor technologies employed in HCV detection. There are a limited number of publications showing electrochemical biosensors being used for the detection of HCV. Due to their simplicity, specificity, and reliability, electrochemical biosensor devices have potential clinical applications in several viral infections.
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5
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Arata H, Hosokawa K, Maeda M. Rapid sub-attomole microRNA detection on a portable microfluidic chip. ANAL SCI 2014; 30:129-35. [PMID: 24420254 DOI: 10.2116/analsci.30.129] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Microfluidic devices are an attractive choice for meeting the requirements of point-of-care microRNA detection. A method using a microfluidic device can drastically shorten the incubation time because the device conveys sample molecules right straight to the surface-immobilized probe DNAs by hydrodynamic force. In this review, we present an overview of a new method for rapid and sensitive microRNA detection from a small sample volume using a power-free microfluidic device driven by degassed poly-dimethylsiloxane (PDMS). Two key technologies for this detection method are summarized. One of the methods relies on the coaxial stacking effect of nucleic acids during sandwich hybridization. This effect is also efficient for stabilizing sandwich hybridization consisting of small DNA and microRNA. The other is the laminar flow-assisted dendritic amplification, which increases the fluorescent signal by supplying two amplification reagents from laminar streams to surface-bound molecules. Utilizing both technologies, microRNA detection is possible with a 0.5 pM detection limit from a 0.5 μL sample corresponding to 0.25 attomoles, with a detection time of 20 min. Since microRNAs are associated with various human diseases, future studies of these technologies might contribute to improved healthcare and may have both industrial and societal impacts.
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6
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Li H, Zhang W, Zhou H. Electrochemical biosensor based on base-stacking-dependent DNA hybridization assay for protein detection. Anal Biochem 2014; 449:26-31. [DOI: 10.1016/j.ab.2013.12.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 11/30/2013] [Accepted: 12/15/2013] [Indexed: 02/07/2023]
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7
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Arata H, Komatsu H, Han A, Hosokawa K, Maeda M. Rapid microRNA detection using power-free microfluidic chip: coaxial stacking effect enhances the sandwich hybridization. Analyst 2012; 137:3234-7. [DOI: 10.1039/c2an16154k] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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8
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Cai S, Lau C, Lu J. Turn-on aptameric system for simple and selective detection of protein via base stacking-dependent DNA hybridization event. Anal Chem 2011; 83:5844-50. [PMID: 21707048 DOI: 10.1021/ac201054m] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Base stacking is employed in an entirely new type of sensing platform for the simple and robust detection of protein. Only in the presence of protein, the aptamer DNA can hybridize stably with the capture DNA to form a stem-loop structure due to the enhancement of base stacking. This leads to a strong chemiluminescence emission for simple protein detection. With the use of a platelet-derived growth factor as a model, a fM detection limit was obtained with a dynamic range that spanned 4 orders of magnitude. Upon modification, the approach presented herein was also extended to detect other types of targets including Hg(2+) ion and adenosine and also other types of labels such as fluorescence nanogold. We believe such advancements will represent a significant step toward improved diagnostics and more personalized medical treatment and environmental monitoring.
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Affiliation(s)
- Sheng Cai
- School of Pharmacy, Fudan University, Shanghai, China
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9
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Cai S, Lau C, Lu J. Sequence-specific detection of short-length DNA via template-dependent surface-hybridization events. Anal Chem 2011; 82:7178-84. [PMID: 20712363 DOI: 10.1021/ac101892t] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Short-length DNA and RNA, such as mature small RNA, which contains only 17-25 nucleotides, are always a problem in hybridization-based detection assays. In this paper, we report a proof-of-concept for a new short-length DNA detection technology which encompasses a design strategy whereby capture and reporter probes that do not hybridize to each other at 20 degrees C can be made to anneal to each other in the presence of a template via the formation of a stable three-component complex. The thermodynamics of this magnetic bead-based DNA biosensor was then investigated in detail by monitoring chemiluminescence (CL) changes in the absence and presence of targets over a temperature profile. The data show that this new biosensor offers the possibility of highly selective and sensitive detection of the short-length target DNA. In view of these advantages, this template-dependent surface-hybridization assay, as a new CL strategy, might create a universal technology for developing simple biosensors in sensitive and selective detection of short-length DNA and RNA.
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Affiliation(s)
- Sheng Cai
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
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10
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Bichenkova EV, Lang Z, Yu X, Rogert C, Douglas KT. DNA-mounted self-assembly: New approaches for genomic analysis and SNP detection. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:1-23. [PMID: 21111076 DOI: 10.1016/j.bbagrm.2010.11.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Revised: 11/07/2010] [Accepted: 11/12/2010] [Indexed: 11/25/2022]
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11
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Prigodich AE, Lee OS, Daniel WL, Seferos DS, Schatz GC, Mirkin CA. Tailoring DNA structure to increase target hybridization kinetics on surfaces. J Am Chem Soc 2010; 132:10638-41. [PMID: 20681682 DOI: 10.1021/ja104859j] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We report a method for increasing the rate of target hybridization on DNA-functionalized surfaces using a short internal complement DNA (sicDNA) strand. The sicDNA causes up to a 5-fold increase in association rate by inducing a conformational change that extends the DNA away from the surface, making it more available to bind target nucleic acids. The sicDNA-induced kinetic enhancement is a general phenomenon that occurred with all sequences and surfaces investigated. Additionally, the process is selective and can be used in multicomponent systems to controllably and orthogonally "turn on" specific sequences by the addition of the appropriate sicDNA. Finally, we show that sicDNA is compatible with systems used in gene regulation, intracellular detection, and microarrays, suggesting several potential therapeutic, diagnostic, and bioinformatic applications.
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Affiliation(s)
- Andrew E Prigodich
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA
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12
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Yuan BF, Zhuang XY, Hao YH, Tan Z. Kinetics of base stacking-aided DNA hybridization. Chem Commun (Camb) 2008:6600-2. [PMID: 19057792 DOI: 10.1039/b812929k] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The association and dissociation rate constants (k(a) and k(d)) of DNA hybridizations involving dual, single or no stacking with different base-pairing sizes were measured, which reveals the advantage of stacking hybridization in both the kinetic and steady state.
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Affiliation(s)
- Bi-feng Yuan
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
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13
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Improved sandwich-hybridization assay for an electrical DNA-chip-based monitoring of bioprocess-relevant marker genes. Appl Microbiol Biotechnol 2008; 78:719-28. [DOI: 10.1007/s00253-008-1347-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2007] [Revised: 12/22/2007] [Accepted: 12/30/2007] [Indexed: 10/22/2022]
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14
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Röder C, König H, Fröhlich J. Species-specific identification of Dekkera/Brettanomyces yeasts by fluorescently labeled DNA probes targeting the 26S rRNA. FEMS Yeast Res 2007; 7:1013-26. [PMID: 17596183 DOI: 10.1111/j.1567-1364.2007.00267.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Sequencing of the complete 26S rRNA genes of all Dekkera/Brettanomyces species colonizing different beverages revealed the potential for a specific primer and probe design to support diagnostic PCR approaches and FISH. By analysis of the complete 26S rRNA genes of all five currently known Dekkera/Brettanomyces species (Dekkera bruxellensis, D. anomala, Brettanomyces custersianus, B. nanus and B. naardenensis), several regions with high nucleotide sequence variability yet distinct from the D1/D2 domains were identified. FISH species-specific probes targeting the 26S rRNA gene's most variable regions were designed. Accessibility of probe targets for hybridization was facilitated by the construction of partially complementary 'side'-labeled probes, based on secondary structure models of the rRNA sequences. The specificity and routine applicability of the FISH-based method for yeast identification were tested by analyzing different wine isolates. Investigation of the prevalence of Dekkera/Brettanomyces yeasts in the German viticultural regions Wonnegau, Nierstein and Bingen (Rhinehesse, Rhineland-Palatinate) resulted in the isolation of 37 D. bruxellensis strains from 291 wine samples.
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Affiliation(s)
- Christoph Röder
- Institute of Microbiology and Wine Research, Johannes Gutenberg University, Mainz, Germany.
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15
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Carter DJ, Cary RB. Lateral flow microarrays: a novel platform for rapid nucleic acid detection based on miniaturized lateral flow chromatography. Nucleic Acids Res 2007; 35:e74. [PMID: 17478499 PMCID: PMC1904290 DOI: 10.1093/nar/gkm269] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Widely used nucleic acid assays are poorly suited for field deployment where access to laboratory instrumentation is limited or unavailable. The need for field deployable nucleic acid detection demands inexpensive, facile systems without sacrificing information capacity or sensitivity. Here we describe a novel microarray platform capable of rapid, sensitive nucleic acid detection without specialized instrumentation. The approach is based on a miniaturized lateral flow device that makes use of hybridization-mediated target capture. The miniaturization of lateral flow nucleic acid detection provides multiple advantages over traditional lateral flow devices. Ten-microliter sample volumes reduce reagent consumption and yield analyte detection times, excluding sample preparation and amplification, of <120 s while providing sub-femtomole sensitivity. Moreover, the use of microarray technology increases the potential information capacity of lateral flow. Coupled with a hybridization-based detection scheme, the lateral flow microarray (LFM) enables sequence-specific detection, opening the door to highly multiplexed implementations for broad-range assays well suited for point-of-care and other field applications. The LFM system is demonstrated using an isothermal amplification strategy for detection of Bacillus anthracis, the etiologic agent of anthrax. RNA from as few as two B. anthracis cells was detected without thermocycling hardware or fluorescence detection systems.
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Affiliation(s)
| | - R. Bruce Cary
- *To whom correspondence should be addressed. Tel: 505 665 6874; Fax: 505 665 3024;
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Liao JC, Mastali M, Li Y, Gau V, Suchard MA, Babbitt J, Gornbein J, Landaw EM, McCabe ERB, Churchill BM, Haake DA. Development of an advanced electrochemical DNA biosensor for bacterial pathogen detection. J Mol Diagn 2007; 9:158-68. [PMID: 17384207 PMCID: PMC1867445 DOI: 10.2353/jmoldx.2007.060052] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Electrochemical sensors have the capacity for rapid and accurate detection of a wide variety of target molecules in biological fluids. We have developed an electrochemical sensor assay involving hybridization of bacterial 16S rRNA to fluorescein-modified detector probes and to biotin-modified capture probes anchored to the sensor surface. Signal is generated by an oxidation-reduction current produced by the action of horseradish peroxidase conjugated to an anti-fluorescein monoclonal Fab. A previous study found that this electrochemical sensor strategy could identify uropathogens in clinical urine specimens. To improve assay sensitivity, we examined the key steps that affect the current amplitude of the electrochemical signal. Efficient lysis and release of 16S rRNA from both gram-negative and -positive bacteria was achieved with an initial treatment with Triton X-100 and lysozyme followed by alkaline lysis, resulting in a 12-fold increase in electrochemical signal compared with alkaline lysis alone. The distance in nucleotides between the target hybridization sites of the detector and capture probes and the location of fluorescein modification on the detector probe contributed to a 23-fold change in signal intensity. These results demonstrate the importance of target-probe and probe-probe interactions in the detection of bacterial 16S rRNA using an electrochemical DNA sensor approach.
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Affiliation(s)
- Joseph C Liao
- Department of Urology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
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17
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Abstract
Multiple oligonucleotides of the same or different sequence, linked end-to-end in tandem can be synthesized in a single automated synthesis. A linker phosphoramidite [R. T. Pon and S. Yu (2004) Nucleic Acids Res., 32, 623–631] is added to the 5′-terminal OH end of a support-bound oligonucleotide to introduce a cleavable linkage (succinic acid plus sulfonyldiethanol) and the 3′-terminal base of the new sequence. Conventional phosphoramidites are then used for the rest of the sequence. After synthesis, treatment with ammonium hydroxide releases the oligonucleotides from the support and cleaves the linkages between each sequence. Mixtures of one oligonucleotide with both 5′- and 3′-terminal OH ends and other oligonucleotides with 5′-phosphorylated and 3′-OH ends are produced, which are deprotected and worked up as a single product. Tandem synthesis can be used to make pairs of PCR primers, sets of cooperative oligonucleotides or multiple copies of the same sequence. When tandem synthesis is used to make two self-complementary sequences, double-stranded structures spontaneously form after deprotection. Tandem synthesis of oligonucleotide chains containing up to six consecutive 20mer (120 bases total), various trinucleotide codons and primer pairs for PCR, or self-complementary strands for in situ formation of double-stranded DNA fragments has been demonstrated.
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Affiliation(s)
- Richard T Pon
- Department of Biochemistry and Molecular Biology, University of Calgary Calgary, AB, Canada T2N 4N1.
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18
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Akutsu JI, Tojo Y, Segawa O, Obata K, Okochi M, Tajima H, Yohda M. Development of an integrated automation system with a magnetic bead-mediated nucleic acid purification device for genetic analysis and gene manipulation. Biotechnol Bioeng 2004; 86:667-71. [PMID: 15137078 DOI: 10.1002/bit.20049] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We have developed an integrated automation system for genetic analysis and gene manipulation. The system, SX-8G Plus, is equipped with an 8-nozzle dispensing unit, a thermal cycler, a cooled reagent reservoir, four tip storage racks, four microplate platforms, buffer reservoirs, an agarose gel electrophoresis unit, a power supply, a pump for exchanging electrophoresis buffer, and a CCD camera. Automation of nucleic acid extraction and purification, the most difficult step in automating genetic analysis and gene manipulation, was realized using magnetic beads with Magtration Technology, which we have previously developed for automating the handling of paramagnetic beads. Using this system, we could perform the automated separation and purification of DNA fragments by agarose gel electrophoresis starting from sample loading. The system would enable the automation of almost all procedures in genetic analysis and gene manipulation.
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Affiliation(s)
- Jun-Ichi Akutsu
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Naka-cho, Koganei, 184-8588, Japan
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19
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Skládal P, dos Santos Riccardi C, Yamanaka H, da Costa PI. Piezoelectric biosensors for real-time monitoring of hybridization and detection of hepatitis C virus. J Virol Methods 2004; 117:145-51. [PMID: 15041211 DOI: 10.1016/j.jviromet.2004.01.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2003] [Revised: 12/16/2003] [Accepted: 01/08/2004] [Indexed: 12/13/2022]
Abstract
The piezoelectric quartz crystal resonators modified with oligonucleotide probes were used for detection of hepatitis C virus (HCV) in serum. The gold electrodes on either rough or smooth surface crystals were modified with a self-assembled monolayer of cystamine. After activation with glutaraldehyde, either avidin or streptavidin were immobilized and used for attachment of biotinylated DNA probes (four different sequences). Piezoelectric biosensors were used in a flow-through setup for direct monitoring of DNA resulting from the reverse transcriptase-linked polymerase chain reaction (RT-PCR) amplification of the original viral RNA. The samples of patients with hepatitis C were analyzed and the results were compared with the standard RT-PCR procedure (Amplicor test kit of Roche, microwell format with spectrophotometric evaluation). The piezoelectric hybridization assay was completed in 10 min and the same sensing surface was suitable for repeated use.
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Affiliation(s)
- Petr Skládal
- Department of Analytical Chemistry, Institute of Chemistry, Universidade Estadual Paulista, Rua Prof. F. Degni s/n, 14801-900 Araraquara, SP, Brazil.
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20
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Barken KB, Gabig-Ciminska M, Holmgren A, Molin S. Effect of unlabeled helper probes on detection of an RNA target by bead-based sandwich hybridization. Biotechniques 2004; 36:124-32. [PMID: 14740494 DOI: 10.2144/04361rr03] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Unlabeled helper oligonucleotides assisting a bead-based sandwich hybridization assay were tested for the optimal placement of the capture and detection probes. The target used was a full-length in vitro synthesized mRNA molecule. Helper probes complementary to regions adjacent to the binding site of the 5′ end attached capture probe were found much more effective than helper probes targeting positions adjacent to the detection probe binding site. The difference is believed to be caused by a disruption of the RNA secondary structure in the area where the capture probe binds, thereby reducing structural interference from the bead. The use of additional helpers showed an additive effect. Using helpers at both sides of the capture and detection probes showed a 15- to 40-fold increase in hybridization efficiency depending on the target, thereby increasing the sensitivity of the hybridization assays. Using an electrical chip linked to the detection probe for the detection of p-aminophenol, which is produced by alkaline phosphatase, a detection limit of 2 × 10−13 M mRNA molecules was reached without the use of a nucleic acid amplification step.
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21
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Cheng J, Liu Y, Hong Y, Wang JJ, Yang Q. Screening and identification of genes trans-regulated by hepatitis C virus NC3 protein with microarray assay. Shijie Huaren Xiaohua Zazhi 2003; 11:930-934. [DOI: 10.11569/wcjd.v11.i7.930] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM To understand the target genes up-regulated or down-regulated by NS3 protein, we compared the differentially expressed genes between the hepatoblastoma cell line HepG2 transfected by pcDNA3.1(-) and pcDNA3.1-NS3, respectively by cDNA microarray technique.
METHODS The NS3 coding DNA fragment was amplified with polymerase chain reaction (PCR) technique by using pBRTM3011 containing the full length of HCV-H cDNA as the template. The expressive vector of pcDNA3.1-NS3 was constructed by routine molecular biological methods. The HepG2 cells were transfected by pcDNA3.1(-) and pcDNA3.1-NS3, respectively using lipofectamine. The total RNA was isolated and reverse transcribed. The cDNAs were subjected for microarray screening with 1 152 cDNA probes.
RESULTS The expressive vector has been constructed and confirmed by restriction enzyme digestion and DNA sequencing analysis. The expression of NS3 protein has been confirmed by Western blot with single chain variable region (scFv) antibody. High quality mRNA and cDNA had been prepared and successful microarray screening had been conducted. From the scanning results, it was found 34 genes were up-regulated and 37 genes were down-regulated by NS3 protein of HCV.
CONCLUSION NS3 protein is a transactivator. The expression of NS3 protein affected the expression spectrum of HCV infected hepatocyte. The microarray is an important technique for the study of transactivating effects for viral proteins.
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Affiliation(s)
- Jun Cheng
- Gene Therapy Research Center, Institute of Infectious Diseases, 302 Hospital of PLA, Beijing, China
| | - Yan Liu
- Gene Therapy Research Center, Institute of Infectious Diseases, 302 Hospital of PLA, Beijing, China
| | - Yuan Hong
- Gene Therapy Research Center, Institute of Infectious Diseases, 302 Hospital of PLA, Beijing, China
| | - Jian-Jun Wang
- Gene Therapy Research Center, Institute of Infectious Diseases, 302 Hospital of PLA, Beijing, China
| | - Qian Yang
- Gene Therapy Research Center, Institute of Infectious Diseases, 302 Hospital of PLA, Beijing, China
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22
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O'Meara D, Ahmadian A, Odeberg J, Lundeberg J. SNP typing by apyrase-mediated allele-specific primer extension on DNA microarrays. Nucleic Acids Res 2002; 30:e75. [PMID: 12140337 PMCID: PMC137093 DOI: 10.1093/nar/gnf074] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
This study reports the development of a microarray-based allele-specific extension method for typing of single nucleotide polymorphisms (SNPs). The use of allele-specific primers has been employed previously to identify single base variations but it is acknowledged that certain mismatches are not refractory to extension. Here we have overcome this limitation by introducing apyrase, a nucleotide-degrading enzyme, to the extension reaction. We have shown previously that DNA polymerases exhibit slower reaction kinetics when extending a mismatched primer compared with a matched primer. This kinetic difference is exploited in the apyrase-mediated allele-specific extension (AMASE) assay, allowing incorporation of nucleotides when the reaction kinetics are fast but degrading the nucleotides before extension when the reaction kinetics are slow. Here we show that five homozygous variants (14% of the total number of variants) that were incorrectly scored in the absence of apyrase were correctly typed when apyrase was included in the extension reaction. AMASE was performed in situ on the oligonucleotide microarrays using fluorescent nucleotides to type 10 SNPs and two indels in 17 individuals generating approximately 200 genotypes. Cluster analysis of these data shows three distinct clusters with clear-cut boundaries. We conclude that SNP typing on oligonucleotide microarrays by AMASE is an efficient, rapid and accurate technique for large-scale genotyping.
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Affiliation(s)
- Deirdre O'Meara
- Department of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Center, S-106 91 Stockholm, Sweden
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23
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Pon RT, Yu S, Sanghvi YS. Tandem oligonucleotide synthesis on solid-phase supports for the production of multiple oligonucleotides. J Org Chem 2002; 67:856-64. [PMID: 11856029 DOI: 10.1021/jo0160773] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
More than one oligonucleotide can be synthesized at a time by linking multiple oligonucleotides end-to-end in a tandem manner on the surface of a solid-phase support. The 5'-terminal hydroxyl position of one oligonucleotide serves as the starting point for the next oligonucleotide synthesis. The two oligonucleotides are linked via a cleavable 3'-O-hydroquinone-O,O'-diacetic acid linker arm (Q-linker). The Q-linker is rapidly and efficiently coupled to the 5'-OH position of immobilized oligonucleotides using HATU, HBTU, or HCTU in the presence of 1 equiv of DMAP. This protocol avoids introduction of phosphate linkages on either the 3'- or 5'-end of oligonucleotides. A single NH(4)OH cleavage step can simultaneously release the products from the surface of the support and each other to produce free 5'- and 3'-hydroxyl termini. Selective cleavage of one oligonucleotide out of two sequences has also been accomplished via a combination of succinyl and Q-linker linker arms. Tandem synthesis of multiple oligonucleotides is useful for producing sets of primers for PCR, DNA sequencing, and other diagnostic applications as well as double-stranded oligonucleotides. Tandem synthesis of the same sequence multiple times increases the yield of material from any single synthesis column for maximum economy in large-scale synthesis. This method can also be combined with reusable solid-phase supports to further reduce the cost of oligonucleotide production.
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Affiliation(s)
- Richard T Pon
- Department of Biochemistry and Molecular Biology, University of Calgary, 3350 Hospital Dr. N.W., Calgary, Alberta, Canada T2N 4N1.
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24
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Halliwell CM, Cass AE. A factorial analysis of silanization conditions for the immobilization of oligonucleotides on glass surfaces. Anal Chem 2001; 73:2476-83. [PMID: 11403288 DOI: 10.1021/ac0010633] [Citation(s) in RCA: 124] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The modification of glass surfaces with (3-mercaptopropyl)trimethoxysilane and the application of this to DNA chip technology are described. A range of factors influencing the silanization method, and hence the number of surface-bound, chemically active thiol groups, were investigated using a design of experiment approach based on analysis of variance. The number of thiol groups introduced on glass substrates were measured directly using a specific radiolabel, [14C]cysteamine hydrochloride. For liquid-phase silanization, the number of surface-bound thiol groups was found to be dependent on both postsilanization thermal curing and silanization time and relatively independent of silane concentration, reaction temperature, and sample pretreatment. Depending on the conditions used in liquid-phase silanization, (1.3-9.0) x 10(12) thiol groups/cm2 on the glass samples were bound. The reliability and repeatability of liquid- and vacuum-phase silanization were also investigated. Eighteen-base oligonucleotide probes were covalently attached to the modified surfaces via a 3'-amino modification on the DNA and subsequent reaction with the cross-linking reagent N-(gamma-maleimidobutyryloxy) succinimide ester (GMBS). The resulting probe levels were determined and found to be stoichiometric with that of the introduced thiol groups. These results demonstrate that silanization of glass surfaces under specific conditions, prior to probe attachment, is of great importance in the development of DNA chips that use the simple concept of the covalent attachment of presynthesized oligonucleotides to silicon oxide surfaces.
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Affiliation(s)
- C M Halliwell
- Department of Biochemistry, Imperial College of Science, Technology and Medicine, University of London, UK
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25
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Riccelli PV, Merante F, Leung KT, Bortolin S, Zastawny RL, Janeczko R, Benight AS. Hybridization of single-stranded DNA targets to immobilized complementary DNA probes: comparison of hairpin versus linear capture probes. Nucleic Acids Res 2001; 29:996-1004. [PMID: 11160933 PMCID: PMC29612 DOI: 10.1093/nar/29.4.996] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
A microtiter-based assay system is described in which DNA hairpin probes with dangling ends and single-stranded, linear DNA probes were immobilized and compared based on their ability to capture single-strand target DNA. Hairpin probes consisted of a 16 bp duplex stem, linked by a T(2)-biotin.dT-T(2) loop. The third base was a biotinylated uracil (U(B)) necessary for coupling to avidin coated microtiter wells. The capture region of the hairpin was a 3' dangling end composed of either 16 or 32 bases. Fundamental parameters of the system, such as probe density and avidin adsorption capacity of the plates were characterized. The target DNA consisted of 65 bases whose 3' end was complementary to the dangling end of the hairpin or to the linear probe sequence. The assay system was employed to measure the time dependence and thermodynamic stability of target hybridization with hairpin and linear probes. Target molecules were labeled with either a 5'-FITC, or radiolabeled with [gamma-(33)P]ATP and captured by either linear or hairpin probes affixed to the solid support. Over the range of target concentrations from 10 to 640 pmol hybridization rates increased with increasing target concentration, but varied for the different probes examined. Hairpin probes displayed higher rates of hybridization and larger equilibrium amounts of captured targets than linear probes. At 25 and 45 degrees C, rates of hybridization were better than twice as great for the hairpin compared with the linear capture probes. Hairpin-target complexes were also more thermodynamically stable. Binding free energies were evaluated from the observed equilibrium constants for complex formation. Results showed the order of stability of the probes to be: hairpins with 32 base dangling ends > hairpin probes with l6 base dangling ends > 16 base linear probes > 32 base linear probes. The physical characteristics of hairpins could offer substantial advantages as nucleic acid capture moieties in solid support based hybridization systems.
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Affiliation(s)
- P V Riccelli
- Department of Chemistry, University of Illinois at Chicago, IL 60607, USA
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26
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Fuchs BM, Glöckner FO, Wulf J, Amann R. Unlabeled helper oligonucleotides increase the in situ accessibility to 16S rRNA of fluorescently labeled oligonucleotide probes. Appl Environ Microbiol 2000; 66:3603-7. [PMID: 10919826 PMCID: PMC92190 DOI: 10.1128/aem.66.8.3603-3607.2000] [Citation(s) in RCA: 227] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Target site inaccessibility represents a significant problem for fluorescence in situ hybridization (FISH) of 16S rRNA with oligonucleotide probes. Here, unlabeled oligonucleotides (helpers) that bind adjacent to the probe target site were evaluated for their potential to increase weak probe hybridization signals in Escherichia coli DSM 30083(T). The use of helpers enhanced the fluorescence signal of all six probes examined at least fourfold. In one case, the signal of probe Eco474 was increased 25-fold with the use of a single helper probe, H440-2. In another case, four unlabeled helpers raised the FISH signal of a formerly weak probe, Eco585, to the level of the brightest monolabeled oligonucleotide probes available for E. coli. The temperature of dissociation and the mismatch discrimination of probes were not significantly influenced by the addition of helpers. Therefore, using helpers should not cause labeling of additional nontarget organisms at a defined stringency of hybridization. However, the helper action is based on sequence-specific binding, and there is thus a potential for narrowing the target group which must be considered when designing helpers. We conclude that helpers can open inaccessible rRNA regions for FISH with oligonucleotide probes and will thereby further improve the applicability of this technique for in situ identification of microorganisms.
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Affiliation(s)
- B M Fuchs
- Max-Planck-Institut für Marine Mikrobiologie, D-28359 Bremen, Germany.
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27
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Schneider BH, Dickinson EL, Vach MD, Hoijer JV, Howard LV. Highly sensitive optical chip immunoassays in human serum. Biosens Bioelectron 2000; 15:13-22. [PMID: 10826639 DOI: 10.1016/s0956-5663(00)00056-7] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Over the past decade the ability of refractometric optical sensors to quantitatively measure a wide range of biomolecules has been demonstrated. These include proteins, nucleic acids, microorganisms, and in competitive formats small molecules such as drugs and pesticides. Furthermore, by using high refractive index nanoparticles to amplify the biomolecular binding signal, sensitivities approaching those of well established diagnostic assays have been achieved. However, to date it has not been possible to show rapid detection of analytes in complex bodily fluids such as serum, in a one-step procedure, due to the interference resulting from non-specific binding (NSB) to the sensor surface. We have carried out preliminary work on the control of interference due to NSB using an optical chip based on the Hartman interferometer. This interferometer configuration employs a reference sensing region that can be functionalized separately from the specific sensing region. Optical chips were stored dry after surface functionalization, and rehydrated in serum. The observed level of background drift in serum was reduced by an order of magnitude when an exposed reference was used, compared to a reference which was blind to the sample. An additional 70% reduction in signal drift in serum was achieved by controlling the surface chemistry of the optical chip using a biotin-poly(ethylene glycol) (PEG) blocking agent. This functionalization procedure was combined with a sandwich assay using gold nanoparticles to develop a one-step assay for human chorionic gonadotropin (hCG) in human serum with a detection limit of 0.1 ng/ml for a 35 min assay.
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28
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Niemeyer CM, Boldt L, Ceyhan B, Blohm D. Evaluation of single-stranded nucleic acids as carriers in the DNA-directed assembly of macromolecules. J Biomol Struct Dyn 1999; 17:527-38. [PMID: 10636087 DOI: 10.1080/07391102.1999.10508383] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Current developments in nanosciences indicate that the self-assembly of macromolecules, such as proteins or metallic nanoclusters, can be conveniently achieved by means of nucleic acid hybridization. Within this context, we here report on the evaluation of single-stranded nucleic acids to be utilized as carrier backbones in DNA-directed self-assembly. A microplate solid-phase hybridization assay is described which allows rapid experimental determination of the hybridization efficiencies of various sequence stretches within a given nucleic acid carrier strand. As demonstrated for two DNA fragments of different sequence, the binding efficiencies of several oligonucleotides depend on the formation of specific secondary structure elements within the carrier molecule. A correlation of sequence-specific hybridization capability with modeled secondary structure is also obvious from experiments using the fluorescence gel-shift analysis. Electrophoretic studies on the employment of helper oligonucleotides in the formation of supramolecular conjugates of several oligonucleotide-tagged proteins indicate, that structural constraints can be minimized by disruption of intramolecular secondary structures of the carrier molecule. To estimate the influences of the chemical nature of the carrier, gel-shift experiments are carried out to compare a 170mer RNA molecule with its DNA analogue. Ternary aggregates, containing two protein components bound to the carrier, are formed with a greater efficiency on the DNA instead of the RNA carrier backbone.
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Affiliation(s)
- C M Niemeyer
- Universität Bremen, FB 2-UFT, Biotechnology and Molecular Genetics, Germany.
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29
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Abstract
The utilization of optical biosensors to study molecular interactions continues to expand. In 1998, 384 articles relating to the use of commercial biosensors were published in 130 different journals. While significant strides in new applications and methodology were made, a majority of the biosensor literature is of rather poor quality. Basic information about experimental conditions is often not presented and many publications fail to display the experimental data, bringing into question the credibility of the results. This review provides suggestions on how to collect, analyze and report biosensor data.
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Affiliation(s)
- D G Myszka
- University of Utah, Salt Lake City, UT 84132, USA.
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30
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Nilsson P, O'meara D, Edebratt F, Persson B, Uhlén M, Lundeberg J, Nygren P. Quantitative investigation of the modular primer effect for DNA and peptide nucleic acid hexamers. Anal Biochem 1999; 269:155-61. [PMID: 10094787 DOI: 10.1006/abio.1999.4000] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The effect on oligonucleotide-template duplex stability upon cohybridization of adjacently annealing oligonucleotides, the modular primer effect, was studied with biosensor technology. DNA and peptide nucleic acid (PNA) hexamer modules and sensor chip-immobilized template DNA strands were designed for analysis of nick, overlap, and gap modular hybridization situations. The fast hybridization kinetics for such hexamer modules allowed for the determination of apparent duplex affinities from equilibrium responses. The results showed that the hybridizational stability of modular hexamer pairs is strongly dependent on the positioning, concentration, and inherent affinity of the adjacently annealing hexamer module. Up to 80-fold increases in apparent affinities could be observed for adjacent modular oligonucleotide pairs compared to affinities determined for single hexamer oligonucleotide hybridizations. Interestingly, also for coinjections of different module combinations where DNA hexamer modules were replaced by their PNA counterparts, a modular primer effect was observed. The introduction of a single base gap between two hexamer modules significantly reduced the stabilization effect, whereas a gap of two bases resulted in a complete loss of the effect. The results suggest that the described biosensor-based methodology should be useful for the selection of appropriate modules and working concentrations for use in different modular hybridization applications.
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Affiliation(s)
- P Nilsson
- Department of Biotechnology, KTH-Royal Institute of Technology, Stockholm, SE-100 44, Sweden
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31
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Turková J. Oriented immobilization of biologically active proteins as a tool for revealing protein interactions and function. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 1999; 722:11-31. [PMID: 10068131 DOI: 10.1016/s0378-4347(98)00434-4] [Citation(s) in RCA: 270] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The advantages of oriented immobilization of biologically active proteins are good steric accessibilities of active binding sites and increased stability. This not only may help to increase the production of preparative procedures but is likely to promote current knowledge about how the living cells or tissues operate. Protein inactivation starts with the unfolding of the protein molecule by the contact of water with hydrophobic clusters located on the surface of protein molecules, which results in ice-like water structure. Reduction of the nonpolar surface area by the formation of a suitable biospecifc complex or by use of carbohydrate moieties thus may stabilize proteins. This review discusses oriented immobilization of antibodies by use of immobilized protein A or G. The section about oriented immobilization of proteins by use of their suitable antibodies covers immobilization of enzymes utilizing their adsorption on suitable immunosorbents prepared using monoclonal or polyclonal antibodies, preparation of bioaffinity adsorbent for the isolation of concanavalin A and immobilization of antibodies by use of antimouse immunoglobulin G, Fc-specific (i.e. specific towards the constant region of the molecule). In the further section immobilization of antibodies and enzymes through their carbohydrate moieties is described. Oriented immobilization of proteins can be also based on the use of boronate affinity gel or immobilized metal ion affinity chromatography technique. Biotin-avidin or streptavidin techniques are mostly used methods for oriented immobilization. Site-specific attachment of proteins to the surface of solid supports can be also achieved by enzyme, e.g., subtilisin, after introduction a single cysteine residue by site-directed mutagenesis.
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Affiliation(s)
- J Turková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague
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32
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O'Meara D, Yun Z, Sönnerborg A, Lundeberg J. Cooperative oligonucleotides mediating direct capture of hepatitis C virus RNA from serum. J Clin Microbiol 1998; 36:2454-9. [PMID: 9705373 PMCID: PMC105143 DOI: 10.1128/jcm.36.9.2454-2459.1998] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A novel method for direct capture of hepatitis C virus (HCV) RNA from clinical samples has been developed. This approach takes advantage of the cooperative interactions between adjacently hybridized oligonucleotides. Here, this cooperative effect was combined with solid-phase technology, whereby a capture probe was covalently coupled to magnetic beads and a second probe, which anneals adjacent to the capture probe site, was prehybridized in solution to the target. When these contiguously hybridized probes were used for the extraction of HCV RNA from clinical samples, the capture efficiency was increased up to 25-fold in comparison to capture with a single probe. The applicability of this sample preparation assay was further investigated by performing a comparative study with both a conventional guanidinium extraction method and a commercial quantitative assay.
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Affiliation(s)
- D O'Meara
- Department of Biochemistry and Biotechnology, Royal Institute of Technology (KTH), Stockholm, Sweden
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