The Experts below are selected from a list of 210 Experts worldwide ranked by ideXlab platform
Ulrich J Krull - One of the best experts on this subject based on the ideXlab platform.
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a paper based resonance energy transfer Nucleic Acid Hybridization assay using upconversion nanoparticles as donors and quantum dots as acceptors
Analytica Chimica Acta, 2015Co-Authors: Samer Doughan, Uvaraj Uddayasankar, Ulrich J KrullAbstract:Abstract Monodisperse aqueous upconverting nanoparticles (UCNPs) were covalently immobilized on aldehyde modified cellulose paper via reduction amination to develop a luminescence resonance energy transfer (LRET)-based Nucleic Acid Hybridization assay. This first account of covalent immobilization of UCNPs on paper for a bioassay reports an optically responsive method that is sensitive, reproducible and robust. The immobilized UCNPs were decorated with oligonucleotide probes to capture HPRT1 housekeeping gene fragments, which in turn brought reporter conjugated quantum dots (QDs) in close proximity to the UCNPs for LRET. This sandwich assay could detect unlabeled oligonucleotide target, and had a limit of detection of 13 fmol and a dynamic range spanning nearly 3 orders of magnitude. The use of QDs, which are excellent LRET acceptors, demonstrated improved sensitivity, limit of detection, dynamic range and selectivity compared to similar assays that have used molecular fluorophores as acceptors. The selectivity of the assay was attributed to the decoration of the QDs with polyethylene glycol to eliminate non-specific adsorption. The kinetics of Hybridization were determined to be diffusion limited and full signal development occurred within 3 min.
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camera based ratiometric fluorescence transduction of Nucleic Acid Hybridization with reagentless signal amplification on a paper based platform using immobilized quantum dots as donors
Analytical Chemistry, 2014Co-Authors: Omair M Noor, Ulrich J KrullAbstract:Paper-based diagnostic assays are gaining increasing popularity for their potential application in resource-limited settings and for point-of-care screening. Achievement of high sensitivity with precision and accuracy can be challenging when using paper substrates. Herein, we implement the red-green-blue color palette of a digital camera for quantitative ratiometric transduction of Nucleic Acid Hybridization on a paper-based platform using immobilized quantum dots (QDs) as donors in fluorescence resonance energy transfer (FRET). A nonenzymatic and reagentless means of signal enhancement for QD-FRET assays on paper substrates is based on the use of dry paper substrates for data acquisition. This approach offered at least a 10-fold higher assay sensitivity and at least a 10-fold lower limit of detection (LOD) as compared to hydrated paper substrates. The surface of paper was modified with imidazole groups to assemble a transduction interface that consisted of immobilized QD-probe oligonucleotide conjugates....
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paper based solid phase multiplexed Nucleic Acid Hybridization assay with tunable dynamic range using immobilized quantum dots as donors in fluorescence resonance energy transfer
Analytical Chemistry, 2013Co-Authors: Omair M Noor, Ulrich J KrullAbstract:A multiplexed solid-phase Nucleic Acid Hybridization assay on a paper-based platform is presented using multicolor immobilized quantum dots (QDs) as donors in fluorescence resonance energy transfer (FRET). The surface of paper was modified with imidazole groups to immobilize two types of QD-probe oligonucleotide conjugates that were assembled in solution. Green-emitting QDs (gQDs) and red-emitting QDs (rQDs) served as donors with Cy3 and Alexa Fluor 647 (A647) acceptors. The gQD/Cy3 FRET pair served as an internal standard, while the rQD/A647 FRET pair served as a detection channel, combining the control and analytical test zones in one physical location. Hybridization of dye-labeled oligonucleotide targets provided the proximity for FRET sensitized emission from the acceptor dyes, which served as an analytical signal. Hybridization assays in the multicolor format provided a limit of detection of 90 fmol and an upper limit of dynamic range of 3.5 pmol. The use of an array of detection zones was designed t...
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paper based solid phase Nucleic Acid Hybridization assay using immobilized quantum dots as donors in fluorescence resonance energy transfer
Analytical Chemistry, 2013Co-Authors: Omair M Noor, Anna Shahmuradyan, Ulrich J KrullAbstract:A paper-based solid-phase assay is presented for transduction of Nucleic Acid Hybridization using immobilized quantum dots (QDs) as donors in fluorescence resonance energy transfer (FRET). The surface of paper was modified with imidazole groups to immobilize QD–probe oligonucleotide conjugates that were assembled in solution. Green-emitting QDs (gQDs) were FRET-paired with Cy3 acceptor. Hybridization of Cy3-labeled oligonucleotide targets provided the proximity required for FRET-sensitized emission from Cy3, which served as an analytical signal. The assay exhibited rapid transduction of Nucleic Acid Hybridization within minutes. Without any amplification steps, the limit of detection of the assay was found to be 300 fmol with the upper limit of the dynamic range at 5 pmol. The implementation of glutathione-coated QDs for the development of Nucleic Acid Hybridization assay integrated on a paper-based platform exhibited excellent resistance to nonspecific adsorption of oligonucleotides and showed no reducti...
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multiplexed interfacial transduction of Nucleic Acid Hybridization using a single color of immobilized quantum dot donor and two acceptors in fluorescence resonance energy transfer
Analytical Chemistry, 2010Co-Authors: Russ W Algar, Ulrich J KrullAbstract:A multiplexed solid-phase assay for the detection of Nucleic Acid Hybridization was developed on the basis of a single color of immobilized CdSe/ZnS quantum dot (QD) as a donor in fluorescence resonance energy transfer (FRET). This work demonstrated that two channels of detection did not necessitate two different QD donors. Two probe oligonucleotides were coimmobilized on optical fibers modified with QDs, and a sandwich assay was used to associate the acceptor dyes with interfacial Hybridization events without target labeling. FRET-sensitized acceptor emission provided an analytical signal that was concentration dependent down to 10 nM. Changes in the ratio of coimmobilized probe oligonucleotides were found to yield linear changes in the relative amounts of acceptor emission. These changes were compared to previous studies that used mixed films of two QD donors for two detection channels. The analysis indicated that probe dilution effects were primarily driven by changes in acceptor number density and tha...
Omair M Noor - One of the best experts on this subject based on the ideXlab platform.
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camera based ratiometric fluorescence transduction of Nucleic Acid Hybridization with reagentless signal amplification on a paper based platform using immobilized quantum dots as donors
Analytical Chemistry, 2014Co-Authors: Omair M Noor, Ulrich J KrullAbstract:Paper-based diagnostic assays are gaining increasing popularity for their potential application in resource-limited settings and for point-of-care screening. Achievement of high sensitivity with precision and accuracy can be challenging when using paper substrates. Herein, we implement the red-green-blue color palette of a digital camera for quantitative ratiometric transduction of Nucleic Acid Hybridization on a paper-based platform using immobilized quantum dots (QDs) as donors in fluorescence resonance energy transfer (FRET). A nonenzymatic and reagentless means of signal enhancement for QD-FRET assays on paper substrates is based on the use of dry paper substrates for data acquisition. This approach offered at least a 10-fold higher assay sensitivity and at least a 10-fold lower limit of detection (LOD) as compared to hydrated paper substrates. The surface of paper was modified with imidazole groups to assemble a transduction interface that consisted of immobilized QD-probe oligonucleotide conjugates....
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paper based solid phase multiplexed Nucleic Acid Hybridization assay with tunable dynamic range using immobilized quantum dots as donors in fluorescence resonance energy transfer
Analytical Chemistry, 2013Co-Authors: Omair M Noor, Ulrich J KrullAbstract:A multiplexed solid-phase Nucleic Acid Hybridization assay on a paper-based platform is presented using multicolor immobilized quantum dots (QDs) as donors in fluorescence resonance energy transfer (FRET). The surface of paper was modified with imidazole groups to immobilize two types of QD-probe oligonucleotide conjugates that were assembled in solution. Green-emitting QDs (gQDs) and red-emitting QDs (rQDs) served as donors with Cy3 and Alexa Fluor 647 (A647) acceptors. The gQD/Cy3 FRET pair served as an internal standard, while the rQD/A647 FRET pair served as a detection channel, combining the control and analytical test zones in one physical location. Hybridization of dye-labeled oligonucleotide targets provided the proximity for FRET sensitized emission from the acceptor dyes, which served as an analytical signal. Hybridization assays in the multicolor format provided a limit of detection of 90 fmol and an upper limit of dynamic range of 3.5 pmol. The use of an array of detection zones was designed t...
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paper based solid phase Nucleic Acid Hybridization assay using immobilized quantum dots as donors in fluorescence resonance energy transfer
Analytical Chemistry, 2013Co-Authors: Omair M Noor, Anna Shahmuradyan, Ulrich J KrullAbstract:A paper-based solid-phase assay is presented for transduction of Nucleic Acid Hybridization using immobilized quantum dots (QDs) as donors in fluorescence resonance energy transfer (FRET). The surface of paper was modified with imidazole groups to immobilize QD–probe oligonucleotide conjugates that were assembled in solution. Green-emitting QDs (gQDs) were FRET-paired with Cy3 acceptor. Hybridization of Cy3-labeled oligonucleotide targets provided the proximity required for FRET-sensitized emission from Cy3, which served as an analytical signal. The assay exhibited rapid transduction of Nucleic Acid Hybridization within minutes. Without any amplification steps, the limit of detection of the assay was found to be 300 fmol with the upper limit of the dynamic range at 5 pmol. The implementation of glutathione-coated QDs for the development of Nucleic Acid Hybridization assay integrated on a paper-based platform exhibited excellent resistance to nonspecific adsorption of oligonucleotides and showed no reducti...
Hyunmin Yi - One of the best experts on this subject based on the ideXlab platform.
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fabrication of uniform dna conjugated hydrogel microparticles via replica molding for facile Nucleic Acid Hybridization assays
Analytical Chemistry, 2010Co-Authors: Christina L. Lewis, Changhyung Choi, Hyunmin YiAbstract:We identify and investigate several critical parameters in the fabrication of single-stranded DNA conjugated poly(ethylene glycol) (PEG) microparticles based on replica molding (RM) for highly uniform and robust Nucleic Acid Hybridization assays. The effects of PEG-diacrylate, probe DNA, and photoinitiator concentrations on the overall fluorescence and target DNA penetration depth upon Hybridization are examined. Fluorescence and confocal microscopy results illustrate high conjugation capacity of the probe and target DNA, femtomole sensitivity, and sequence specificity. Combined, these findings demonstrate a significant step toward simple, robust, and scalable procedures to manufacture highly uniform and high-capacity Hybridization assay particles in a well-controlled manner by exploiting many advantages that the batch processing-based RM technique offers. We envision that the results presented here may be readily applied to rapid and high-throughput Hybridization assays for a wide variety of applications...
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Hierarchical assembly of viral nanotemplates with encoded microparticles via Nucleic Acid Hybridization.
Langmuir, 2008Co-Authors: Christina L. Lewis, Nicholas E. Horelik, Daniel C. Pregibon, Patrick S. Doyle, Hyunmin YiAbstract:: We demonstrate hierarchical assembly of tobacco mosaic virus (TMV)-based nanotemplates with hydrogel-based encoded microparticles via Nucleic Acid Hybridization. TMV nanotemplates possess a highly defined structure and a genetically engineered high density thiol functionality. The encoded microparticles are produced in a high throughput microfluidic device via stop-flow lithography (SFL) and consist of spatially discrete regions containing encoded identity information, an internal control, and capture DNAs. For the Hybridization-based assembly, partially disassembled TMVs were programmed with linker DNAs that contain sequences complementary to both the virus 5' end and a selected capture DNA. Fluorescence microscopy, atomic force microscopy (AFM), and confocal microscopy results clearly indicate facile assembly of TMV nanotemplates onto microparticles with high spatial and sequence selectivity. We anticipate that our Hybridization-based assembly strategy could be employed to create multifunctional viral-synthetic hybrid materials in a rapid and high-throughput manner. Additionally, we believe that these viral-synthetic hybrid microparticles may find broad applications in high capacity, multiplexed target sensing.
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patterned assembly of genetically modified viral nanotemplates via Nucleic Acid Hybridization
Nano Letters, 2005Co-Authors: Hyunmin Yi, Saira Nisar, Michael A Powers, William E Bentley, Gregory F Payne, Reza Ghodssi, Gary W Rubloff, Michael T Harris, James N CulverAbstract:The patterning of nanoparticles represents a significant obstacle in the assembly of nanoscale materials and devices. In this report, cysteine residues were genetically engineered onto the virion surface of tobacco mosaic virus (TMV), providing attachment sites for fluorescent markers. To pattern these viruses, labeled virions were partially disassembled to expose 5‘ end RNA sequences and hybridized to virus-specific probe DNA linked to electrodeposited chitosan. Electron microscopy and RNAase treatments confirmed the patterned assembly of the virus templates onto the chitosan surface. These findings demonstrate that TMV nanotemplates can be dimensionally assembled via Nucleic Acid Hybridization.
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a robust technique for assembly of Nucleic Acid Hybridization chips based on electrochemically templated chitosan
Analytical Chemistry, 2004Co-Authors: Hyunmin Yi, Gregory F Payne, Reza Ghodssi, Gary W Rubloff, Liqun Wu, William E BentleyAbstract:A Nucleic Acid Hybridization assay was assembled onto a robust and readily addressable silicon-based chip using polysaccharide chitosan as a scaffold for the covalent coupling of probe DNA to the chip's surface. Chitosan is a unique polymer, ideally suited for this application because its net charge and solubility are pH dependent. Specifically in this work, gold-patterned electrodes were created using standard photolithographic techniques, chitosan was electrodeposited in a spatially resolved manner onto the polarized electrodes, probe DNA was covalently assembled onto the chitosan, and both DNA:DNA and DNA:mRNA Hybridization detection schemes were evaluated. Hybridization of target Nucleic Acid was quantifiable, reproducible, and robust; the surface was regenerated and rehybridized up to eight times without loss of signal. Finally, transcriptional upregulation of the Escherichia coli chaperone, DnaK, which is an indicator of cellular stress, was observed using the Hybridization chip sandwich assay. Thus...
Akira Shimadzu - One of the best experts on this subject based on the ideXlab platform.
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optimization of excimer forming two probe Nucleic Acid Hybridization method with pyrene as a fluorophore
Nucleic Acids Research, 1998Co-Authors: Masayuki Masuko, Katsuyoshi Ebata, Hiroyuki Ohtani, Akira ShimadzuAbstract:A previously presented homogeneous assay method, named the excimer-forming two-probe Nucleic Acid Hybridization (ETPH) method, is based on specific excimer formation between two pyrenes attached at the neighboring terminals of two sequential probe oligonucleotides complementary to a single target. In this study, we investigated assay conditions and optimal molecular design of probes for intense excimer emission using a pyrenemethyliodoacetamide-introduced 16mer probe, a pyrene butanoic Acid-introduced 16merprobe and a target 32mer. The length of the linker between the pyrene residue and the terminal sugar moiety remarkably influenced the quantum efficiency of excimer emission; the pair of linker arms of these two probes was optimal. The quantum efficiency was also dependent upon the concentrations of dimethylformamide and NaCl added to the assay solution. Spectroscopic measurements and T m analysis showed that an optimal configuration of the two pyrene residues for intense excimer emission might be affected by pyrene-pyrene interaction, pyrene-duplex interaction (intercalation/stacking) and solvent conditions as a whole. We then demonstrated the practicality of the ETPH method with the optimal Hybridization conditions thus attained by determining that the concentration of 16S rRNA in extracts from Vibrio mimicus ATCC 33655 cells in exponential growth phase is 18 500 16S rRNA molecules/cell on average.
Russ W Algar - One of the best experts on this subject based on the ideXlab platform.
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multiplexed interfacial transduction of Nucleic Acid Hybridization using a single color of immobilized quantum dot donor and two acceptors in fluorescence resonance energy transfer
Analytical Chemistry, 2010Co-Authors: Russ W Algar, Ulrich J KrullAbstract:A multiplexed solid-phase assay for the detection of Nucleic Acid Hybridization was developed on the basis of a single color of immobilized CdSe/ZnS quantum dot (QD) as a donor in fluorescence resonance energy transfer (FRET). This work demonstrated that two channels of detection did not necessitate two different QD donors. Two probe oligonucleotides were coimmobilized on optical fibers modified with QDs, and a sandwich assay was used to associate the acceptor dyes with interfacial Hybridization events without target labeling. FRET-sensitized acceptor emission provided an analytical signal that was concentration dependent down to 10 nM. Changes in the ratio of coimmobilized probe oligonucleotides were found to yield linear changes in the relative amounts of acceptor emission. These changes were compared to previous studies that used mixed films of two QD donors for two detection channels. The analysis indicated that probe dilution effects were primarily driven by changes in acceptor number density and tha...
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interfacial transduction of Nucleic Acid Hybridization using immobilized quantum dots as donors in fluorescence resonance energy transfer
Langmuir, 2009Co-Authors: Russ W Algar, Ulrich J KrullAbstract:Fluorescence resonance energy transfer (FRET) using immobilized quantum dots (QDs) as energy donors was explored as a transduction method for the detection of Nucleic Acid Hybridization at an interface. This research was motivated by the success of the QD-FRET-based transduction of Nucleic Acid Hybridization in solution-phase assays. This new work represents a fundamental step toward the assembly of a biosensor, where immobilization of the selective chemistry on a surface is desired. After immobilizing QD-probe oligonucleotide conjugates on optical fibers, a demonstration of the retention of selectivity was achieved by the introduction of acceptor (Cy3)-labeled single-stranded target oligonucleotides. Hybridization generated the proximity required for FRET, and the resulting fluorescence spectra provided an analytical signal proportional to the amount of target. This research provides an important framework for the future development of Nucleic Acid biosensors based on QDs and FRET. The most important fin...
