1
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Boissinot K, Peytavi R, Chapdelaine S, Geissler M, Boissinot M, Martel EA, Béliveau-Viel D, Gravel JF, Malic L, Veres T, Boudreau D, Bergeron MG. Real-time monitoring of bead-based DNA hybridization in a microfluidic system: study of amplicon hybridization behavior on solid supports. Analyst 2021; 146:4226-4234. [PMID: 34095908 DOI: 10.1039/d1an00394a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA hybridization phenomena occurring on solid supports are not understood as clearly as aqueous phase hybridizations and mathematical models cannot predict some empirically obtained results. Ongoing research has identified important parameters but remains incomplete to accurately account for all interactions. It has previously been shown that the length of the overhanging (dangling) end of the target DNA strand following hybridization to the capture probe is correlated to interactions with the complementary strand in solution which can result in unbinding of the target and its release from the surface. We have developed an instrument for real-time monitoring of DNA hybridization on spherical particles functionalized with oligonucleotide capture probes and arranged in the form of a tightly packed monolayer bead bed inside a microfluidic cartridge. The instrument is equipped with a pneumatic module to mediate displacement of fluid on the cartridge. We compared this system to both conventional (passive) and centrifugally-driven (active) microfluidic microarray hybridization on glass slides to establish performance levels for the detection of single nucleotide polymorphisms. The system was also used to study the effect of the dangling end's length in real-time when the immobilized target DNA is exposed to the complementary strand in solution. Our findings indicate that increasing the length of the dangling end leads to desorption of target amplicons from bead-bound capture probes at a rate approaching that of the initial hybridization process. Finally, bead bed hybridization was performed with Streptococcus agalactiae cfb gene amplicons obtained from randomized clinical samples, which allowed for identification of group B streptococci within 5-15 min. The methodology presented here is useful for investigating competitive hybridization mechanisms on solid supports and to rapidly validate the suitability of microarray capture probes.
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Affiliation(s)
- Karel Boissinot
- Centre de recherche en infectiologie de l'Université Laval, Axe Maladies infectieuses et immunitaires, Centre de recherche du CHU de Québec-Université Laval, 2705 boulevard Laurier, Québec, QC G1V 4G2, Canada. and Département de microbiologie-infectiologie et immunologie, Faculté de médecine, Université Laval, 1050 avenue de la Médecine, Québec, QC G1V 0A6, Canada
| | - Régis Peytavi
- Centre de recherche en infectiologie de l'Université Laval, Axe Maladies infectieuses et immunitaires, Centre de recherche du CHU de Québec-Université Laval, 2705 boulevard Laurier, Québec, QC G1V 4G2, Canada. and Département de microbiologie-infectiologie et immunologie, Faculté de médecine, Université Laval, 1050 avenue de la Médecine, Québec, QC G1V 0A6, Canada
| | - Sébastien Chapdelaine
- Centre d'optique, photonique et laser (COPL), Université Laval, 2375 rue de la Terrasse, Québec, QC G1V 0A6, Canada
| | - Matthias Geissler
- Life Sciences Division, National Research Council of Canada, 75 boulevard de Mortagne, Boucherville, QC J4B 6Y4, Canada.
| | - Maurice Boissinot
- Centre de recherche en infectiologie de l'Université Laval, Axe Maladies infectieuses et immunitaires, Centre de recherche du CHU de Québec-Université Laval, 2705 boulevard Laurier, Québec, QC G1V 4G2, Canada.
| | - Eric A Martel
- Centre de recherche en infectiologie de l'Université Laval, Axe Maladies infectieuses et immunitaires, Centre de recherche du CHU de Québec-Université Laval, 2705 boulevard Laurier, Québec, QC G1V 4G2, Canada.
| | - David Béliveau-Viel
- Centre d'optique, photonique et laser (COPL), Université Laval, 2375 rue de la Terrasse, Québec, QC G1V 0A6, Canada
| | - Jean-François Gravel
- Centre d'optique, photonique et laser (COPL), Université Laval, 2375 rue de la Terrasse, Québec, QC G1V 0A6, Canada
| | - Lidija Malic
- Life Sciences Division, National Research Council of Canada, 75 boulevard de Mortagne, Boucherville, QC J4B 6Y4, Canada.
| | - Teodor Veres
- Life Sciences Division, National Research Council of Canada, 75 boulevard de Mortagne, Boucherville, QC J4B 6Y4, Canada.
| | - Denis Boudreau
- Centre d'optique, photonique et laser (COPL), Université Laval, 2375 rue de la Terrasse, Québec, QC G1V 0A6, Canada and Département de chimie, Université Laval, 1045 avenue de la Médecine, Québec, QC G1V 0A6, Canada
| | - Michel G Bergeron
- Centre de recherche en infectiologie de l'Université Laval, Axe Maladies infectieuses et immunitaires, Centre de recherche du CHU de Québec-Université Laval, 2705 boulevard Laurier, Québec, QC G1V 4G2, Canada. and Département de microbiologie-infectiologie et immunologie, Faculté de médecine, Université Laval, 1050 avenue de la Médecine, Québec, QC G1V 0A6, Canada
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2
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Abstract
Hybridization between nucleic acid strands immobilized on a solid support with partners in solution is widely practiced in bioanalytical technologies and materials science. An important fundamental aspect of understanding these reactions is the role played by immobilization in the dynamics of duplex formation and disassembly. This report reviews and analyzes literature kinetic data to identify commonly observed trends and to correlate them with probable molecular mechanisms. The analysis reveals that while under certain conditions impacts from immobilization are minimal so that surface and solution hybridization kinetics are comparable, it is more typical to observe pronounced offsets between the two scenarios. In the forward (hybridization) direction, rates at the surface commonly decrease by one to two decades relative to solution, while in the reverse direction rates of strand separation at the surface can exceed those in solution by tens of decades. By recasting the deviations in terms of activation barriers, a consensus of how immobilization impacts nucleation, zipping, and strand separation can be conceived within the classical mechanism in which duplex formation is rate limited by preassembly of a nucleus a few base pairs in length, while dehybridization requires the cumulative breakup of base pairs along the length of a duplex. Evidence is considered for how excess interactions encountered on solid supports impact these processes.
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Affiliation(s)
- Eshan Treasurer
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Rastislav Levicky
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
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3
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Toward a Quantitative Relationship between Nanoscale Spatial Organization and Hybridization Kinetics of Surface Immobilized Hairpin DNA Probes. ACS Sens 2021; 6:371-379. [PMID: 32945167 DOI: 10.1021/acssensors.0c01278] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Hybridization of DNA probes immobilized on a solid support is a key process for DNA biosensors and microarrays. Although the surface environment is known to influence the kinetics of DNA hybridization, so far it has not been possible to quantitatively predict how hybridization kinetics is influenced by the complex interactions of the surface environment. Using spatial statistical analysis of probes and hybridized target molecules on a few electrochemical DNA (E-DNA) sensors, functioning through hybridization-induced conformational change of redox-tagged hairpin probes, we developed a phenomenological model that describes how the hybridization rates for single probe molecules are determined by the local environment. The predicted single-molecule rate constants, upon incorporation into numerical simulation, reproduced the overall kinetics of E-DNA sensor surfaces at different probe densities and different degrees of probe clustering. Our study showed that the nanoscale spatial organization is a major factor behind the counterintuitive trends in hybridization kinetics. It also highlights the importance of models that can account for heterogeneity in surface hybridization. The molecular level understanding of hybridization at surfaces and accurate prediction of hybridization kinetics may lead to new opportunities in development of more sensitive and reproducible DNA biosensors and microarrays.
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4
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Hong S, Samson AAS, Song JM. Application of fluorescence resonance energy transfer to bioprinting. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115749] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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5
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Nobusawa K, Okamoto N, Chong KSL, Lin X, Iwahori K, Yamashita I. Dispersed Gold Nanoparticle Array Produced by Apoferritins Utilizing Biomineralization and Chemical Conversion. ACS OMEGA 2017; 2:1424-1430. [PMID: 31457514 PMCID: PMC6641008 DOI: 10.1021/acsomega.6b00550] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 03/21/2017] [Indexed: 05/12/2023]
Abstract
A new method for producing a dispersed gold nanoparticle (Au NP) array to anchor probe DNAs onto a DNA-sensing electrode has been developed. A homogenous gold sulfide (Au2S) core (precursor of Au NP) was biomineralized in the cavity of a mutant apoferritin (K98E) with enhanced negative outer-surface charges. We employed a slow chemical reaction system utilizing a stable cationic gold complex. K98E could attract the gold complex, and Au2S NPs were synthesized. K98E enabled dispersed placement of the synthesized Au2S core onto a cationic 3-aminopropyltriethoxysilane (APTES) layer on a substrate. UV-ozone treatment eliminated the protein shells and APTES layer. X-ray photoelectron spectroscopy confirmed that the Au2S core was reduced to Au NPs under the same treatment. Atomic force microscopy (AFM) clearly showed that the combination of apoferritin versatility, chemical system design, and UV-ozone treatment successfully produced a dispersed Au NP array on the substrate.
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Affiliation(s)
- Kazuyuki Nobusawa
- Graduate
School of Engineering, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Naofumi Okamoto
- Graduate
School of Materials Science, Nara Institute
of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Karen Siew Ling Chong
- Institute
of Materials Research and Engineering, Agency
for Science, Technology and Research, 2 Fusionopolis Way, Innovis, #08-03, 138634 Singapore
| | - Xi Lin
- Biomedical
Sciences Institute, Agency for Science,
Technology and Research, 61 Biopolis Drive, #03-12 Proteos, 138673 Singapore
| | - Kenji Iwahori
- Graduate
School of Materials Science, Nara Institute
of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Ichiro Yamashita
- Graduate
School of Materials Science, Nara Institute
of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
- Graduate
School of Engineering, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
- E-mail:
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6
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von der Haar M, Heuer C, Pähler M, von der Haar K, Lindner P, Scheper T, Stahl F. Optimization of Cyanine Dye Stability and Analysis of FRET Interaction on DNA Microarrays. BIOLOGY 2016; 5:biology5040047. [PMID: 27916881 PMCID: PMC5192427 DOI: 10.3390/biology5040047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/10/2016] [Accepted: 11/24/2016] [Indexed: 01/27/2023]
Abstract
The application of DNA microarrays for high throughput analysis of genetic regulation is often limited by the fluorophores used as markers. The implementation of multi-scan techniques is limited by the fluorophores' susceptibility to photobleaching when exposed to the scanner laser light. This paper presents combined mechanical and chemical strategies which enhance the photostability of cyanine 3 and cyanine 5 as part of solid state DNA microarrays. These strategies are based on scanning the microarrays while the hybridized DNA is still in an aqueous solution with the presence of a reductive/oxidative system (ROXS). Furthermore, the experimental setup allows for the analysis and eventual normalization of Förster-resonance-energy-transfer (FRET) interaction of cyanine-3/cyanine-5 dye combinations on the microarray. These findings constitute a step towards standardization of microarray experiments and analysis and may help to increase the comparability of microarray experiment results between labs.
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Affiliation(s)
- Marcel von der Haar
- Institute of Technical Chemistry, Leibniz University Hanover, Callinstr. 5, 30167 Hanover, Germany.
| | - Christopher Heuer
- Institute of Technical Chemistry, Leibniz University Hanover, Callinstr. 5, 30167 Hanover, Germany.
| | - Martin Pähler
- Institute of Technical Chemistry, Leibniz University Hanover, Callinstr. 5, 30167 Hanover, Germany.
| | - Kathrin von der Haar
- Institute of Technical Chemistry, Leibniz University Hanover, Callinstr. 5, 30167 Hanover, Germany.
| | - Patrick Lindner
- Institute of Technical Chemistry, Leibniz University Hanover, Callinstr. 5, 30167 Hanover, Germany.
| | - Thomas Scheper
- Institute of Technical Chemistry, Leibniz University Hanover, Callinstr. 5, 30167 Hanover, Germany.
| | - Frank Stahl
- Institute of Technical Chemistry, Leibniz University Hanover, Callinstr. 5, 30167 Hanover, Germany.
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7
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Capaldo P, Alfarano SR, Ianeselli L, Zilio SD, Bosco A, Parisse P, Casalis L. Circulating Disease Biomarker Detection in Complex Matrices: Real-Time, In Situ Measurements of DNA/miRNA Hybridization via Electrochemical Impedance Spectroscopy. ACS Sens 2016. [DOI: 10.1021/acssensors.6b00262] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Pietro Capaldo
- Elettra-Sincrotrone Trieste S.C.p.A., Area
Science Park, Strada Statale 14 km 163.5, 34149 Basovizza, Trieste, Italy
| | | | - Luca Ianeselli
- Elettra-Sincrotrone Trieste S.C.p.A., Area
Science Park, Strada Statale 14 km 163.5, 34149 Basovizza, Trieste, Italy
| | - Simone Dal Zilio
- CNR-IOM, Laboratorio TASC, Area
Science Park, Strada Statale 14 km 163.5, 34149 Basovizza, Trieste, Italy
| | - Alessandro Bosco
- Elettra-Sincrotrone Trieste S.C.p.A., Area
Science Park, Strada Statale 14 km 163.5, 34149 Basovizza, Trieste, Italy
| | - Pietro Parisse
- Elettra-Sincrotrone Trieste S.C.p.A., Area
Science Park, Strada Statale 14 km 163.5, 34149 Basovizza, Trieste, Italy
- INSTM-ST Unit, Area Science Park,
Strada Statale 14 km 163.5, 34149 Basovizza, Trieste, Italy
| | - Loredana Casalis
- Elettra-Sincrotrone Trieste S.C.p.A., Area
Science Park, Strada Statale 14 km 163.5, 34149 Basovizza, Trieste, Italy
- INSTM-ST Unit, Area Science Park,
Strada Statale 14 km 163.5, 34149 Basovizza, Trieste, Italy
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8
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Abstract
Evidence is presented that binding isotherms, simple or biphasic, can be extracted directly from noninterpreted, complex 2D NMR spectra using principal component analysis (PCA) to reveal the largest trend(s) across the series. This approach renders peak picking unnecessary for tracking population changes. In 1:1 binding, the first principal component captures the binding isotherm from NMR-detected titrations in fast, slow, and even intermediate and mixed exchange regimes, as illustrated for phospholigand associations with proteins. Although the sigmoidal shifts and line broadening of intermediate exchange distorts binding isotherms constructed conventionally, applying PCA directly to these spectra along with Pareto scaling overcomes the distortion. Applying PCA to time-domain NMR data also yields binding isotherms from titrations in fast or slow exchange. The algorithm readily extracts from magnetic resonance imaging movie time courses such as breathing and heart rate in chest imaging. Similarly, two-step binding processes detected by NMR are easily captured by principal components 1 and 2. PCA obviates the customary focus on specific peaks or regions of images. Applying it directly to a series of complex data will easily delineate binding isotherms, equilibrium shifts, and time courses of reactions or fluctuations.
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Affiliation(s)
- Jia Xu
- Department of Biochemistry, University of Missouri , 117 Schweitzer Hall, Columbia, Missouri 65211, United States
| | - Steven R Van Doren
- Department of Biochemistry, University of Missouri , 117 Schweitzer Hall, Columbia, Missouri 65211, United States
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9
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Yan Y, Samai S, Bischoff KL, Zhang J, Ginger DS. Photocontrolled DNA Hybridization Stringency with Fluorescence Detection in Heterogeneous Assays. ACS Sens 2016. [DOI: 10.1021/acssensors.5b00233] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | | | - Kristi L. Bischoff
- Mel
and Enid Zuckerman College of Public Heath, University of Arizona, Tucson, Arizona 85724, United States
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10
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von der Haar M, Preuß JA, von der Haar K, Lindner P, Scheper T, Stahl F. The Impact of Photobleaching on Microarray Analysis. BIOLOGY 2015; 4:556-72. [PMID: 26378589 PMCID: PMC4588150 DOI: 10.3390/biology4030556] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/20/2015] [Accepted: 09/08/2015] [Indexed: 02/06/2023]
Abstract
DNA-Microarrays have become a potent technology for high-throughput analysis of genetic regulation. However, the wide dynamic range of signal intensities of fluorophore-based microarrays exceeds the dynamic range of a single array scan by far, thus limiting the key benefit of microarray technology: parallelization. The implementation of multi-scan techniques represents a promising approach to overcome these limitations. These techniques are, in turn, limited by the fluorophores’ susceptibility to photobleaching when exposed to the scanner’s laser light. In this paper the photobleaching characteristics of cyanine-3 and cyanine-5 as part of solid state DNA microarrays are studied. The effects of initial fluorophore intensity as well as laser scanner dependent variables such as the photomultiplier tube’s voltage on bleaching and imaging are investigated. The resulting data is used to develop a model capable of simulating the expected degree of signal intensity reduction caused by photobleaching for each fluorophore individually, allowing for the removal of photobleaching-induced, systematic bias in multi-scan procedures. Single-scan applications also benefit as they rely on pre-scans to determine the optimal scanner settings. These findings constitute a step towards standardization of microarray experiments and analysis and may help to increase the lab-to-lab comparability of microarray experiment results.
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Affiliation(s)
- Marcel von der Haar
- Institute of Technical Chemistry, Leibniz University Hanover, Callinstr. 5, 30167 Hanover, Germany.
| | - John-Alexander Preuß
- Institute of Technical Chemistry, Leibniz University Hanover, Callinstr. 5, 30167 Hanover, Germany.
| | - Kathrin von der Haar
- Institute of Technical Chemistry, Leibniz University Hanover, Callinstr. 5, 30167 Hanover, Germany.
| | - Patrick Lindner
- Institute of Technical Chemistry, Leibniz University Hanover, Callinstr. 5, 30167 Hanover, Germany.
| | - Thomas Scheper
- Institute of Technical Chemistry, Leibniz University Hanover, Callinstr. 5, 30167 Hanover, Germany.
| | - Frank Stahl
- Institute of Technical Chemistry, Leibniz University Hanover, Callinstr. 5, 30167 Hanover, Germany.
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11
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Romanov V, Davidoff SN, Miles AR, Grainger DW, Gale BK, Brooks BD. A critical comparison of protein microarray fabrication technologies. Analyst 2015; 139:1303-26. [PMID: 24479125 DOI: 10.1039/c3an01577g] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Of the diverse analytical tools used in proteomics, protein microarrays possess the greatest potential for providing fundamental information on protein, ligand, analyte, receptor, and antibody affinity-based interactions, binding partners and high-throughput analysis. Microarrays have been used to develop tools for drug screening, disease diagnosis, biochemical pathway mapping, protein-protein interaction analysis, vaccine development, enzyme-substrate profiling, and immuno-profiling. While the promise of the technology is intriguing, it is yet to be realized. Many challenges remain to be addressed to allow these methods to meet technical and research expectations, provide reliable assay answers, and to reliably diversify their capabilities. Critical issues include: (1) inconsistent printed microspot morphologies and uniformities, (2) low signal-to-noise ratios due to factors such as complex surface capture protocols, contamination, and static or no-flow mass transport conditions, (3) inconsistent quantification of captured signal due to spot uniformity issues, (4) non-optimal protocol conditions such as pH, temperature, drying that promote variability in assay kinetics, and lastly (5) poor protein (e.g., antibody) printing, storage, or shelf-life compatibility with common microarray assay fabrication methods, directly related to microarray protocols. Conventional printing approaches, including contact (e.g., quill and solid pin), non-contact (e.g., piezo and inkjet), microfluidics-based, microstamping, lithography, and cell-free protein expression microarrays, have all been used with varying degrees of success with figures of merit often defined arbitrarily without comparisons to standards, or analytical or fiduciary controls. Many microarray performance reports use bench top analyte preparations lacking real-world relevance, akin to "fishing in a barrel", for proof of concept and determinations of figures of merit. This review critiques current protein-based microarray preparation techniques commonly used for analytical and function-based proteomics and their effects on array-based assay performance.
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Affiliation(s)
- Valentin Romanov
- Wasatch Microfluidics, LLC, 825 N. 300 W., Suite C325, Salt Lake City, UT, USA.
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12
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Liu Y, Duan C, Zhang C, Yang X, Zhao Y, Dong R, Zhou J, Gai Z. Evaluation of a viral microarray based on simultaneous extraction and amplification of viral nucleotide acid for detecting human herpesviruses and enteroviruses. PLoS One 2015; 10:e0117626. [PMID: 25774509 PMCID: PMC4361642 DOI: 10.1371/journal.pone.0117626] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Accepted: 12/29/2014] [Indexed: 12/17/2022] Open
Abstract
In this study, a viral microarray based assay was developed to detect the human herpesviruses and enteroviruses associated with central nervous system infections, including herpes simplex virus type 1, type 2 (HSV1 and HSV2), Epstein-Barr virus (EBV), cytomegalovirus (CMV), enterovirus 71 (EV71), coxsackievirus A 16 (CA16) and B 5(CB5). The DNA polymerase gene of human herpesviruses and 5’-untranslated region of enteroviruses were selected as the targets to design primers and probes. Human herpesviruses DNA and enteroviruses RNA were extracted simultaneously by using a guanidinium thiocyanate acid buffer, and were subsequently amplified through a biotinylated asymmetry multiplex RT-PCR with the specific primer of enteroviruses. In total, 90 blood samples and 49 cerebrospinal fluids samples with suspected systemic or neurological virus infections were investigated. Out of 139 samples, 66 were identified as positive. The specificities of this multiplex RT-PCR microarray assay were over 96% but the sensitivities were various from 100% for HSV1, HSV2, EV71 and CB5, 95.83% for CMV, 80% for EBV to 71.43% for CA16 in comparison with reference standards of TaqMan qPCR/qRT-PCR. The high Kappa values (>0.90) from HSV1, HSV2, CMV, EV71 and CB5 were obtained, indicating almost perfect agreement in term of the 5 viruses detection. But lower Kappa values for EBV (0.63) and CA16 (0.74) displayed a moderate to substantial agreement. This study provides an innovation of simultaneous extraction, amplification, hybridization and detection of DNA viruses and RNA viruses with simplicity and specificity, and demonstrates a potential clinical utility for a variety of viruses’ detection.
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Affiliation(s)
- Yi Liu
- Pediatric Research Institute, Qilu Children’s Hospital of Shandong University, Ji’nan, China
| | - Chunhong Duan
- Department of Pediatrics, Qilu Children’s Hospital of Shandong University, Ji’nan, China
| | - Chunxiu Zhang
- Shanghai Biochip National Engineering Research Center, Shanghai, China
| | - Xiaomeng Yang
- Pediatric Research Institute, Qilu Children’s Hospital of Shandong University, Ji’nan, China
| | - Yan Zhao
- Clinical Central Laboratory, Maternal and Children's Health Care Institute of Jinan, Jinan, China
| | - Rui Dong
- Pediatric Research Institute, Qilu Children’s Hospital of Shandong University, Ji’nan, China
| | - Jiajing Zhou
- Shanghai Biochip National Engineering Research Center, Shanghai, China
| | - Zhongtao Gai
- Pediatric Research Institute, Qilu Children’s Hospital of Shandong University, Ji’nan, China
- Department of Pediatrics, Qilu Children’s Hospital of Shandong University, Ji’nan, China
- * E-mail:
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13
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Rao AN, Grainger DW. BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE. Biomater Sci 2014; 2:436-471. [PMID: 24765522 PMCID: PMC3992954 DOI: 10.1039/c3bm60181a] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Both clinical and analytical metrics produced by microarray-based assay technology have recognized problems in reproducibility, reliability and analytical sensitivity. These issues are often attributed to poor understanding and control of nucleic acid behaviors and properties at solid-liquid interfaces. Nucleic acid hybridization, central to DNA and RNA microarray formats, depends on the properties and behaviors of single strand (ss) nucleic acids (e.g., probe oligomeric DNA) bound to surfaces. ssDNA's persistence length, radius of gyration, electrostatics, conformations on different surfaces and under various assay conditions, its chain flexibility and curvature, charging effects in ionic solutions, and fluorescent labeling all influence its physical chemistry and hybridization under assay conditions. Nucleic acid (e.g., both RNA and DNA) target interactions with immobilized ssDNA strands are highly impacted by these biophysical states. Furthermore, the kinetics, thermodynamics, and enthalpic and entropic contributions to DNA hybridization reflect global probe/target structures and interaction dynamics. Here we review several biophysical issues relevant to oligomeric nucleic acid molecular behaviors at surfaces and their influences on duplex formation that influence microarray assay performance. Correlation of biophysical aspects of single and double-stranded nucleic acids with their complexes in bulk solution is common. Such analysis at surfaces is not commonly reported, despite its importance to microarray assays. We seek to provide further insight into nucleic acid-surface challenges facing microarray diagnostic formats that have hindered their clinical adoption and compromise their research quality and value as genomics tools.
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Affiliation(s)
- Archana N. Rao
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT 84112 USA
| | - David W. Grainger
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT 84112 USA
- Department of Bioengineering, University of Utah, Salt Lake City, UT 84112 USA
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14
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Guarnaccia M, Gentile G, Alessi E, Schneider C, Petralia S, Cavallaro S. Is this the real time for genomics? Genomics 2014; 103:177-82. [DOI: 10.1016/j.ygeno.2014.02.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 01/30/2014] [Accepted: 02/11/2014] [Indexed: 01/22/2023]
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15
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Mummidivarapu VS, Pathak RK, Hinge VK, Dessingou J, Rao CP. A fluorescent di-zinc(II) complex of bis-calix[4]arene conjugate as chemosensing-ensemble for the selective recognition of ATP. Supramol Chem 2014. [DOI: 10.1080/10610278.2013.868897] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
| | - Rakesh Kumar Pathak
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Vijaya Kumar Hinge
- Department of Biosciences & Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
| | - Jayaraman Dessingou
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Chebrolu Pulla Rao
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
- Department of Biosciences & Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
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Daniel C, Roupioz Y, Gasparutto D, Livache T, Buhot A. Solution-phase vs surface-phase aptamer-protein affinity from a label-free kinetic biosensor. PLoS One 2013; 8:e75419. [PMID: 24069412 PMCID: PMC3775802 DOI: 10.1371/journal.pone.0075419] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 08/12/2013] [Indexed: 01/04/2023] Open
Abstract
Aptamers are selected DNA ligands that target biomolecules such as proteins. In recent years, they are showing an increasing interest as potential therapeutic agents or recognition elements in biosensor applications. In both cases, the need for characterizing the mating between the target and the aptamer either in solution or immobilized on a surface, is pressing. In this context, we have developed a kinetic biosensor made of micro-arrayed anti-thrombin aptamers to assess the kinetic parameters of this interaction. The binding of label-free thrombin on the biosensor was monitored in real-time by Surface Plasmon Resonance imaging. Remarkable performances were obtained for the quantification of thrombin without amplification (sub-nanomolar limit of detection and linear range of quantification to two orders of magnitude). The independent determinations of both the solution- and surface-phase affinities, respectively KDSol and KDSurf, revealed distinct values illustrating the importance of probes, targets or surface interactions in biosensors. Interestingly, KDSurf values depend on the aptamer grafting density and linearly extrapolate towards KDSol for highly diluted probes. This suggests a lesser impact of the surface compared to the probe or target cooperativity interactions since the latter decrease with a reduced grafting density.
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Affiliation(s)
- Camille Daniel
- Laboratoire Structure et Propriétés d’Architectures Moléculaires, UMR 5819 CEA/CNRS/UJF, Institut Nanosciences et Cryogénie, Grenoble, France
| | - Yoann Roupioz
- Laboratoire Structure et Propriétés d’Architectures Moléculaires, UMR 5819 CEA/CNRS/UJF, Institut Nanosciences et Cryogénie, Grenoble, France
| | - Didier Gasparutto
- Service de Chimie Inorganique et Biologique, UMR-E3 CEA/UJF, Institut Nanosciences et Cryogénie, Grenoble, France
| | - Thierry Livache
- Laboratoire Structure et Propriétés d’Architectures Moléculaires, UMR 5819 CEA/CNRS/UJF, Institut Nanosciences et Cryogénie, Grenoble, France
| | - Arnaud Buhot
- Laboratoire Structure et Propriétés d’Architectures Moléculaires, UMR 5819 CEA/CNRS/UJF, Institut Nanosciences et Cryogénie, Grenoble, France
- * E-mail:
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Noor MO, Krull UJ. Paper-based solid-phase multiplexed nucleic acid hybridization assay with tunable dynamic range using immobilized quantum dots as donors in fluorescence resonance energy transfer. Anal Chem 2013; 85:7502-11. [PMID: 23837820 DOI: 10.1021/ac401471n] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
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 to provide improved analytical figures of merit compared to that which could be achieved on one type of array design in terms of relative concentration of multicolor QDs. The hybridization assays showed excellent resistance to nonspecific adsorption of oligonucleotides. Selectivity of the two-plex hybridization assay was demonstrated by single nucleotide polymorphism (SNP) detection at a contrast ratio of 50:1. Additionally, it is shown that the use of preformed QD-probe oligonucleotide conjugates and consideration of the relative number density of the two types of QD-probe conjugates in the two-color assay format is advantageous to maximize assay sensitivity and the upper limit of dynamic range.
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Affiliation(s)
- M Omair Noor
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
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Rao AN, Vandencasteele N, Gamble LJ, Grainger DW. High-resolution epifluorescence and time-of-flight secondary ion mass spectrometry chemical imaging comparisons of single DNA microarray spots. Anal Chem 2012; 84:10628-36. [PMID: 23150996 DOI: 10.1021/ac3019334] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA microarray assay performance is commonly compromised by spot-spot probe and signal variations as well as heterogeneity within printed microspots. Accurate metrics for captured DNA target signal rely upon uniform spot distribution of both probe and target DNA to yield reliable hybridized signal. While often presumed, this is neither easily achieved nor often proven experimentally. High-resolution imaging techniques were used to determine spot heterogeneity in identical DNA array microspots comprising varied ratios of unlabeled and dye-labeled DNA probes contact-printed onto commercial arraying surfaces. Epifluorescence imaging data for individual array microspots were correlated with time-of-flight secondary ion mass spectrometry (TOF-SIMS) chemical state imaging of the same spots. Epifluorescence imaging intensity distinguished varying DNA density distributed both within a given spot and from spot to spot. TOF-SIMS chemical analysis confirmed these heterogeneous printed DNA distributions by tracking bound Cy3 dye, DNA base, and phosphate specific ion fragments often correlating to fluorescence patterns within identical spots. TOF-SIMS ion fragments originating from probe DNA and Cy3 dye are enriched in microspot centers, correlating with high fluorescence intensity regions. Both TOF-SIMS and epifluorescence support Marangoni flow effects on spot drying, with high-density DNA-Cy3 located in spot centers and nonhomogeneous DNA distribution within printed spots. Microspot image dimensional analysis results for DNA droplet spreading show differing DNA densities across printed spots. The study directly supports different DNA probe chemical and spatial microenvironments within spots that yield spot-spot signal variations known to affect DNA target hybridization efficiencies and kinetics. These variations critically affect probe-target duplex formation and DNA array signal generation.
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Affiliation(s)
- Archana N Rao
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, Utah 84112-5820, USA
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