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Noun M, Akoumeh R, Abbas I. Cell and Tissue Imaging by TOF-SIMS and MALDI-TOF: An Overview for Biological and Pharmaceutical Analysis. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:1-26. [PMID: 34809729 DOI: 10.1017/s1431927621013593] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The potential of mass spectrometry imaging (MSI) has been demonstrated in cell and tissue research since 1970. MSI can reveal the spatial distribution of a wide range of atomic and molecular ions detected from biological sample surfaces, it is a powerful and valuable technique used to monitor and detect diverse chemical and biological compounds, such as drugs, lipids, proteins, and DNA. MSI techniques, notably matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) and time of flight secondary ion mass spectrometry (TOF-SIMS), witnessed a dramatic upsurge in studying and investigating biological samples especially, cells and tissue sections. This advancement is attributed to the submicron lateral resolution, the high sensitivity, the good precision, and the accurate chemical specificity, which make these techniques suitable for decoding and understanding complex mechanisms of certain diseases, as well as monitoring the spatial distribution of specific elements, and compounds. While the application of both techniques for the analysis of cells and tissues is thoroughly discussed, a briefing of MALDI-TOF and TOF-SIMS basis and the adequate sampling before analysis are briefly covered. The importance of MALDI-TOF and TOF-SIMS as diagnostic tools and robust analytical techniques in the medicinal, pharmaceutical, and toxicology fields is highlighted through representative published studies.
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Affiliation(s)
- Manale Noun
- Lebanese Atomic Energy Commission - NCSR, Beirut, Lebanon
| | - Rayane Akoumeh
- Lebanese Atomic Energy Commission - NCSR, Beirut, Lebanon
| | - Imane Abbas
- Lebanese Atomic Energy Commission - NCSR, Beirut, Lebanon
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2
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Castellanos A, Ramirez CE, Michalkova V, Nouzova M, Noriega FG, Francisco FL. Three Dimensional Secondary Ion Mass Spectrometry Imaging (3D-SIMS) of Aedes aegypti ovarian follicles. JOURNAL OF ANALYTICAL ATOMIC SPECTROMETRY 2019; 34:874-883. [PMID: 31680712 PMCID: PMC6824543 DOI: 10.1039/c8ja00425k] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The mobilization of nutrient reserves into the ovaries of Aedes aegypti mosquitoes after sugar-feeding plays a vital role in the female's reproductive maturation. In the present work, three-dimensional secondary ion mass spectrometry imaging (3D-SIMS) was used to generate ultrahigh spatial resolution (~1 μm) chemical maps and study the composition and spatial distribution of lipids at the single ovarian follicle level (~100 μm in size). 3D-Mass Spectrometry Imaging (3D-MSI) allowed the identification of cellular types in the follicle (oocyte, nurse and follicular cells) using endogenous markers, and revealed that most of the triacyglycerides (TGs) were compartmentalized in the oocyte region. By comparing follicles from water-fed and sugar-fed females (n=2), 3D-MSI-Time of Flight-SIMS showed that TGs were more abundant in ovarian follicles of sugar-fed females; despite relative sample reproducibility per feeding condition, more biological replicates will better support the trends observed. While the current 3D-MSI-TOF-SIMS does not permit MS/MS analysis of the lipid species, complementary LC-MS/MS analysis of the ovarian follicles aided tentative lipid assignments of the SIMS data. The combination of these MS approaches is giving us a first glimpse of the distribution of functionally relevant ovarian lipid molecules at the cellular level. These new tools can be used to investigate the roles of different lipids on follicle fitness and overall mosquito reproductive output.
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Affiliation(s)
- Anthony Castellanos
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, 33199, United States
| | - Cesar E. Ramirez
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, 33199, United States
| | - Veronika Michalkova
- Department of Biological Sciences, Florida International University, Miami, Florida, 33199, United States
| | - Marcela Nouzova
- Department of Biological Sciences, Florida International University, Miami, Florida, 33199, United States
- Institute of Parasitology, Biology Centre CAS, Ceske, Budejovice, Czech Republic; and
| | - Fernando G. Noriega
- Department of Biological Sciences, Florida International University, Miami, Florida, 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, 33199, United States
| | - Fernández-Lima Francisco
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, 33199, United States
- Corresponding author: Francisco A. Fernández-Lima, Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St AHC4-233, Miami, FL 33199, USA;
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Huang C, Wang J, Lv X, Liu L, Liang L, Hu W, Luo C, Wang F, Yuan Q. Redefining Molecular Amphipathicity in Reversing the "Coffee-Ring Effect": Implications for Single Base Mutation Detection. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:6777-6783. [PMID: 29779375 DOI: 10.1021/acs.langmuir.8b01248] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The "coffee ring effect" is a natural phenomenon wherein sessile drops leave ring-shaped structures on the solid surfaces upon drying. It drives a nonuniform deposition of suspended compounds on the substrates, which adversely affects many processes, including surface-assisted biosensing and molecular self-assembly. In this study, we describe how the coffee ring effect can be eliminated by controlling the amphipathicity of the suspended compounds, for example, DNA modified with hydrophobic dye. Specifically, nuclease digestion of the hydrophilic DNA end converts the dye-labeled molecule into an amphipathic molecule (one with comparably weighted hydrophobic and hydrophilic ends) and reverses the coffee ring effect and results in a uniform disk-shaped feature deposition of the dye. The amphipathic product decreases the surface tension of the sessile drops and induces the Marangoni flow, which drives the uniform distribution of the amphipathic dye-labeled product in the drops. As a proof of concept, this strategy was used in a novel enzymatic amplification method for biosensing to eliminate the coffee ring effect on a nitrocellulose membrane and increase assay reliability and sensitivity. Importantly, the reported strategy for eliminating the coffee ring effect can be extended to other sessile drop systems for potentially improving assay reliability and sensitivity.
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Affiliation(s)
- Chi Huang
- Institute of Chemical Biology and Nanomedicine, Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , China
| | | | | | | | - Ling Liang
- Institute of Chemical Biology and Nanomedicine, Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , China
| | | | | | | | - Quan Yuan
- Institute of Chemical Biology and Nanomedicine, Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , China
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4
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Hao X, Josephs EA, Gu Q, Ye T. Molecular conformations of DNA targets captured by model nanoarrays. NANOSCALE 2017; 9:13419-13424. [PMID: 28875997 DOI: 10.1039/c7nr04715k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
An open question in single molecule nanoarrays is how the chemical and morphological heterogeneities of the solid support affect the properties of biomacromolecules. We generated arrays that allowed individually-resolvable DNA molecules to interact with tailored surface heterogeneities and revealed how molecular conformations are impacted by surface interactions.
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Affiliation(s)
- X Hao
- Chemistry and Chemical Biology, University of California, Merced, California 95343, USA.
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5
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Li H, Brewer G, Ongo G, Normandeau F, Omeroglu A, Juncker D. Immunohistochemistry Microarrays. Anal Chem 2017; 89:8620-8625. [DOI: 10.1021/acs.analchem.7b00807] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Huiyan Li
- Biomedical
Engineering Department, ‡McGill University and Genome Quebec Innovation
Centre, §Department of Pathology, McGill University Health Centre, and ∥Department of
Neurology and Neurosurgery, McGill University, Montreal, Quebec H3A0G1, Canada
| | - Gabrielle Brewer
- Biomedical
Engineering Department, ‡McGill University and Genome Quebec Innovation
Centre, §Department of Pathology, McGill University Health Centre, and ∥Department of
Neurology and Neurosurgery, McGill University, Montreal, Quebec H3A0G1, Canada
| | - Grant Ongo
- Biomedical
Engineering Department, ‡McGill University and Genome Quebec Innovation
Centre, §Department of Pathology, McGill University Health Centre, and ∥Department of
Neurology and Neurosurgery, McGill University, Montreal, Quebec H3A0G1, Canada
| | - Frederic Normandeau
- Biomedical
Engineering Department, ‡McGill University and Genome Quebec Innovation
Centre, §Department of Pathology, McGill University Health Centre, and ∥Department of
Neurology and Neurosurgery, McGill University, Montreal, Quebec H3A0G1, Canada
| | - Atilla Omeroglu
- Biomedical
Engineering Department, ‡McGill University and Genome Quebec Innovation
Centre, §Department of Pathology, McGill University Health Centre, and ∥Department of
Neurology and Neurosurgery, McGill University, Montreal, Quebec H3A0G1, Canada
| | - David Juncker
- Biomedical
Engineering Department, ‡McGill University and Genome Quebec Innovation
Centre, §Department of Pathology, McGill University Health Centre, and ∥Department of
Neurology and Neurosurgery, McGill University, Montreal, Quebec H3A0G1, Canada
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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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Xing X, Liu W, Li T, Xing S, Fu X, Wu D, Liu D, Wang Z. A portable optical waveguide resonance light-scattering scanner for microarray detection. Analyst 2015; 141:199-205. [PMID: 26567521 DOI: 10.1039/c5an01839k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In the present work, a portable and low-cost planar waveguide based resonance light scattering (RLS) scanner (termed as: PW-RLS scanner) has been developed for microarray detection. The PW-RLS scanner employs a 2 × 4 white light emitting diode array (WLEDA) as the excitation light source, a folded optical path with a complementary metal oxide semiconductor (CMOS) as the signal/image acquisition device and stepper motors with gear drives as the mechanical drive system. The biological binding/recognizing events on the microarray can be detected with an evanescent waveguide-directed illumination and light-scattering label (e.g., nanoparticles) while the microarray slide acts as an evanescent waveguide substrate. The performance of the as-developed PW-RLS scanner has been evaluated by analyzing type 2 diabetes mellitus (T2DM) risk genes. Highly selective and sensitive (less than 1% allele frequency at the attomole-level) T2DM risk gene detection is achieved using single-stranded DNA functionalized gold nanoparticles (ssDNA-GNPs) as detection probes. Additionally, the successful simultaneous analysis of 15 T2DM patient genotypes suggests that the device has great potential for the realization of a personalized diagnostic test for a given disease or patient follow-up.
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Affiliation(s)
- Xuefeng Xing
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China.
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8
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Gajos K, Petrou P, Budkowski A, Awsiuk K, Bernasik A, Misiakos K, Rysz J, Raptis I, Kakabakos S. Imaging and spectroscopic comparison of multi-step methods to form DNA arrays based on the biotin-streptavidin system. Analyst 2015; 140:1127-39. [PMID: 25535629 DOI: 10.1039/c4an00929k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Three multi-step multi-molecular approaches using the biotin-streptavidin system to contact-print DNA arrays on SiO2 surfaces modified with (3-glycidoxypropyl)trimethoxysilane are examined after each deposition/reaction step by atomic force microscopy, X-ray photoelectron spectroscopy and time of flight secondary ion mass spectrometry. Surface modification involves the spotting of preformed conjugates of biotinylated oligonucleotides with streptavidin onto surfaces coated with biotinylated bovine serum albumin b-BSA (approach I) or the spotting of biotinylated oligonucleotides onto a streptavidin coating, the latter prepared through a reaction with immobilized b-BSA (approach II) or direct adsorption (approach III). AFM micrographs, quantified by autocorrelation and height histogram parameters (e.g. roughness), reveal uniform coverage after each modification step with distinct nanostructures after the reaction of biotinylated BSA with streptavidin or of a streptavidin conjugate with biotinylated oligonucleotides. XPS relates the immobilization of biomolecules with covalent binding to the epoxy-silanized surface. Protein coverage, estimated from photoelectron attenuation, shows that regarding streptavidin the highest and the lowest immobilization efficiency is achieved by following approaches I and III, respectively, as confirmed by TOF-SIMS microanalysis. The size of the DNA spot reflects the contact radius of the printed droplet and increases with protein coverage (and roughness) prior to the spotting, as epoxy-silanized surfaces are hardly hydrophilic. Representative TOF-SIMS images show sub-millimeter spots: uniform for approach I, doughnut-like (with a small non-zero minimum) for approach II, both with coffee-rings or peak-shaped for approach III. Spot features, originating from pinned contact lines and DNA surface binding and revealed by complementary molecular distributions (all material, DNA, streptavidin, BSA, epoxy, SiO2), indicate two modes of droplet evaporation depending on the details of each applied approach.
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Affiliation(s)
- Katarzyna Gajos
- M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland.
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9
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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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10
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Passarelli MK, Newman CF, Marshall PS, West A, Gilmore IS, Bunch J, Alexander MR, Dollery CT. Single-Cell Analysis: Visualizing Pharmaceutical and Metabolite Uptake in Cells with Label-Free 3D Mass Spectrometry Imaging. Anal Chem 2015; 87:6696-702. [PMID: 26023862 DOI: 10.1021/acs.analchem.5b00842] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Detecting metabolites and parent compound within a cell type is now a priority for pharmaceutical development. In this context, three-dimensional secondary ion mass spectrometry (SIMS) imaging was used to investigate the cellular uptake of the antiarrhythmic agent amiodarone, a phospholipidosis-inducing pharmaceutical compound. The high lateral resolution and 3D imaging capabilities of SIMS combined with the multiplex capabilities of ToF mass spectrometric detection allows for the visualization of pharmaceutical compound and metabolites in single cells. The intact, unlabeled drug compound was successfully detected at therapeutic dosages in macrophages (cell line: NR8383). Chemical information from endogenous biomolecules was used to correlate drug distributions with morphological features. From this spatial analysis, amiodarone was detected throughout the cell, with the majority of the compound found in the membrane and subsurface regions and absent in the nuclear regions. Similar results were obtained when the macrophages were doped with amiodarone metabolite, desethylamiodarone. The fwhm lateral resolution measured across an intracellular interface in high lateral resolution ion images was approximately 550 nm. Overall, this approach provides the basis for studying cellular uptake of pharmaceutical compounds and their metabolites on the single cell level.
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Affiliation(s)
- Melissa K Passarelli
- †National Centre of Excellence in Mass Spectrometry Imaging (NiCE-MSI), National Physical Laboratory (NPL), Teddington, Middlesex, TW11 0LW, United Kingdom
| | | | | | | | - Ian S Gilmore
- †National Centre of Excellence in Mass Spectrometry Imaging (NiCE-MSI), National Physical Laboratory (NPL), Teddington, Middlesex, TW11 0LW, United Kingdom
- §University of Nottingham, School of Pharmacy University Park, Nottingham, NG7 2RD, United Kingdom
| | - Josephine Bunch
- †National Centre of Excellence in Mass Spectrometry Imaging (NiCE-MSI), National Physical Laboratory (NPL), Teddington, Middlesex, TW11 0LW, United Kingdom
- §University of Nottingham, School of Pharmacy University Park, Nottingham, NG7 2RD, United Kingdom
| | - Morgan R Alexander
- §University of Nottingham, School of Pharmacy University Park, Nottingham, NG7 2RD, United Kingdom
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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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Gao R, Choi N, Chang SI, Lee EK, Choo J. Real-time analysis of diaquat dibromide monohydrate in water with a SERS-based integrated microdroplet sensor. NANOSCALE 2014; 6:8781-6. [PMID: 24954446 DOI: 10.1039/c4nr01269k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
We report the fast and sensitive trace analysis of diaquat dibromide monohydrate (DQ) in water using a surface-enhanced Raman scattering (SERS)-based microdroplet sensor. This sensor is composed of two compartments: the first one is for droplet generation for fresh silver nanoparticle (AgNP) synthesis and the second for droplet merging for SERS detection. Silver ions were nucleated and grown to large size AgNPs in droplets, and then each droplet was synchronously merged with another droplet containing DQ for SERS detection. This two-phase liquid-liquid segmented flow system prevented memory effects caused by the precipitation of nanoparticle aggregates on channel walls because the aqueous droplets were isolated by a continuous oil phase. The limit of detection (LOD) of DQ in water was determined to be below 5 nM, which satisfies the maximum contaminant level defined by the United States EPA. This method was also validated successfully in DQ-spiked tap water. The SERS-based integrated sensing system is expected to be useful as an in-the-field sensing platform for fast and reproducible trace analysis of environmental pollutants in water.
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Affiliation(s)
- Rongke Gao
- Department of Bionano Technology, Hanyang University, Ansan 426-791, South Korea.
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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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Noor MO, Petryayeva E, Tavares AJ, Uddayasankar U, Algar WR, Krull UJ. Building from the “Ground” Up: Developing interfacial chemistry for solid-phase nucleic acid hybridization assays based on quantum dots and fluorescence resonance energy transfer. Coord Chem Rev 2014. [DOI: 10.1016/j.ccr.2013.08.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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15
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Ianeselli L, Grenci G, Callegari C, Tormen M, Casalis L. Development of stable and reproducible biosensors based on electrochemical impedance spectroscopy: three-electrode versus two-electrode setup. Biosens Bioelectron 2013; 55:1-6. [PMID: 24355458 DOI: 10.1016/j.bios.2013.11.067] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 11/25/2013] [Indexed: 01/05/2023]
Abstract
This work focuses on the development of electrochemical impedance biosensors based on capacitance readout, for the detection of biomolecules in small sample volumes. We performed electrochemical impedance spectroscopy (EIS) measurements of DNA hybridization in electrochemical cells with microfabricated gold electrodes. The time stability of the device was tested in two different configurations: two microelectrodes in a microfluidic channel; two microelectrodes plus a reference electrode in an electrochemical cell. Our results demonstrate that the three-electrode setup is more stable, more reproducible, and suitable for real-time measurements. In the last part of the work we perform a test study of DNA hybridization in real time, and we show that the three-electrode configuration can measure the process in situ and in real time.
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Affiliation(s)
| | - Gianluca Grenci
- CNR-IOM, Laboratorio TASC, Area Science Park, Basovizza, Strada Statale 14 km 163.5, Trieste I-34149, Italy
| | - Carlo Callegari
- Elettra-Sincrotrone Trieste S.C.p.A., S.S. 14 km 163.5, In Area Science Park, Basovizza, Trieste 34149, Italy
| | - Massimo Tormen
- CNR-IOM, Laboratorio TASC, Area Science Park, Basovizza, Strada Statale 14 km 163.5, Trieste I-34149, Italy
| | - Loredana Casalis
- Elettra-Sincrotrone Trieste S.C.p.A., S.S. 14 km 163.5, In Area Science Park, Basovizza, Trieste 34149, Italy.
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16
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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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17
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Tong L, Wu J, Li J, Ju H, Yan F. Hybridization chain reaction engineered DNA nanopolylinker for amplified electrochemical sensing of biomarkers. Analyst 2013; 138:4870-6. [PMID: 23846116 DOI: 10.1039/c3an00824j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A DNA nanopolylinker was designed as a three dimensional nanoprobe with high loading of signal molecules for amplifying the biosensing signal. The nanoprobe was prepared by hybridization chain reaction engineering dsDNA polymerization on initiator DNA modified Au nanoparticle with two kinds of small molecule, for example, FITC-labeled DNA hairpins. The core-shell conjugate that was formed contained approximately 320 FITC molecules for further binding of signal molecules. With a sandwich-type immunoreaction and a biotin-streptavidin affinity reaction, the biotinylated core-shell nanoprobe was immobilized on the immunosensor surface, and the FITC molecules then bound enzyme labeled anti-FITC antibody to catalyze a silver deposition process, leading to a novel cascade signal amplification strategy. By combining the proposed strategy with stripping analysis of the deposited silver, an ultrasensitive immunoassay method for biomarker detection was developed. Under optimal conditions, this method showed a linear detection range over 5 orders of magnitude for carcinoembryonic antigen with a detection limit of 1.2 fg mL(-1) (about 18 molecules in 5.0 μL sample). The preparation of DNA nanopolylinker was simple and economic, and it could be used as a universal and multifarious probe for different bioanalytical techniques and showed the promising potential of the signal amplification strategy in the future design of biosensing methodology.
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Affiliation(s)
- Liu Tong
- State Key Laboratory of Analytical Chemistry for Life Science, Department of Chemistry, Nanjing University, Nanjing 210093, PR China
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18
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Rao AN, Rodesch CK, Grainger DW. Real-time fluorescent image analysis of DNA spot hybridization kinetics to assess microarray spot heterogeneity. Anal Chem 2012; 84:9379-87. [PMID: 23043216 DOI: 10.1021/ac302165h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Current microarray assay technology predominately uses fluorescence as a detectable signal end point. This study assessed real-time in situ surface hybridization capture kinetics for single printed DNA microspots on solid array surfaces using fluorescence. The influence of the DNA target and probe cyanine dye position on oligo-DNA duplex formation behavior was compared in solution versus surface-hybridized single DNA printed spots using fluorescence resonance energy transfer (FRET) analysis. Fluorophore Cy3/Cy5 fluorescence intensities were analyzed both through the printed hybridized DNA spot thickness and radially across single-spot surfaces. Confocal single-spot imaging shows that real-time in situ hybridization kinetics with constant target concentrations changes as a function of the printed probe density. Target-specific imaging in single spots exhibits a heterogeneous printed probe radial density that influences hybridization spatially and temporally via radial hemispherical diffusion of dye-labeled target from the outside edge of the spot to the interior. FRET of the surface-captured target occurs irrespective of the probe/target fluorophore position, resulting from excess printed probe density and spot thickness. Both heterogeneous probe density distributions in printed spots and the fluorophore position on short DNA oligomers influence duplex formation kinetics, hybridization efficiencies, and overall fluorescence intensity end points in surface-capture formats. This analysis is important to understanding, controlling, and quantifying the array assay signal essential to reliable application of the surface-capture format.
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Affiliation(s)
- Archana N Rao
- Department of Pharmaceutics and Pharmaceutical Chemistry, School of Medicine, University of Utah, Salt Lake City, Utah 84112, United States
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