Imaging TOF-SIMS analysis of oligonucleotide microarrays

Cheran, Larisa-Emilia; Vukovich, Dajana; Thompson, Michael

doi:10.1039/b209827j

Cited by 14 publications

(12 citation statements)

References 8 publications

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“…The surfaces patterned with oligonucleotides were analyzed by time-of-flight secondary ion mass spectrometry (ToF-SIMS). 134.03 (A À , adenine) and m/z = 110.01 (C À , cytosine)) 48 immobilized in a patterned fashion following the mask's features.…”

Section: Resultsmentioning

confidence: 99%

Photo-induced chemistry for the design of oligonucleotide conjugates and surfaces

et al. 2016

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Section: Resultsmentioning

confidence: 99%

Photo-induced chemistry for the design of oligonucleotide conjugates and surfaces

et al. 2016

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“…In this type of analysis, mass spectrometry was used for sequencing; for example, exons of the p53 gene and for genotyping . In 2003, Cheran et al used imaging time‐of‐flight secondary‐ion mass spectrometry (TOF‐SIMS) for the recognition of the spatial distribution of DNA strands. Meanwhile, MALDI‐MS imaging is the method of choice in obtaining much of information for many different reaction sites.…”

Section: Miniaturized Synthesis and Molecule Librariesmentioning

confidence: 99%

Miniaturized and Automated Synthesis of Biomolecules—Overview and Perspectives

et al. 2019

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Chemical synthesis is performed by reacting different chemical building blocks with defined stoichiometry, while meeting additional conditions, such as temperature and reaction time. Such a procedure is especially suited for automation and miniaturization. Life sciences lead the way to synthesizing millions of different oligonucleotides in extremely miniaturized reaction sites, e.g., pinpointing active genes in whole genomes, while chemistry advances different types of automation. Recent progress in matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS) imaging could match miniaturized chemical synthesis with a powerful analytical tool to validate the outcome of many different synthesis pathways beyond applications in the life sciences. Thereby, due to the radical miniaturization of chemical synthesis, thousands of molecules can be synthesized. This in turn should allow ambitious research, e.g., finding novel synthesis routes or directly screening for photocatalysts. Herein, different technologies are discussed that might be involved in this endeavor. A special emphasis is given to the obstacles that need to be tackled when depositing tiny amounts of materials to many different extremely miniaturized reaction sites.

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“…Different techniques have been developed to prepare such arrays, including printing [1][2][3] and photolithography 4 as the most popular approaches. Different techniques have been developed to prepare such arrays, including printing [1][2][3] and photolithography 4 as the most popular approaches.…”

Section: Introductionmentioning

confidence: 99%

“…[1][2][3]5,6 Both techniques rely on surface-sensitive characteristic signals 7 that reveal the chemical state and atomic concentration (XPS) or the molecular composition (TOF-SIMS). Especially two methods with unique specificity and sensitivity namely X-ray Photoelectron Spectroscopy (XPS) and Time-of-Flight Secondary Ion Mass Spectrometry (TOF-SIMS) have been widely applied to examine DNA spots.…”

Section: Introductionmentioning

confidence: 99%

Imaging and spectroscopic comparison of multi-step methods to form DNA arrays based on the biotin–streptavidin system

Gajos

Petrou²,

Budkowski

et al. 2015

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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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Imaging TOF-SIMS analysis of oligonucleotide microarrays

Cited by 14 publications

References 8 publications

Photo-induced chemistry for the design of oligonucleotide conjugates and surfaces

Photo-induced chemistry for the design of oligonucleotide conjugates and surfaces

Miniaturized and Automated Synthesis of Biomolecules—Overview and Perspectives

Imaging and spectroscopic comparison of multi-step methods to form DNA arrays based on the biotin–streptavidin system

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