Immobilization Techniques for Microarray: Challenges  and Applications

Nimse, Satish Balasaheb; Song, Ki-Bong; Sonawane, Mukesh Digambar; Sayyed, Danishmalik Rafiq; Kim, Taisun

doi:10.3390/s141222208

Cited by 154 publications

(124 citation statements)

References 118 publications

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“…Moreover, this drop in probes density was more severe with amino-modified slides than with epoxysilane slides whatever the deposition technology. This data confirms that a surface chemistry permitting covalent linkage of the biomolecules is favoring high probe immobilization efficiency at low concentration of deposited probes [34,35]. We also noticed that the diminution of fluorescence intensity versus probes concentration on epoxysilane slides by the InnoStamp 40 ® technology followed a bell-shaped curve, with a maximum at the probe concentration of 0.5–1 µM.…”

Section: Resultssupporting

confidence: 82%

Automated and Multiplexed Soft Lithography for the Production of Low-Density DNA Microarrays

Fredonnet

Foncy

Cau³

et al. 2016

Microarrays

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Microarrays are established research tools for genotyping, expression profiling, or molecular diagnostics in which DNA molecules are precisely addressed to the surface of a solid support. This study assesses the fabrication of low-density oligonucleotide arrays using an automated microcontact printing device, the InnoStamp 40®. This automate allows a multiplexed deposition of oligoprobes on a functionalized surface by the use of a MacroStampTM bearing 64 individual pillars each mounted with 50 circular micropatterns (spots) of 160 µm diameter at 320 µm pitch. Reliability and reuse of the MacroStampTM were shown to be fast and robust by a simple washing step in 96% ethanol. The low-density microarrays printed on either epoxysilane or dendrimer-functionalized slides (DendriSlides) showed excellent hybridization response with complementary sequences at unusual low probe and target concentrations, since the actual probe density immobilized by this technology was at least 10-fold lower than with the conventional mechanical spotting. In addition, we found a comparable hybridization response in terms of fluorescence intensity between spotted and printed oligoarrays with a 1 nM complementary target by using a 50-fold lower probe concentration to produce the oligoarrays by the microcontact printing method. Taken together, our results lend support to the potential development of this multiplexed microcontact printing technology employing soft lithography as an alternative, cost-competitive tool for fabrication of low-density DNA microarrays.

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Section: Resultssupporting

confidence: 82%

Automated and Multiplexed Soft Lithography for the Production of Low-Density DNA Microarrays

Fredonnet

Foncy

Cau³

et al. 2016

Microarrays

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“…Aptamer strands coupled through this suboptimal interaction occupy a larger effective volume on the surface of the magnetic particles, which not only jeopardizes the hybridization with the complementary sequence, but also decreases the total amount of aptamer on the particle surface resulting in fewer DNA strands that can be coupled onto a given space [10]. This suboptimal efficiency of covalent carbodiimide crosslinking for DNA immobilization on a carboxylated surface was previously observed in other applications such as immuno-PCR [43] and DNA microarrays [44], in which parameters such as pH, ionic strength and reaction time seemed to play an important role in immobilization efficiency.…”

Section: Quantification Of Magnetic Particle Surface Coveragementioning

confidence: 83%

Evaluation of different strategies for magnetic particle functionalization with DNA aptamers

2016

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The optimal bio-functionalization of magnetic particles is essential for developing magnetic particle-based bioassays. Whereas functionalization with antibodies is generally well established, immobilization of DNA probes, such as aptamers, is not yet fully explored. In this work, four different types of commercially available magnetic particles, coated with streptavidin, maleimide or carboxyl groups, were evaluated for their surface coverage with aptamer bioreceptors, efficiency in capturing target protein and non-specific protein adsorption on their surface. A recently developed aptamer against the peanut allergen, Ara h 1 protein, was used as a model system. Conjugation of biotinylated Ara h 1 aptamer to the streptavidin particles led to the highest surface coverage, whereas the coverage of maleimide particles was 25% lower. Carboxylated particles appeared to be inadequate for DNA functionalization. Streptavidin particles also showed the greatest target capturing efficiency, comparable to the one of particles functionalized with anti-Ara h 1 antibody. The performance of streptavidin particles was additionally tested in a sandwich assay with the aptamer as a capture receptor on the particle surface. While the limit of detection obtained was comparable to the same assay system with antibody as capture receptor, it was superior to previously reported values using the same aptamer in similar assay schemes with different detection platforms. These results point to the promising application of the Ara h 1 aptamer-functionalized particles in bioassay development.

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“…This indicates that the surface density of the streptavidin cannot be increased further with higher concentration, owing to an issue of steric hindrance. 45 We may have to also consider that the probe DNA suffers from the crowding effect when the surface density is excessively high, 25, 48 which impairs the target DNA hybridization. It is certain that our standard DNA laser is in the optimal range for detecting small quantities of target DNA molecules and there is not much scope to improve its efficiency.…”

Section: Resultsmentioning

confidence: 99%

Digital DNA detection based on a compact optofluidic laser with ultra-low sample consumption

et al. 2016

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DNA lasers self-amplify optical signals from DNA analyte as well as thermodynamic differences between sequences, allowing quasi-digital DNA detection. However, these systems have drawbacks, such as relatively large sample consumption and complicated dye labelling. Moreover, although the lasing signal can detect the target DNA, it is superimposed on an unintended fluorescence background, which persists for non-target DNA samples as well. From an optical point of view, it is thus not truly digital detection and requires spectral analysis to identify the target. In this work, we propose and demonstrate an optofluidic laser that has a single layer of DNA molecules as gain material. A target DNA produces intensive laser emission comparable to existing DNA lasers, while any unnecessary fluorescence background is successfully suppressed. As a result, the target DNA can be detected with a single laser pulse, in a truly digital manner. Since the DNA molecules cover only a single layer on the surface of the laser microcavity, the DNA sample consumption is a few orders-of-magnitude lower than that of existing DNA lasers. Furthermore, the DNA molecules are stained by simply immersing the microcavity in the intercalating dye solution, and thus the proposed DNA laser is free of any complex dye-labelling process prior to analysis.

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Immobilization Techniques for Microarray: Challenges and Applications

Cited by 154 publications

References 118 publications

Automated and Multiplexed Soft Lithography for the Production of Low-Density DNA Microarrays

Automated and Multiplexed Soft Lithography for the Production of Low-Density DNA Microarrays

Evaluation of different strategies for magnetic particle functionalization with DNA aptamers

Digital DNA detection based on a compact optofluidic laser with ultra-low sample consumption

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