Abstract
The structural characterization of glass slides surface-modified with 3-azidopropyltrimethoxysilane and used for anchoring nucleic acids, resulting in the so-called DNA microarrays, is presented. Depending on the silanization conditions, the slides were found to show different oligonucleotide binding efficiency, thus, an attempt was made to correlate this efficiency with the structural characteristics of the silane layers. Atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS) and X-ray reflectometry (XRR) measurements provided information on the surface topography, chemical composition and thickness of the silane films, respectively. The surface for which the best oligonucleotides binding efficiency is observed, has been found to consist of a densely-packed silane layer, decorated with a high-number of additional clusters that are believed to host exposed azide groups.
Highlights
IntroductionDNA microarrays are ordered matrices of oligonucleotides or larger deoxyribonucleic acid (DNA) fragments attached to activated solid surfaces, usually in the form of glass slides [1]
We showed that CuAAC reaction can be applied as a method for the preparation of deoxyribonucleic acid (DNA) microarrays through oligonucleotides immobilization on glass supports surface-functionalized using 3-azidopropyltrimethoxysilane (AzPTMS) [24]
In order to determine to preferred orientation of the second silane molecular layer on top of the first one, we performed molecular docking studies in which we looked for an optimal spatial arrangement of a silane molecule located close to the surface of a silane layer formed by 9 molecules exposing azide groups
Summary
DNA microarrays are ordered matrices of oligonucleotides or larger deoxyribonucleic acid (DNA) fragments attached to activated solid surfaces, usually in the form of glass slides [1]. They enable high-throughput screening of biomolecular interactions, allowing the analysis of the level of gene expression, studies of the genome structure, identification of a genetic polymorphism or detection of viral, bacterial and fungal pathogens. Microarray experiments require minimum amounts of samples, which is an important factor in genetic studies. Microarrays became essential tools in many research areas, such as medicine, pharmacology, biochemistry, genetics and microbiology
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