An Efficient Binding Chemistry for Glass Polynucleotide Microarrays

A variety of methods have been described for making synthetic polynucleotide microarrays. These include in situ synthesis directly on the array surface, for example, by photolithography or ink-jet printing technologies, and the application of presynthesized polynucleotides that are derivatized with...

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Bibliographic Details
Published in:Bioconjugate chemistry 2002-01, Vol.13 (1), p.97-103
Main Authors: Lee, Paul H, Sawan, Samuel P, Modrusan, Zora, Arnold, Lyle J, Reynolds, Mark A
Format: Article
Language:English
Subjects:
Algorithms
Cross-Linking Reagents
DNA - chemistry
DNA - genetics
Glass
In Situ Hybridization
Oligonucleotide Array Sequence Analysis - methods
Polyethyleneimine - chemistry
RNA Probes
RNA, Messenger - biosynthesis
Saccharomyces cerevisiae - genetics
Spectroscopy, Fourier Transform Infrared
Surface Properties
Triazines
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Summary:A variety of methods have been described for making synthetic polynucleotide microarrays. These include in situ synthesis directly on the array surface, for example, by photolithography or ink-jet printing technologies, and the application of presynthesized polynucleotides that are derivatized with various nucleophiles or electrophiles. In the latter case, a variety of surface chemistries have been developed, and several are available commercially. These chemistries must be compatible with nanoliter-scale volumes of polynucleotide reagents, which contact the array over a small portion of their surface. We reasoned that a three-dimensional polymer coating could potentially offer greater surface contact and higher binding efficiency. Here we describe a polyethylenimine-based coating chemistry that provides exceptional binding and hybridization characteristics. In our preferred process, size-fractionated polyethylenimine polymers are cross-linked onto an aminopropylsilanated glass surface in the presence of cyanuric chloride. The resulting three-dimensional coating binds polynucleotides through a mixture of covalent and noncovalent interactions as evidenced by comparisons between 5‘-aminoalkyl modified and unmodified polynucleotides. Binding and hybridization comparisons are presented including analogous two-dimensional electrophilic and electrostatic chemistries.
ISSN:1043-1802
1520-4812
DOI:10.1021/bc015523q