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Molecular interactions on microarrays

Nature Genetics volume 21, pages 5–9 (1999)Cite this article

Abstract

The structural features of nucleic acid probes tethered to a solid support and the molecular basis of their interaction with targets in solution have direct implications for the hybridization process. We discuss how arrays of oligonucleotides provide powerful tools to study the molecular basis of these interactions on a scale which is impossible using conventional analysis.

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Figure 1: The density of oligonucleotides on the surface is approximately 10 pmol per mm2 on aminated polypropylene, approximately 0.1 pmol per mm2 on glass after ammonia deprotection—–equivalent to one molecule per 39 square angstroms.
Figure 2: Long target sequences are likely to fold in on themselves as a result of intramolecular Watson–Crick base pairing.
Figure 3: Short targets are better able than large targets to interact with tethered oligonucleotides: they are less likely to have bases hidden from duplex formation by intramolecular base pairing; and, as they are less bulky, they will more readily penetrate the closely packed lawn of oligonucleotides.
Figure 4: A 32P–labelled RNA transcript of rat Ox40, encoding a cell surface glycoprotein, hybridized to a scanning array in 3.

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  1. Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK

    Edwin Southern, Kalim Mir & Mikhail Shchepinov

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  2. Kalim Mir
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Southern, E., Mir, K. & Shchepinov, M. Molecular interactions on microarrays. Nat Genet 21 (Suppl 1), 5–9 (1999). https://doi.org/10.1038/4429

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