Use of a multi-thermal washer for DNA microarrays simplifies probe design and gives robust genotyping assays

J. Petersen, Lena Poulsen, S. Petronis, H. Birgens, Hans Martin Dufva

    Research output: Contribution to journalJournal articleResearchpeer-review

    Abstract

    DNA microarrays are generally operated at a single condition, which severely limits the freedom of designing probes for allele-specific hybridization assays. Here, we demonstrate a fluidic device for multi-stringency posthybridization washing of microarrays on microscope slides. This device is called a multi-thermal array washer (MTAW), and it has eight individually controlled heating zones, each of which corresponds to the location of a subarray on a slide. Allele-specific oligonucleotide probes for nine mutations in the beta-globin gene were spotted in eight identical subarrays at positions corresponding to the temperature zones of the MTAW. After hybridization with amplified patient material, the slides were mounted in the MTAW, and each subarray was exposed to different temperatures ranging from 22 to 40 degrees C. When processed in the MTAW, probes selected without considering melting temperature resulted in improved genotyping compared with probes selected according to theoretical melting temperature and run under one condition. In conclusion, the MTAW is a versatile tool that can facilitate screening of a large number of probes for genotyping assays and can also enhance the performance of diagnostic arrays.
    Original languageEnglish
    JournalNucleic Acids Research
    Volume36
    Issue number2
    ISSN0305-1048
    DOIs
    Publication statusPublished - 2008

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