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Nucleic Acids Research Advance Access originally published online on December 6, 2007
Nucleic Acids Research 2008 36(2):e10; doi:10.1093/nar/gkm1081
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Nucleic Acids Research, 2008, Vol. 36, No. 2 e10
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

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

Jesper Petersen1, Lena Poulsen2, Sarunas Petronis3, Henrik Birgens1 and Martin Dufva2,*

1Department of Haematology, Herlev Hospital, University of Copenhagen, Herlev Ringvej 75, DK-2730 Herlev, Denmark, 2Microarray Group, Department of Micro and Nanotechnology, Technical University of Denmark, Oersteds Plads, Bld. 345 East, DK-2800 Kongens Lyngby, Denmark and 3Department of Applied Physics, Fysikgården 4, Chalmers University of Technology, SE-412 96 Göteborg, Sweden

*To whom correspondence should be addressed. Tel: +45 4525 6324; Fax: +45 4588 7762; Email: mdu{at}mic.dtu.dk

Received October 4, 2007. Revised November 16, 2007. Accepted November 16, 2007.

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°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.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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