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Jets: a modification to speed flexible oligonucleotide array construction

The Pharmacogenomics Journal volume 1, pages 163–165 (2001)Cite this article

We have come a long way since the days of Northern blots. With the completion, or near completion, of multiple genome sequencing projects, DNA microarray technology is emerging as an extremely powerful and fundamental tool that can be used to explore genetic and molecular pathways associated with disease and other cellular processes.1,2 Translation of this information to the clinical arena will result in improvements in patient diagnostics and treatments.3,4,5 The application of array technology to biological questions is quickly transforming scientific paradigm, from one that formerly centered on the analysis of a relatively few biological measurements to one that supports the simultaneous exploration of thousands of events. While array technology is a powerful tool for both researchers and clinicians, its utility is hindered by the expense of, and difficulties associated with, custom modification of the arrays. In a recent article published in Nature Biotechnology, Hughes et al describe the adaptation of ink-jet technology for the in situ synthesis of small quantities of unique 60-mer oligonucleotides directly onto glass slides.6 This ‘second generation’ ink-jet oligonucleotide synthesizer is based on the approach described by Blanchard et al.7 It will greatly facilitate array modification by eliminating the time necessary for large-scale cDNA or oligonucleotide synthesis, reorganization of microtiter dishes, re-spotting of the DNA elements, or the generation of new photolithographic masks. With this new application of ink-jet technology, small quantities of oligonucleotides, specified by the user, can be synthesized directly onto the array. This permits a rapid customization that can meet the widely varying needs of investigators.

The prototypic microarray contains thousands of DNA elements (cDNAs or oligonucleotides) that are spotted or synthesized onto a solid substrate.8 These DNA elements correspond to the sequence of known genes (or predicted genes) identified through the efforts of the genome projects. Microarrays are typically constructed using two different approaches. The first approach was described by Pat Brown of Stanford University and involves mechanical spotting of cDNA fragments or oligonucleotides (60 to 70-mers) onto a solid substrate.9 Deposition of the DNA is accomplished using robotics equipped with micropins or by ink-jet print heads; small volumes are transferred from microtiter wells to the surface of the slide.10 While researchers using this ‘spotting’ approach are able to customize the array format in order to meet the laboratories’ needs, this modification is cumbersome and requires continuous, large-scale production of new reagents (oligonucleotide synthesis or PCR amplification), the generation of new stock titer plates, and respotting.

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Authors and Affiliations

  1. Department of Cell Biology, University of Alabama at Birmingham, AL, USA

    B Yoder

  2. Human Genetics and Nutrition Sciences, University of Alabama at Birmingham, AL, USA

    S M Sell

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  1. B Yoder
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  2. S M Sell
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Correspondence to B Yoder.

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Yoder, B., Sell, S. Jets: a modification to speed flexible oligonucleotide array construction. Pharmacogenomics J 1, 163–165 (2001). https://doi.org/10.1038/sj.tpj.6500032

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