A novel design of whole-genome microarray probes for <it>Saccharomyces cerevisiae </it>which minimizes cross-hybridization

• Main Authors: Brino Laurent, Dujon Bernard, Tekaia Fredj, Talla Emmanuel
• Format: Article
• Language: English
• Published: BMC 2003-09-01
• Series: BMC Genomics
• Online Access: http://www.biomedcentral.com/1471-2164/4/38

<p>Abstract</p> <p>Background</p> <p>Numerous DNA microarray hybridization experiments have been performed in yeast over the last years using either synthetic oligonucleotides or PCR-amplified coding sequences as probes. The design and quality of the microarray probes are of critical importance for hybridization experiments as well as subsequent analysis of the data.</p> <p>Results</p> <p>We present here a novel design of <it>Saccharomyces cerevisiae </it>microarrays based on a refined annotation of the genome and with the aim of reducing cross-hybridization between related sequences. An effort was made to design probes of similar lengths, preferably located in the 3'-end of reading frames. The sequence of each gene was compared against the entire yeast genome and optimal sub-segments giving no predicted cross-hybridization were selected. A total of 5660 novel probes (more than 97% of the yeast genes) were designed. For the remaining 143 genes, cross-hybridization was unavoidable. Using a set of 18 deletant strains, we have experimentally validated our cross-hybridization procedure. Sensitivity, reproducibility and dynamic range of these new microarrays have been measured. Based on this experience, we have written a novel program to design long oligonucleotides for microarray hybridizations of complete genome sequences.</p> <p>Conclusions</p> <p>A validated procedure to predict cross-hybridization in microarray probe design was defined in this work. Subsequently, a novel <it>Saccharomyces cerevisiae </it>microarray (which minimizes cross-hybridization) was designed and constructed. Arrays are available at Eurogentec S. A. Finally, we propose a novel design program, <it>OliD</it>, which allows automatic oligonucleotide design for microarrays. The <it>OliD </it>program is available from authors.</p>