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

BMC Genomics. 2003 Sep 22;4(1):38. doi: 10.1186/1471-2164-4-38.


Background: 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.

Results: We present here a novel design of Saccharomyces cerevisiae 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.

Conclusions: A validated procedure to predict cross-hybridization in microarray probe design was defined in this work. Subsequently, a novel Saccharomyces cerevisiae microarray (which minimizes cross-hybridization) was designed and constructed. Arrays are available at Eurogentec S. A. Finally, we propose a novel design program, OliD, which allows automatic oligonucleotide design for microarrays. The OliD program is available from authors.

Publication types

  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Base Sequence
  • DNA Primers
  • Gene Expression Profiling / methods*
  • Genomics
  • Oligonucleotide Array Sequence Analysis / methods*
  • Oligonucleotide Probes* / chemistry
  • Polymerase Chain Reaction
  • Reproducibility of Results
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins / biosynthesis
  • Saccharomyces cerevisiae Proteins / genetics
  • Sequence Alignment
  • Software


  • DNA Primers
  • Oligonucleotide Probes
  • Saccharomyces cerevisiae Proteins