Probing Gene Expression: Sequence-Specific Hybridization on Microarrays

Abstract

Background: DNA microarrays are routinely used to monitor the transcriptlevelsof thousands of genes simultaneously. However, the array design, hybridizationconditions, and oligodeoxyribonucleotide probe sequence impact theperformance of the DNA microarray platform and must be consideredby dataanalysis.Results: We analyzed the signal intensities of GeneChip microarraysin terms ofa microscopic binding model. It considers specific and non-specifictranscripts,which both compete for duplex formation with perfect match (PM) andmismatch(MM) oligonucleotide probes. Intensity simulations enable us to judgetheaccuracy and precision of gene expression measures. The accuracy oftheestimated fold changes ranks according to PM-MM>PM>MM whereas theprecision decreases with PM?MM>PM-MM where PM-MM denotes therespective intensity difference.Conclusions: MM probes possess the potency to correct the intensityof therespective PM probe for the non-specific background. The middle baserelatedbias of the MM intensity must however be considered by improved algorithmsofdata analysis. Moreover, the knowledge of base pair interactions suggeststosubstitute the complementary mismatches on GeneChips by alternativerules ofMM design.