Base pair interactions and hybridization isotherms of matched and mismatched oligonucleotide probes on microarrays

The microarray technology enables the expression degree of thousands of genes to be estimated at once by the measurement of the abundance of the respective messenger RNA. This method is based on the sequence specific binding of RNA to DNA probes and its detection using fluorescent labels. The raw intensity data are affected by the sequence-specific affinity of probe and RNA for duplex formation, by the background intensity due to nonspecific hybridization at small transcript concentrations and by the saturation of the probes at high transcript concentration owing to surface adsorption. We address these issues using a binding model which describes specific and nonspecific hybridization in terms of a competitive two-species Langmuir isotherm and DNA/RNA duplex formation in terms of sequence-specific, single-base related interactions. The GeneChip microarrays technology uses pairs of so-called perfect match (PM) and mismatch (MM) oligonucleotide probes to estimate the amount of nonspecific hybridization. The mean affinity of the probes decrease according to PM(specific) > MM(specific) >> PM(nonspecific) approximate to MM(nonspecific). The stability of specific and nonspecific DNA/RNA duplexes is mainly determined by Watson Crick (WC) pairings. Mismatched self-complementary pairings in the middle of the MM sequence only weakly contribute to the duplex stability. The asymmetry of base pair interaction in the DNA/RNA hybrid duplexes gives rise to a duplet-like symmetry of the PM - MM intensity difference at dominating nonspecific hybridization and a triplet-like symmetry at specific hybridization. The signal intensities of the PM and MM probes and their difference are assessed in terms of sensitivity and specificity. The presented results imply the refinement of existing algorithms of probe level analysis to correct microarray data for nonspecific background intensities and saturation on the basis of the probe sequence.