Inst. f. Informatik   
Uni Leipzig

Bioinformatics Preprint 04-004

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Interactions in oligonucleotide hybrid duplexes on microarrays

Hans Binder, Toralf Kirsten, Ivo L. Hofacker, Markus Loeffler, Peter F. Stadler

Submitted for publication in:
J.Phys.Chem B

The interactions in RNA/DNA hybrid duplexes on microarrays have been investigated because of their importance for chip design and the analysis of gene expression data. We investigated Affymetrix GeneChip© intensity data in terms of chip averaged sensitivities over all perfect match (PM) and mismatch (MM) probes possessing a common triple of neighboured bases in the middle of their sequence to estimate the contribution of matched Watson-Crick (WC) and mismatched self complementary (SC) base pairs to DNA/RNA duplex stability. This approach provides a modelindependent estimation of base-specific contributions to the probe sensitivities. We found that biotinylated and fluorescently labelled SC pairs always increase the sensitivity compared with the nonlabelled ones. In contrast, labels attached to nucleotide bases forming WC pairs in most cases decrease their binding affinity and thus decrease the sensitivity of the probe. Single base related mean sensitivity values rank in ascending order according to C > T > G ~ A for SC pairs and C > G ~ T > A for WC pairs. The bases adjacent to the middle base considerably modify the sensitivity as a consequence of stacking interactions and sterical effects. Linear combination of the triple averaged probe sensitivities provide nearest neighbour (NN) sensitivity terms which rank in a similar order as the respective NN free energy terms obtained from thermodynamic studies on the stability of RNA/DNA duplexes in solution. Systematic deviations between both data sets can be mostly attributed to the labelling of the target RNA in the chip experiments. Our results provide a set of molecular NN and single base related interaction parameters which consider specific properties of duplex formation in microarray hybridisation experiments such as fluorescence labelling and selfcomplementary mismatches. Our results are useful for the optimisation of oligonucleotide probe sequences in chip design and for the interpretation of microarray probe intensities in gene expression analysis.

DNA/RNA duplex formation, purine-pyrimidine asymmetry, self-complementary base pairs, labelled nucleotides, nearest-neighbour interactions, gene expression analysis

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