  MOTIVATION: The use of oligonucleotide microarray technology requires a very
detailed attention to the design of specific probes spotted on the solid phase.
These problems are far from being commonplace since they refer to complex
physicochemical constraints. Whereas there are more and more publicly available
programs for microarray oligonucleotide design, most of them use the same
algorithm or criteria to design oligos, with only little variation. RESULTS: We
show that classical approaches used in oligo design software may be inefficient
under certain experimental conditions, especially when dealing with complex
target mixtures. Indeed, our biological model is a human obligate parasite, the
microsporidia Encephalitozoon cuniculi. Targets that are extracted from
biological samples are composed of a mixture of pathogen transcripts and host
cell transcripts. We propose a new approach to design oligonucleotides which
combines good specificity with a potentially high sensitivity. This approach is
original in the biological point of view as well as in the algorithmic point of
view. We also present an experimental validation of this new strategy by
comparing results obtained with standard oligos and with our composite oligos.
A specific E.cuniculi microarray will overcome the difficulty to discriminate
the parasite mRNAs from the host cell mRNAs demonstrating the power of the
microarray approach to elucidate the lifestyle of an intracellular pathogen
using mix mRNAs.
