OligoArray

OligoArray designs gene-specific oligonucleotide probes for genome-scale microarray experiments to enable specific hybridization-based expression analysis.

Key Features:

• Genome-scale probe design: Computes gene-specific oligonucleotides for genome-wide microarrays.
• Thermodynamic secondary-structure prediction: Uses a thermodynamic approach to predict oligonucleotide secondary structures.
• Hybridization specificity calculation: Calculates hybridization specificity for unique probes within a mixture of labeled probes to minimize cross-hybridization.
• Prevention of stable secondary structures: Selects probes that avoid formation of stable secondary structures that could interfere with probe labeling and hybridization.
• Tm control via length adjustment: Allows adjustment of oligonucleotide length to achieve a narrow melting temperature (Tm) range for consistent hybridization conditions.
• Microarray probe compatibility: Generates probes suitable for spotted or in situ synthesized microarray slides.
• Demonstrated scalability: Designed 75,764 oligonucleotides representing 26,140 Arabidopsis thaliana transcripts, providing at least one specific oligonucleotide for 93% of transcripts.

Scientific Applications:

• Genome-scale expression analysis: Enables genome-wide expression profiling by producing specific probes for organisms with fully sequenced genomes without dependence on cDNA or oligonucleotide libraries.
• Microarray probe set development: Supports development of probe sets for spotted and in situ synthesized oligonucleotide microarrays used in transcriptomic experiments.
• Transcript-specific probe design in model organisms: Applied to design transcript-specific probes in Arabidopsis thaliana, demonstrating high coverage of annotated transcripts.

Methodology:

Computes gene-specific oligonucleotides using a thermodynamic approach that predicts secondary structures, calculates hybridization specificity within mixtures of labeled probes, and adjusts oligonucleotide length to target a narrow melting temperature (Tm) range.