Alternative Splicing Probe Design

Jivan's alternative splicing database includes oligonucleotide probes specific to each splice site and each exon or exonic portion that undergoes alternative splicing. (exon-exon junction or exon-intron junction). The choice of probes for a particular microarray or PCR application depends on a variety of factors. Junction probes are capable of directly detecting any splicing event&em;including alternative exons, retained introns, alternative acceptor or donor sites leading to trimmed and extended exons&em;covering the whole spliceome.

For Jivan's SpliceExpress™ arrays, oligonucleotide probes range in length from 34 to 42 bases (T. Clark, C. Sugnet, M. Ares Jr., Science, 296, 907 (2002)) to achieve an isothermal target melting temperature (T_m) of approximately 67° array-wide. Unlike technologies that rely on probes complementary to exons and junctions, Jivan uses sense-strand oligos to hybridize to the complement of exons and junctions within labeled cRNA or cDNA. Further optimization balances the melting temperature of a probe on each side of the splice site for greater sensitivity and specificity in order to differentiate between multiple splice isoforms.

Each SpliceExpress™ splice array contains probes for a collection of genes carefully selected for comprehensiveness and relevance based on publications, automated analysis and manual curation.