Can I use Stellaris® RNA FISH Probes to distinguish RNAs from genes with high homology?

Studies by LGC Biosearch Technologies and our collaborators have shown that RNAs from genes with high homology can be distinguished by Stellaris RNA FISH. Most gene homology resides in the coding region, and if the untranslated regions can be used as targets, then targets with high overall homology can be more easily discriminated. Under the conditions of hybridization in the Stellaris RNA FISH method, oligonucleotides containing two or more mismatches to the target sequence will hybridize only weakly. To identify and eliminate cross-reacting sequences, we recommend applying bioinformatic approaches like BLAST or a multiple sequence alignment.