Can I design a Stellaris FISH RNA probe set to detect small RNAs?

The Stellaris™ Probe Designer software, available on our website, outputs a probe set with up to 48 oligonucleotides which are each 18-22 nucleotides long. A target of at least 1 kb in length is needed for the design of a full 48-oligonucleotide probe set. By reducing the number of probes in a set, the Stellaris technology can be used with target sequences as short as 600 nucleotides. If your sequence is significantly shorter, then the Stellaris method is less likely to provide for reliable single molecule detection. A shorter sequence may also be suitable if your target is found in clusters, such as at the site of transcription, or in Cajal Bodies. No matter what your design challenge might be, we want to help further your research with Stellaris, so please reach out to our design team at techsupport@biosearchtech.com to learn more about whether your target of interest can be detected by Stellaris RNA FISH.