DNA FISH uses denaturation to expose chromosomal DNA. Probes then hybridise to specific genomic loci or chromosomal regions to detect copy number, structural variants, or gene fusions. RNA FISH targets intact mRNA or non-coding RNA in fixed, non-denatured cells. Stellaris RNA FISH uses pools of short tiled oligonucleotides that co-localise on a single transcript. This produces a spot bright enough for single-molecule counting without signal amplification.
Cell-based Analysis
FISH Probes and Fluorescence In Situ Hybridisation Reagents
FISH probes for single-molecule RNA and DNA target localisation in cells
FISH reagents bind directly to complementary nucleic acid targets in your sample while the cellular architecture stays intact. Fluorescent reporters then mark the exact location under your standard epifluorescence or confocal microscope. This resolves targets down to individual molecules or specific chromosomal loci.
myTags FISH Probes, developed by Daicel Arbor Biosciences, are custom-designed synthetic oligonucleotide probes. They detect and visualise complementary genomic targets in your FISH and other applications.
Stellaris RNA FISH is an RNA visualisation method developed by LGC Biosearch Technologies. It allows simultaneous detection, localisation and quantification of individual RNA molecules at the cellular level in fixed samples using fluorescence microscopy.
Choosing the right FISH probe for your target
- Custom or off-the-shelf probe sets? Custom FISH probes can target the specific sequence you are interested in. Off-the-shelf probe sets are pre-designed probe sets targeting highly requested sequences and controls.
- DNA or RNA FISH? The Stellaris probe sets target RNA sequences. myTags probe sets can be designed for targeting either DNA or RNA in your samples.
- Number of probes needed? The number of probes in the designed probe set depends on the length of your target sequence and the required specificity. Stellaris FISH probes offer a maximum of 48 probes per probe set. A minimum of 25 probes is recommended. For myTags FISH probes, the number of probes per probe set is almost unlimited for your design, ranging up to more than 100,000.
- Length of probes? Stellaris RNA FISH probes have an approximate length of 18 to 22 bp. myTags probes are longer, with an approximate length of 43 to 47 bp each.
- Labelling? A label for your Stellaris RNA FISH probes is available, such as FAM, CAL, Quasar, TAMRA, Amine or Biotin. myTags FISH probes can be ordered pre-labelled or immortal (unlabelled), with labels such as FAM, Alexa 488, ATTO, TAMRA, Digoxigenin or Biotin available.
- Design? If you have already designed your probe sequences, synthesis can proceed directly. If you have not designed them yet, the Arbor design team can take over myTags FISH probe design. For Stellaris FISH probes, BioCat's design team can also help, though you remain responsible for design approval.
Applications
Single-molecule RNA localisation and quantification
Stellaris RNA FISH probes count individual mRNA molecules in your fixed cells, resolving subcellular localisation and expression patterns.
Chromosomal locus detection and copy-number analysis
Custom myTags DNA FISH probes target genomic loci to detect gene amplifications, deletions and copy-number changes in your cells and tissue.
Structural variant and gene-fusion confirmation
Custom FISH probe pairs flank a predicted breakpoint or fusion junction, confirming chromosomal rearrangements from your sequencing data.
Pathogen RNA detection
Custom RNA FISH probes target viral or microbial RNA, letting you visualise infection at single-cell resolution. This complements PCR-based pathogen detection.
Chromosome painting and comparative cytogenetics
Large custom myTags probe sets span whole chromosomes or arms, supporting karyotype analysis and chromosomal structure studies.
Splice variant and isoform-specific detection
Probes against specific exons or exon junctions distinguish spliced isoforms at single-molecule resolution, extending your transcriptome profiling.
Frequently asked questions
myTags FISH probes are custom-designed and can target either DNA or RNA sequences, with probe lengths of 43 to 47 bp and probe set sizes ranging up to more than 100,000 probes. Stellaris RNA FISH probes target RNA only, are shorter at 18 to 22 bp, and are limited to a maximum of 48 probes per set, with 25 recommended as a minimum. Both can be ordered as a custom design, or, for Stellaris, chosen from pre-designed sets for common targets.
For Stellaris RNA FISH, a minimum of 25 probes tiling the target transcript is recommended, up to a maximum of 48. Each probe contributes partial fluorescence. Co-localisation of all probes on a single mRNA produces a diffraction-limited spot bright enough to distinguish from background with standard widefield or confocal microscopes.
Yes. Sequential IF-FISH or FISH-IF workflows are established methods. The order of immunofluorescence and FISH depends on the protocol. Some workflows stain protein first. Others perform RNA FISH first, or use integrated protocols that preserve both RNA and epitopes. This avoids probe denaturation conditions damaging protein epitopes. The best order still depends on fixation method, target abundance, and the specific probe chemistry used.
Parent category: Cell-based assay kits
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