Super-Resolution Microscopes

Single Molecule FISH (smFISH) Imaging

Image and quantify RNA with single-molecule sensitivity

A Fluorescence Localization and Imaging Technique for RNA Visualization

RNA transcripts are a critical piece of the central dogma of biology yet are difficult to image due to their requirement for specific, fluorescent labeling and nanoscopic size. Bruker’s Vutara single-molecule localization microscope (SMLM) and fully integrated SRX software enables users to easily conduct smFISH imaging and analysis experiments.

Bruker offers the tools necessary for successful smFISH experiments including our:

What is Single Molecule FISH (smFISH)? 

Single molecule fluorescence in situ hybridization (smFISH) — also known as smRNA FISH or RNA FISH — is a cutting-edge technique for studying gene expression in single cells. This technique is similar to FISH in that it is used to visualize DNA, either specific genes or portions of genes, but differs in its unique ability to image and quantify individual RNA molecules. The applications of smFISH transcend life sciences disciplines and include, among others, genomics, cancer biology, neuroscience, and more.

Key advantages of smFISH

  1. Enables visualization and quantification of specifically labeled RNA molecules at single-molecule resolution; and
  2. Supports single-cell gene expression experiments through time and space.

P E O P L E   A L S O   A S K:

Why use smFISH vs. FISH?

If the research question requires investigation and visualization of RNA instead of DNA, smFISH is the most optimized technique. Fluorescence in-situ hybridization (FISH) operates under the same principles as smFISH — the hybridization of complementary fluorescent probes to a target sequence. However, FISH is optimized for targeting DNA sequences, such as entire genes or portions of genes.

How can I learn more about super-resolution microscopy?

Visit our Super-Resolution Microscopy Knowledge Pack, which contains a bundle of information. Inside, you will find the Bruker Super-Resolution eBook, several full-length protocol papers, and a full-length webinar. These resources are freely available and can be accessed on the Super-Resolution Microscopy Knowledge Pack page.


What is smFISH Used For?

Visualize and quantify specifically labeled RNA with single-molecule resolution

Performing smFISH experiments with the Vutara not only allows for quantification of RNA, but also enables the visualization of the target RNA at subcellular resolution. The ability to image the RNA within the cell opens avenues to studying RNA distribution and localization in relation to other markers or proteins. The combination of the imaging and quantification with smFISH can also be used as a readout for prediction of protein content. The advantage of RNA imaging with smFISH with the Vutara is unique from RNA sequencing data, which only provides quantitative values of RNA abundance.

Early passage normal diploid lung fibroblasts labeled against non-coding RNA MALAT1 using Stellaris® FISH Probes end-labeled with Quasar® 670. Data courtesy of Marco De Cecco at Brown University.

Investigate spatio-temporal gene expression patterns

RNA imaging with smFISH enables quantitative and qualitative gene expression experiments within single cells. With smFISH, researchers can measure cellular mRNA and perform spatial localization and quantification in locations such as the cytoplasm and nucleus. Single RNA molecules can be traced over time for temporal analysis.

How Does smFISH Work?

With smFISH, RNA targets are imaged via the hybridization and of many short, fluorescently labeled oligonucleotide probes.

How to detect mRNA with smFISH

  1. Design smFISH probes that are complementary to the target RNA and will be coupled with a fluorophore for imaging
  2. Prepare sample for imaging (can be live or fixed)
  3. Hybridize smFISH probes to target RNA in sample
  4. Collect images with the Vutara VXL in large FOV mode
  5. Analyze your data. Localize, quantify, and visualize molecules with software

Frequently Asked Questions

Understanding smFISH

What is the difference between smFISH and FISH?

Fluorescence in situ hybridization (FISH) is a technique used for the visualization of DNA, either specific genes or portions of genes, within a cell. This technique works via the use of probes that hybridize to the desired genomic region of interest and are labeled with fluorescent dye that is visible with SMLM. FISH is a powerful tool to investigate genomics questions, as it supports chromatin tracing applications. Like FISH, single molecule fluorescence in situ hybridization (smFISH) is a technique optimized for studying gene expression in single cells but is distinct in its ability to localize and quantify individual RNA molecules. With smFISH, RNA targets are imaged via the application of many short, labeled oligonucleotide probes that fluoresce when hybridized to the target sequence.

How does smFISH RNA visualization compare to other RNA visualization techniques?

The advantage of our smFISH module is that it provides both visualization and quantification of RNA within the sample — unlike other techniques like RNA sequencing that only provide quantitative RNA abundance values.

Performing smFISH

What are the advantages of Vutara VXL for smFISH experiments?

The advantage of using Vutara’s smFISH module is that it provides both visualization and quantification of RNA within the sample — unlike other techniques like RNA sequencing that only provide quantitative RNA abundance values.

What software is available for smFISH experiments?

Advanced software is necessary to analyze smFISH data collected with SMLM. Bruker’s SRX software contains internal analysis tools, including those for segmentation and statistics, and is compatible with external open-source code. This software also features statistical analysis of distribution of smFISH probes in the cytosol and nucleus.

How are samples prepared for smFISH experiments?

Bruker provides a variety of protocols for SMLM methods like smFISH. You can find them here.

An additional protocol for sample preparation and imaging with probes can be found here:

Trcek, T., Lionnet, T., Shroff, H. et al. mRNA quantification using single-molecule FISH in Drosophila embryos. Nat Protoc 12, 1326–1348 (2017).

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