Main Menu (Mobile)- Block

Main Menu - Block

CASFISH: DNA labeling with CRISPR/Cas9

janelia7_blocks-janelia7_node_tool_type_list | block
node_title | node_title

CASFISH: DNA labeling with CRISPR/Cas9

node:body | entity_field

About the Innovation

Genomic DNA in cells is highly folded and organized in three dimensions. Detection and visualization of genomic DNA are widely accomplished by using various fluorescence in situ hybridization (FISH) methods. However, despite enhancements to DNA FISH methods, the use of chemicals or heat in the process results in denaturation of the DNA and potentially affects the integrity of the biological structure, which limits research related to the understanding of gene expression. 

Researchers at HHMI’s Janelia Research Campus have developed a novel method that can be used to rapidly detect DNA sequences in a more sensitive manner and without denaturation, resulting in the newest development in FISH technology since the discovery of fluorescent probes. The method uses a bacterial protein, CRISPR/Cas9 protein, to detect endogenous DNA sequences in fixed and unfixed material. Researchers can use the CASFISH method to detect short DNA sequences in cells in situ through a designed complex of Cas9 protein modified to only bind DNA with single-guide RNA (labeled or unlabeled), selected from the set of available genomic sequences.

Because the protein is the generic reporter, it can be labeled with any means, fluorescent proteins, dyes, quantum dots, gold particles, or other analytes consistent with microscopy or other appropriate detection methods. CASFISH provides researchers with simpler, more efficient, and robust in situ imaging of cellular DNA. The method has been demonstrated in a laboratory study in the visualization of non-repetitive genomic sequences. Scientists could use the novel method in the detection and visualization of genomic DNA sequences in cells and tissues.


• Rapidly detects DNA sequences more sensitively and without denaturation

Reduces both the deleterious effects and inconvenience of sample preparation

• Does not require the use of chemicals, heat, or fixation


• Provides detection and visualization of cellular DNA for gene expression research and other genomics research

• Could potentially be used directly on tissues for the rapid diagnosis of disease


Commercial License or Non-Profit Research



In the top 5% of all research outputs scored by Altmetric.

183 total citations on Dimensions.

183 total citations on Dimensions.

Direct access to publication.

Patent Protection:

For inquiries, please reference:

CASFISH, Janelia 2014-041

node:field_image | entity_field
individual_tool_resources | views
janelia_helper-janelia7_publication_list | block
janelia7_blocks-janelia7_tool_collaborators | block
janelia7_blocks-janelia7_program_administration | block


Michael Perham
addtoany-addtoany_button | block

Share this Tool