CRISPR-Based Imaging System Detects Target Gene Loci in Live Cells

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Shaojie Zhang, Ph.D.
Ardalan Naseri, Ph.D.
Hanhui Ma, Ph.D.
Huisman Maximiliaan, Ph.D.
Thoru Pederson, Ph.D.
Li-Chun Tu, Ph.D.
Zuoshang Xu, Ph.D.
Chunxing Yang, Ph.D.
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US Patent Pending
Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow
Nature biotechnology, vol. 34,5 (2016): 528-30. DOI:10.1038/nbt.3526

Key points

  • Detects and labels multiple gene loci simultaneously in a single assay
  • Enables scientists to track in real-time the chromosome dynamics in live cells
  • Can be used for diagnosis of genetic diseases that have DNA repeat expansions


Researchers at the University of Central Florida and the University of Massachusetts have developed a CRISPR-based system for detecting DNA repeat expansion sequences—genetic mutations that cause diseases such as amyotrophic lateral sclerosis (ALS). The CRISPR Arrayed Repeat Detection System (CARDS) can detect multiple mutated genes simultaneously in a single assay. Additionally, the system’s unique CRISPRainbow technology enables scientists to simultaneously label as many as six target loci in live cells with a distinctive color. Overall, the system provides a means to resolve the 3D genome in live cells and track chromosome dynamics in real-time.

Technical Details

Based on the CRISPR technology, CARDS locates, labels and tracks the movements of DNA without editing/cutting the genome. CARDS tags specific locations along the genome by using its unique CRISPRainbow technology, a novel combination of a nuclease-dead Cas9 (dCas9) protein and an engineered single-guide RNA (sgRNA) sequence. A mutation in the dCas9 protein makes the nuclease inactive so that it only binds to the DNA but does not cleave it. The scaffolds of the sgRNA bind sets of fluorescent proteins that can be further combined to generate additional colors. For example, the technology can be used to simultaneously label six distinct chromosomal loci with different colors (such as red, green, blue, yellow, cyan and magenta) and observed in real-time with fluorescence microscopy.


  • Simultaneous imaging of multiple gene loci in live cells
  • Tracks chromosome dynamics in real time
  • Less costly and technically easier to implement than FISH (fluorescent in situ hybridization)

Market Application

  • Clinical diagnostics of genetic diseases
  • Genomics
  • Imaging


Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow, Nature Biotechnology, vol. 34,5 (2016): 528-30. DOI:10.1038/nbt.3526,

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