Single-Stranded Nucleic Acid Detection And Imaging System Using Cas9

Tech ID: 24729 / UC Case 2015-090-0

Patent Status

Country Type Number Dated Case
United States Of America Published Application 20180002736 01/04/2018 2015-090
European Patent Office Published Application 3250689 12/06/2017 2015-090
Patent Cooperation Treaty Published Application WO2016123243 08/04/2016 2015-090

Brief Description

Genome editing using CRISPR/Cas9 has enabled rapid and accessible alteration of specific genomic loci in many organisms. A flexible means to target nucleic acids would allow alteration and imaging of endogenous RNA transcripts, for example, analogous to CRISPR/Cas-based genomic tools, but most nucleic acid targeting methods rely on incorporation of exogenous tags.


UC Berkeley researchers discovered compositions and methods for labeling a single stranded target nucleic acid with the use of a Cas9 protein; a Cas9 guide RNA; and a quenched PAMmer (a single stranded oligonucleotide having a protospacer adjacent motif (PAM) sequence.  The PAMmer also contains a detectable label and a quencher moiety that quenches the detectable label.  Cas9 cleavage of the PAMmer is predicted on complete Cas9 sgRNA: target complementarity and thus is highly specific.  The inventors have used the methods and compositions to track RNA in living cells in a programmable manner without genetically encoded tags.

Suggested uses

  • Detection of endogenous and foreign single-stranded nucleic acids (e.g., in cell culture, patient samples, and environmental samples)
  • Fixed and live-cell imaging of single-stranded nucleic acids


  • Ultra-low background and thus fewer false positive signals
  • Highly specific and sensitive detection


Programmable RNA Tracking in Live Cells with CRISPR/Cas9

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  • Doudna, Jennifer A.

Other Information


Imaging, Cas9

Categorized As