CRISPR Cas9 System Activity Detection

In the CRISPR-Cas9 system, different guide RNA (gRNA) can be designed based on the target gene. The DNA cutting efficiency of Cas9 can vary depending on the gRNA and target gene. It is therefore important to be able to accurately verify the activity of the CRISPR-Cas9 system in a given assay, in order to maximize the cleavage and gene knock-in/knock-out efficiency of CRISPR-Cas9. Synbio Technologies provides SSA activity assays, in vitro cleavage activity assays, and endogenous activity assays to detect gRNA activity.

SSA activity assays

Single-strand annealing(SSA)assays can verify whether the target gRNA plasmid can mediate Cas9 to cut naked DNA and are a common method to assess the activity of CRISPR-Cas9. The plasmid-based SSA assay contains two inactive luciferase-encoding fragments, which contain a stop codon and a segment of gRNA in the middle of the target sequence. If CRISPR-Cas9 can recognize and cleave the target site, the resultant double-stranded break can be repaired by the SSA mechanism, rescuing the now-active luciferase gene. Thus the SSA assay can be used to predict the cleavage activity of CRISPR-Cas9 by fluorescence detection.

Construction of plasmid-based SSA
Construction of plasmid-based SSA
Result of SSA assays
Result of SSA assays

Auxiliary product: construction of plasmid-based SSA activity kit (catalog no.: k0001)

Verification of in vitro cleavage assay

The target DNA sequence is digested with Cas9 in vitro to obtain two DNA fragments. Agarose gel electrophoresis allows analysis of gRNA-mediated DNA cleavage by comparing the yield of the smaller, digested fragments to the remaining undigested target DNA. Verification of in vitro cleavage is another way to determine the activity and efficiency of CRISPR-Cas9.

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Auxiliary product: in vitro gRNA target cleavage activity detection kit (catalog no.: k0002)

Endogenous Activity Assay

Surveyor method is called mismatch endonuclease assay, using the endonuclease T7E1 endonuclease. The suitable primers are first designed on both sides of the target, after which the DNA containing potentially mismatched mutation sites is amplified by PCR. T7E1 endonuclease can recognize and cleave mismatched DNA heteroduplexes. The digested product is finally analyzed by agarose gel electrophoresis to estimate the ratio of the cleavage and un-cleaved bands, reflecting the activity of CRISPR-Cas9.

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Comparison of different activity assay services:

Assay services Differentiation
SSA activity assay Easy to design, simple to use, cost-effective
in vitro cleavage activity assay Easy to use, only target design is needed
Cell-free assay system, cost effective
Endogenous activity assay Fast turnaround time, accelerated validation process


Service Specifications:

Service Name Service Specifications Timeline Deliverables
SSA activity assay
  • gRNA target primer design and synthesis
  • pSSA-luc vector construction
  • Cell transfection
Inquiry Assay Report
in vitro cleavage activity assay
  • In vitro transcription gRNA
  • CRISPR-Cas9 in vitro cleavage reaction
Inquiry Assay Report
Endogenous Activity Assay
  • Genome extraction
  • Target primer design
  • T7E1 enzyme digestion
Inquiry Assay Report