Using recombinant Cas9 nuclease to assess locus modification in genome editing experiments (#M0386)


In vitro digestion of PCR amplicons with Cas9 ribonucleoproteins (Cas9 Nuclease) is a sensitive assay for detecting indels. Unlike mismatch detection assays, Cas9 has the additional advantage of determining targeting efficiencies above 50%. This is of value as targeting efficiency in genome editing experiments increases and for detection of biallelic editing in isolated cell colonies or tissues, and was previously only achievable using specialized PCR or amplicon sequencing approaches.

Required Materials:

  • Q5® Hot Start High-Fidelity 2X Master Mix (NEB #M0494)
  • Purified genomic DNA from targeted cells
  • PCR primers to amplify a ~1 kb region containing the target site
    • The target site should be offset from the center of the amplicon so that digestion produces easily resolvable DNA fragments
    • PCR primer design is critical. Please visit NEB's Tools and Resources page to optimize your primer design using the NEB Tm Calculator
  • A PCR thermocycler with programmable temperature ramp rate
  • DNA purification system (optional)
  • Spectrophotometer, fluorometer, or other method of DNA quantitation
  • Agilent Bioanalyzer®, QIAgen QIAxcel®, or agarose gel electrophoresis
  • Cas9 Nuclease, S. pyogenes (NEB #M0386S/L)
  • NEBuffer r3.1
  • sgRNA containing the targeting sequence in the region of interest
    • sgRNAs can be generated by in vitro transcription using the EnGen® sgRNA Synthesis Kit, S. pyogenes (NEB #E3322) and a single oligonucleotide or the HiScribe T7 Quick High-Yield RNA synthesis Kit (NEB #E2050) using linearized plasmid, PCR products, or oligonucleotides as templates.
    • sgRNAs must contain the target sequences (20 nucleotides) adjacent to the Protospacer Adjacent Motif (PAM, NGG) in the target DNA. (1,2)

Before You Start:

  • We strongly recommend wearing gloves and using nuclease-free tubes and reagents to avoid RNase contamination. Further recommendations for avoiding ribonuclease contamination can be found here.
  • Reactions are typically 20 μl, but can be scaled up as needed. Reactions should be assembled in nuclease-free microfuge tubes or PCR strip tubes.
  • It is essential to keep the molar ratio of Cas9 and sgRNA per target site at or near 10:10:1 to obtain the best cleavage efficiency. A calculator can be found here.
  • Prepare 1 μM sgRNA by diluting the stock with nuclease-free water on ice.


For genomic DNA extraction, purification and PCR amplification, please follow the manufacturer’s protocol.


  1. Set up a 50 µl PCR reaction using ~100 ng of genomic DNA as a template. For each amplicon set up 3 PCR reactions using the following templates
    1. gDNA from targeted cells (e.g., Cas9 or TALEN transfected cells)
    2. gDNA from negative control cells (e.g., non-specific DNA transfected cells)
    3. water (e.g., no template control)
    PCR using Q5 High-Fidelity DNA Polymerase
    Q5® Hot Start High-Fidelity 2X Master Mix (M0494S) 25 µl 1X
    10 µM Forward Primer 2.5 µl 0.5 µM
    10 µM Reverse Primer 2.5 µl 0.5 µM
    Template DNA variable ~100 ng
    Nuclease-free water To 50 µl

  2. Gently mix the reaction. Collect all liquid to the bottom of the tube by a quick spin if necessary. Transfer PCR tubes to a PCR machine and begin thermocycling.

  3. Cycling Conditions
    Initial Denaturation 98°C 30 seconds
    35 cycles

    98°C 5 seconds
    *50-72°C 10 seconds
    72°C 20 seconds
    Final Extension 72°C 2 minutes
    Hold 4-10°C
    *Use of the NEB Tm Calculator is highly recommended.

    Note: Q5 Hot Start High-Fidelity 2X Master Mix does not require a separate activation step. Standard Q5 cycling conditions are recommended.
  4. Analyze a small amount of the PCR product to verify size and appropriate amplification.
  5. Measure the concentration of the purified PCR products by Qubit® dsDNA BR Assay or other relevant system. A yield of > 25 ng DNA/μL is sufficient.

  6. *Cas9 Nuclease cleavage efficiency may be altered in the presence of certain PCR buffers. In general, efficiency tends to decrease as the amount of buffer increases. If > 2 µl of PCR product will be necessary for the cleavage reaction, consider purifying the PCR product prior to digestion.
      Cas9 digestion with sgRNA:

  1. Pre-loading sgRNA to Cas9 Nuclease
    NEBuffer r3.1 2µl
    1 µM sgRNA 2 µl (100 nM final)
    1 µM Cas9 Nuclease, S.pyogenes (M0386S/L) 2 µl (100 nM final)
    Nuclease-free Water 14-x µl
    Incubation Time & Temperature 5 – 10 minutes at room temperature

  3. Digestion of PCR product
    Reaction from Step1 20-x µl
    PCR product x µl (50 ng-200 ng DNA)*
    Incubation Time & Temperature 30 minutes at 37⁰C
    * < 2 μl PCR product per 20 μl is recommended. The ratio of Cas9:sgRNA:target should be near 10:10:1.

Purification is optional. If desired, we recommend either digestion with with 1 μl Proteinase K, Molecular Biology Grade (NEB #P8107S) for 15-30 minutes at 37⁰C or column purification. These steps can be of use if nonspecific binding or high background interfer with fragment analysis.


Analyze the fragmented PCR products by gel electrophoresis or other fragment analysis methods.

Calculate the estimated gene modification using the following formula:

% modification = 100 x ([uncut DNA] / [uncut DNA]+[fragment1]+[fragment2])


  1. Jinek et al. (2012) Science 337 (6096) 816-821.
  2. Larson et al. (2013) Nature Protocol (8) 2180-2196.
  3. Gagnon, J.A. et al. (2014) PLos ONE (9) e98186.

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