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  • MspJI

    cloned at neb recombinant incubation temp heat inactivation EpiMark Icon
    Catalog #SizeConcentrationPriceQtyAdd to Cart
    R0661S200 units5,000 units/ml$105.00Add to Cart
    R0661L1,000 units5,000 units/ml$425.00Add to Cart
    Epigenetic Analysis (EpiMark® Validated) Products,
    Methylation Dependent Restriction Enzymes for Epigenetics,
    Restriction Endonucleases: H-M
    Methylated DNA Analysis,
    Restriction Enzyme Digestion,
    Restriction Enzymes for Epigenetics


    MspJI, an EpiMark®, validated product is a modification-dependent endonuclease that recognizes mCNNR sites and generates a double-stranded DNA break on the 3´ side of the modified cytosine at N9/N13. The recognized cytosine modifications include C5-methylation (5-mC) and C5-hydroxymethylation (5-hmC) (1).

    This enzyme is provided with an Enzyme Activator Solution which may be used for efficient digestion by MspJI.

    The most common epigenetic modifications found in eukaryotic organisms are methylation marks at CpG or CHG sites. A subset of these modified sites are recognized and cleaved by MspJI.

    At fully methylated CpG sites:
    5´ . . . Y N mC G N R . . . 3´
    3´ . . . R N G mC N Y . . . 5´

    or CHG sites:
    5´ . . . Y mC H G R . . . 3´
    3´ . . . R G D mC Y . . . 5´

    R = A or G
    Y = C or T
    H = A or C or T (not G)
    D = A or G or T (not C) 

    MspJI recognizes each hemi-methylated site individually and cleaves bidirectionally to generate 32-base or 31-base fragments, respectively. These fragments contain the central methylated site and have 4-base 5´ overhangs at each end. MspJI does not cleave unmodified DNA.

    Product Source

    An E. coli strain that carries the synthetic MspJI gene from Mycobacterium species JLS.

    Reagents Supplied

    The following reagents are supplied with this product:

    Store at (°C)Concentration
    CutSmart® Buffer-2010X
    Enzyme Activator Solution30X

    Properties and Usage

    Unit Definition

    One unit is defined as the amount of enzyme required to digest 1 µg of pBR322 (dcm+) DNA in 1 hour at 37°C in a total reaction volume of 50 µl.

    Reaction Conditions

    1X CutSmart® Buffer
    Supplement with 1X Enzyme Activator Solution
    Incubate at 37°C

    1X CutSmart® Buffer:
    50 mM Potassium Acetate
    20 mM Tris-acetate
    10 mM Magnesium Acetate
    100 μg/ml BSA
    pH 7.9 @ 25°C

    Activity in NEBuffers

    NEBuffer 1.1: 10%
    NEBuffer 2.1: 10%
    NEBuffer 3.1: 10%
    CutSmart® Buffer: 100%

    Diluent Compatibility

    Storage Temperature


    Storage Conditions

    10 mM Tris-HCl
    300 mM NaCl
    1 mM DTT
    0.1 mM EDTA
    500 μg/ml BSA
    50% Glycerol
    pH 7.4 @ 25°C

    Heat Inactivation

    65°C for 20 min

    Methylation Sensitivity

    dam methylation: Not Sensitive
    dcm methylation: Not Sensitive
    CpG Methylation: Not Sensitive


    1. Use of excess enzyme inhibits cleavage. Optimization of the amount of enzyme needed for complete digestion may be required for each substrate DNA. Excess of enzyme or prolonged digestion time in the presence of Enzyme Activator Solution may cause star activity.
    2. Star activity may result from extended digestion.


    1. Zheng, Y. et al. (2010). Nucl. Acids Res. doi:10, 1093/nar/gkq327.
    2. U.S. Publication No. 2010-0167942 Unpublished observation


    1. How can I access the old NEBuffer Activity Chart?
    2. Why is my Restriction Enzyme not cutting DNA?
    3. Why do I see a DNA smear on an agarose gel after a restriction digest?
    4. Why do I see additional DNA bands on my gel after a restriction digest?
    5. How many nucleotides do I have to add adjacent to the RE recognition site in order to get efficient cutting?


    1. Genomic DNA Digestion using MspJI (R0661)
    2. Optimizing Restriction Endonuclease Reactions
    3. Double Digest Protocol with Standard Restriction Enzymes

    Selection Charts

    Usage Guidelines & Tips

    Troubleshooting Guides

    Interactive Tools

    NEB Publications

    • Xiaojun Huang, Hanlin Lu, Jun-Wen Wang, Liqin Xu, Siyang Liu, Jihua Sun, Jun Wang, Fei Gao (2013). High-throughput sequencing of methylated cytosine enriched by modification-dependent restriction endonuclease MspJI BMC Genetics. 14:56, PubMedID: 23773292, DOI: 10.1186/1471-2156-14-56
    • Horton, J.R., Mabuchi, M., Cohen-Karni, D., Zhang, X., Griggs, R., Samaranayake, M., Roberts, R.J., Zheng, Y. and Cheng, X. (2012). Stucture and cleavage activity of the tetrameric MspJI DNA modification-dependent restriction endonuclease. Nucleic Acids Research. 40(19), 9763-9773. PubMedID: 22848107


    • McKernan KJ, Spangler J, Zhang L, Tadigotla V, McLaughlin S, Warner J, Zare A, Boles RG (2014). Expanded genetic codes in next generation sequencing enable decontamination and mitochondrial enrichment PLoS One. 9(5), e96492. PubMedID: 24788618, DOI: 10.1371/journal.pone.0096492
    • Cohen-Karni, D, et al. (2011). The MspJI family of modification-dependent restriction endonucleases for epigenetic studies Proc. Natl. Acad. Sci. . PubMedID: 21690366, DOI: 10.1073/pnas.1018448108

    Quality Control

    Quality Control Assays

    The following Quality Control Tests are performed on each new lot and meet the specifications designated for the product. Individual lot data can be found on the Product Summary Sheet/Datacard or Manual which can be found in the Supporting Documents section of this page. Further information regarding NEB product quality can be found here.
    • Exonuclease Activity (Radioactivity Release):
      The product is tested in a reaction containing a radiolabeled mixture of single and double-stranded DNA. After incubation for 4 hours the exonuclease activity is determined by the % release of radioactive nucleotides.
    • Non-Specific DNase Activity (16 hour):
      The product is tested for non-specific nuclease degradation in a reaction containing a DNA substrate. After incubation for 16 hours there is no detectable degradation of the DNA substrate as determined by agarose gel electrophoresis.
    • RNase Activity (2 Hour Digestion):
      The product is tested in a reaction containing a RNA substrate.  After incubation for 2 hour there is no detectable degradation of the RNA substrate as determined by gel electrophoresis.

    Certificate of Analysis

    The Certificate of Analysis (COA) is a signed document that includes the storage temperature, expiration date and quality control's for an individual lot. The following file naming structure is used to name these document files: [Product Number]_[Size]_[Version]_[Lot Number]


    The Specification sheet is a document that includes the storage temperature, shelf life and the specifications designated for the product. The following file naming structure is used to name these document files: [Product Number]_[Size]_[Version]

    Safety Data Sheet

    The following is a list of Safety Data Sheet (SDS) that apply to this product to help you use it safely.