NEBNext® dsDNA Fragmentase®

Updated Protocol and Components

NEBNext dsDNA Fragmentase is an enzyme-based reagent that shears DNA to produce fragments of the desired sizes in a time-dependent manner, for next generation sequencing library preparation protocols

  • dsDNA Fragmentase provides random fragmentation, similar to mechanical methods (1,2)

Ordering Information

  • 50 reactions
  • 250 reactions
  • Product Information

    NEBNext® dsDNA Fragmentase generates dsDNA breaks in a time-dependent manner to yield 50–1,000 bp DNA fragments depending on reaction time. NEBNext dsDNA Fragmentase contains two enzymes, one randomly generates nicks on dsDNA and the other recognizes the nicked site and cuts the opposite DNA strand across from the nick, thereby producing dsDNA breaks. The resulting DNA fragments contain short overhangs, 5´-phosphates, and 3´-hydroxyl groups. The random nicking activity of NEBNext dsDNA Fragmentase has been confirmed by preparation of libraries for next-generation sequencing. A comparison of the sequencing results between libraries prepared with genomic DNA sheared with NEBNext dsDNA Fragmentase and with mechanical shearing demonstrates that NEBNext dsDNA Fragmentase does not introduce any detectable bias during sequencing library preparation and no difference in sequence coverage is observed between the two methods.

    For larger volume requirements, customized and bulk packaging is available by purchasing through the OEM/Bulks department at NEB. Please contact for further information.

    Reaction Definition:  One reaction is defined as the amount of NEBNext dsDNA Fragmentase required to convert 1 µg of purified HeLa cell gDNA in 20 µl of 1X NEBNext dsDNA Fragmentase Reaction Buffer v2 into short (100–300 bp) DNA fragments in 30 minutes at 37°C.


    Figure 1: Fragmentation of E. coli gDNA
    Figure 1: Fragmentation of E. coli gDNA.
    E. coli gDNA was fragmented with NEBNext dsDNA Fragmentase for the indicated times and purified on MinElute® columns.
    Figure 2: Fragmentation
    Figure 2: Fragmentation
    Fragmentation of 5,10 and 20 kb amplicons with NEBNext dsDNA Fragmentase.

    Reagents Supplied

    The following reagents are supplied with this product:

    Store at (°C) Concentration
    NEBNext® dsDNA Fragmentase® Reaction Buffer v2 -20 10 X
    Magnesium Chloride (MgCl2) (200 mM) -20
    Product Categories:
    DNA Library Prep
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