NEBNext® dsDNA Fragmentase® is an enzyme-based solution used for the fragmentation of DNA. dsDNA Fragmentase generates 100-800bp fragments in a time dependent manner. The solution 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, producing dsDNA breaks. The resulting DNA fragments contain short overhangs, 5´-phosphates, and 3´-hydroxyl groups. This nicking activity has been shown to be random. Comparison of sequencing data from libraries prepared with DNA sheared mechanically or by dsDNA Fragmentase (Figure 1) demonstrates that the dsDNA Fragmentase does not introduce any detectable bias. In addition, no difference in sequence coverage is observed between these methods. dsDNA Fragmentase can be used with genomic DNA, PCR products and whole genome amplified DNA, of any degree of GC content.
NEBNext dsDNAFragmentase® generates fragments in the 100–300 bp range more effectively than nebulization.
Figure 1: Relative size distribution of E. coli DNA fragments with dsDNAFragmentase vs. Nebulization as seen using the Bioanalyzer 2100. The dsDNAFragmentase sample was incubated for 30 minutes at 37°C with 0.05 µg of DNA per µl of dsDNAFragmentase in 1X Fragmentase Reaction Buffer with 100 µg/ml BSA. The Nebulizer sample was prepared by nebulization of DNA in 50% glycerol for 6 minutes at 35 psi. NEBNext® and Fragmentase® are registered trademarks of New England Biolabs, Inc.