Product Class: Other

NEBNext® dsDNA Fragmentase®
NEBU

For most applications, especially where time-tunable fragmentation or preservation of methylation is needed, we recommend NEBNext UltraShear®.

Note: NEBNext dsDNA Fragmentase now has an updated protocol and components list.

Product Introduction

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)

Note: NEBNext dsDNA Fragmentase is not part of the NEBNext Ultra™ II FS (Fragmentation System) reagents.

Catalog # Size Concentration
M0348S 50.0 reactions
M0348L 250.0 reactions

Product Information

Description





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 custom@neb.com 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.
This product is related to the following categories:

Reagents Supplied

Reagents Supplied

The following reagents are supplied with this product:

NEB # Component Name Component # Stored at (°C) Amount Concentration

Properties & Usage

Reaction Conditions

1X NEBNext® dsDNA Fragmentase® Reaction Buffer v2

1X NEBNext® dsDNA Fragmentase® Reaction Buffer v2
20 mM Tris-HCl
15 mM MgCl2
50 mM NaCl
0.1 mg/ml BSA
0.15% Triton® X-100
(pH 7.5 @ 25°C)

Application Features

  • Generation of dsDNA fragments for sequencing on next generation sequencing platforms
  • Generation of dsDNA fragments for libraries

Protocols, Manuals & Usage

Protocols

  1. Digestion with NEBNext dsDNA Fragmentase (M0348)

FAQs & Troubleshooting

FAQs

  1. When dsDNA Fragmentase (NEB #M0348) was changed to include Fragmentase Buffer v2,  was there any change to the dsDNA Fragmentase enzyme itself?
  2. What sequencing platforms can DNA fragments produced using dsDNA Fragmentase (NEB #M0348) be used for?
  3. What types of DNA are suitable for fragmentation using ds DNA Fragmentase (NEB #M0348)?
  4. What type of ends does dsDNA Fragmentase (NEB #M0348) create?
  5. Can dsDNA Fragmentase (NEB #M0348) be heat inactivated?
  6. Can I add ligase to my samples after using dsDNA Fragmentase (NEB #M0348) to seal any nicks?
  7. Does the fragmentation reagent included in NEBNext Ultra® II FS DNA kits contain NEBNext dsDNA Fragmentase®?

Quality, Safety & Legal

Quality Assurance Statement

Quality Control tests are performed on each new lot of NEB product to meet the specifications designated for it. Specifications and individual lot data from the tests that are performed for this particular product can be found and downloaded on the Product Specification Sheet, Certificate of Analysis, data card or product manual. Further information regarding NEB product quality can be found here.

Specifications

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]

Certificate Of Analysis

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

Safety DataSheets

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

Legal and Disclaimers

Products and content are covered by one or more patents, trademarks and/or copyrights owned or controlled by New England Biolabs, Inc (NEB). The use of trademark symbols does not necessarily indicate that the name is trademarked in the country where it is being read; it indicates where the content was originally developed. The use of this product may require the buyer to obtain additional third-party intellectual property rights for certain applications. For more information, please email busdev@neb.com.

This product is intended for research purposes only. This product is not intended to be used for therapeutic or diagnostic purposes in humans or animals.

New England Biolabs (NEB) is committed to practicing ethical science – we believe it is our job as researchers to ask the important questions that when answered will help preserve our quality of life and the world that we live in. However, this research should always be done in safe and ethical manner. Learn more.

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