DNA Fragmentation

DNA fragmentation is the breaking of DNA molecules into smaller pieces. Fragmentation of DNA is an early step in next generation sequencing workflows, and methods of DNA fragmentation include:

  • Enzyme-based treatments fragment DNA by the simultaneous cleavage of both strands, or by generation of nicks on each strand of dsDNA to produce dsDNA breaks.
  • Acoustic shearing using short wavelength acoustic energy focuses transmission of high-frequency acoustic energy on the DNA sample and can be performed isothermally. The transducer is bowl shaped so that waves converge at the target of interest.
  • Sonication using specialized sonicators subjects DNA to longer wavelength, unfocused acoustic energy, and requires cooling periods between sonication bursts.
  • DNA can be sheared by the use of centrifugal force to move DNA through a hole of a specific size. The rate of centrifugation determines the degree of DNA fragmentation.
  • Point-sink shearing, a type of hydrodynamic shearing, uses a syringe pump to create hydrodymanic shear forces by moving DNA through a tube with a tight constriction, such that the DNA breaks, with the size of the constriction and the flow rate of the liquid determining the DNA fragment size.
  • Needle shearing creates shearing forces by passing DNA through a small gauge needle.
  • Nebulization uses compressed air to force DNA through a small hole in a nebulizer unit, and the fragmented, aerosolized DNA is collected. DNA fragment size is determined by the pressure used.

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Protocols for DNA Fragmentation