DNA fragmentation is the breaking of DNA molecules into smaller pieces. Fragmentation of DNA is an early step in next generation sequencing workflows, as well in the creation of DNA inserts for expression libraries. Methods of DNA fragmentation include:
- Acoustic shearing is the transmission of high-frequency acoustic energy waves delivered to a DNA library. The transducer is bowl shaped so that waves converge at the target of interest.
- Nebulization forces DNA through a small hole in a nebulizer unit, which results in the formation of a fine mist that is collected. Fragment size is determined by the pressure of the gas used to push the DNA through the nebulizer.
- Sonication, a type of hydrodynamic shearing,subjects DNA to hydrodynamic shearing by exposure to brief periods of sonication, usually resulting in 700bp fragments.Point-sink shearing, a type of hydrodynamic shearing, uses a syringe pump to create hydrodymanic shear forces by pushing a DNA library through a small abrupt contraction. About 90% of fragment lengths fall within a two-fold range.
- Needle shearing creates shearing forces by passing DNA libraries through a small gauge needle.
- French pressure cells pass DNA through a narrow valve under high pressure to create high shearing forces.
- Enzyme-based treatments fragment DNA either by the simultaneous cleavage of both strands, or by generation of nicks on each strand of dsDNA to produce dsDNA breaks.