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.
Improving Enzymatic DNA Fragmentation for Next Generation Sequencing Library Construction