What are the methods used to create DNA fragments?

Methods used for creating DNA fragments can be split into two basic categories -mechanical shearing and enzyme-based.

Mechanical Shearing Fragmentation Methods

The most commonly used mechanical shearing methods for creating DNA fragments include:

• Focused acoustic shearing - In this technique, the DNA sample is exposed to focused transmission of high-frequency, short wavelength acoustic energy. This generates smaller-sized DNA fragments. The size of DNA fragments can be controlled by varying both the duration and intensity of the acoustic waves.
• Hydrodynamic shearing - This technique involves applying hydrodynamic shear forces by pushing DNA through the small opening of a syringe. This is the preferred method for generating larger-sized DNA fragments. DNA fragment size can be controlled by varying the speed at which the DNA is pushed through the syringe. 
• Nebulization - In this method, compressed air is used to force DNA through a small orifice in a specially-designed nebulizer unit. The amount of pressure used determines the size of DNA fragments that are created. This technique is most suitable for small numbers of samples.

Enzyme-Based Fragmentation Methods

Enzyme-based fragmentation involves using enzymes to create DNA fragments. Three most commonly used enzymes include:

• Restriction enzymes - Restriction enzymes create either blunt-ended or overhanging double-stranded breaks on binding their recognition site. 
• Nicking enzymes - Nicking enzymes cut only one strand of a double-stranded DNA at a specific recognition nucleotide sequence known as a restriction site, generating DNA fragments that are nicked rather than cleaved.
• Transposons - Transposons create DNA fragments by cleaving DNA at random sites and inserting a short double-stranded oligonucleotide on both ends of the cleaved DNA.