Fragmentation - The long, thin threads which consist of duplex DNA molecules are sufficiently rigid to be broken by shear forces solution. Intense sonification with ultrasound can reduce the length to about 300 bp. More controlled shearing can be achieved by high speed stirring in a blender.

Typically high molecular weight DNA can be broken down into fragments of about 8 kb by stirring at 1500 rev/min for 30 min. Breakage occurs essentially at random with respect to DNA sequence. The only problem with this method is that the results or the length of fragment is not reproducible.