The right answer is The digestion of DNA by restriction enzymes.
The fragmentation of the DNA is done by bacterial enzymes called restriction enzymes.
Restriction-enzymes (or endonucleases) recognize and cut the DNA into a specific sequence. These enzymes are naturally produced in bacteria as a defense against bacteriophages - viruses that infect bacteria. The bacterial restriction enzymes cut the DNA of the invasive bacteriophage while leaving the bacterial genomic DNA healthy and safe through the addition of methyl groups.
These enzymes are used in practice at the laboratory level to explore DNA.