AAT Bioquest

What are the enzymes used for DNA fragmentation?

Posted February 22, 2022


There are three types of enzymes used for DNA fragmentation - restriction enzymes, nicking enzymes, and transposases.

Restriction enzymes

Restriction enzymes work by creating either blunt-ended or overhanging double-stranded breaks on binding their recognition site. A recognition site is a DNA sequence with a shape that matches a part of the enzyme. When the restriction enzyme comes in contact with a recognition site, it wraps around the DNA and causes a break in both strands of the DNA molecule, resulting in DNA fragmentation.

Nicking Enzymes

Nicking enzymes cut only one strand of a double-stranded DNA at a specific recognition nucleotide sequence known as a restriction site. This results in DNA molecules that are nicked rather than cleaved.


DNA transposons cause DNA fragmentation by cleaving DNA at random sites and inserting a short double-stranded oligonucleotide on both ends of the cleaved DNA. Transposons use a cut-and-paste mechanism to move from one genomic location to another, often altering the cell’s genetic identity and genome size. 

Additional resources

Subcloning of DNA fragments

ReadiUse™ 100 bp DNA Ladder