AAT Bioquest

What is the difference between endonuclease and exonuclease?

Posted July 22, 2020


Both endonuclease and exonuclease are nuclease enzymes which can hydrolyze polynucleotide chains such as DNA and RNA. The main difference between these enzymes is that endonucleases cleave the phosphodiester bond in the polynucleotide present internal in the polynucleotide chain, whereas exonucleases cleave the phosphodiester bond from the ends.

Accordingly, exonucleases require a free 3’ or 5’ end for their action, and release individual nucleotides after the hydrolytic reaction; while endonucleases do not require such a free end and release oligonucleotide chains after hydrolysis.

Besides, exonucleases are usually sequence non-specific, while endonucleases can be either sequence specific or non-specific. The non-specific endonucleases can cut the phosphodiester bonds between any nucleotides, while the sequence specific ones, known as restriction enzymes, cut at a specific sequence called the restriction site.

Additional resources

Helixyte™ Green *10,000X Aqueous PCR Solution*

6-ROX glycine *25 uM fluorescence reference solution for PCR reactions*

Perdew, G. H., Heuvel, J. P. V., & Peters, J. M. (2008). Regulation of gene expression. Springer Science & Business Media.

Lodish, H., Berk, A., Kaiser, C. A., Krieger, M., Scott, M. P., Bretscher, A., ... & Matsudaira, P. (2008). Molecular cell biology. Macmillan.