What is an Endonuclease?

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  • Written By: Mary McMahon
  • Edited By: O. Wallace
  • Last Modified Date: 11 October 2019
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An endonuclease is a specialized enzyme which is capable of breaking the bonds between nucleic acids in a polynucleotide chain, yielding two fragments. These enzymes can act in both DNA and RNA to cut from within a strand. Certain endonucleases, known as restriction endonucleases, attack specific sites within strands of RNA and DNA, recognizing particular sequences. These enzymes are very valuable in scientific research when people want the ability to edit genetic information, as in genetic engineering.

By contrast, an exonuclease can only cut away genetic material at the end of a strand of DNA or RNA. Endonucleases are used by bacteria and archaea as part of their defensive mechanisms. Some of the earliest observations of these enzymes in action come from research on bacteria, and bacteria are used to produce endonucleases on a large scale for research purposes.


Within a bacterium, an endonuclease is designed to repel viral attacks by chopping up foreign DNA so that it becomes nonfunctional. The organism protects its own DNA from the actions of the endonuclease through a process known as methylation. Methylation prevents the endonuclease from acting, ensuring that the DNA of the organism is left intact. Foreign DNA, however, is not so lucky, and the endonuclease will neatly snip the backbone of the DNA in two places, severing it to create separate strands. Depending on which endonuclease is involved, the events may be “blunt” or “sticky,” referring to where in the strand the DNA or RNA is severed.

Researchers can use known restriction endonucleases to snip DNA in desired target areas, creating a convenient insertion point. New genetic material can be inserted at this point, with the goal of coaxing the expression of an entirely new gene. This can be used to do things like introducing herbicide resistance to crops so that farmers can spray fields to keep down weeds.

Labs which manufacture endonucleases sell their products to researchers and other labs. The lab describes the ways in which a product can act, allowing researchers to determine which product would be most suitable for their desired uses. Working with endonucleases can be tricky, and it requires patience and skill. One could think of an enzyme like a restriction endonuclease as a very small and very finicky set of scissors which can be used to craft a project, but can also malfunction if not handled properly, cutting in the wrong spot or failing to cut at all.


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