Nuclease & Exonuclease Enzyme Function & Activity

Joanna Tatomir, Jeremy Battista
  • Author
    Joanna Tatomir

    Joanna holds a PhD in Biology from the University of Michigan and is currently working towards a degree in Veterinary Medicine at Michigan State University. She has taught a combination of ESL and STEM courses to secondary and university students.

  • Instructor
    Jeremy Battista

    Jeremy has a master of science degree in education.

Understand what nuclease is by learning the nuclease definition. Know the function of nuclease. Understand what is meant by an exonuclease and what does it do. Updated: 12/21/2021

Table of Contents



Genetic molecules such as DNA and RNA are essential for life on Earth. While transcription results in an RNA copy of DNA, translation creates proteins from the amino acid code contained in RNA. In order to copy DNA during transcription, a variety of enzymes are required to facilitate replication. Nucleases represent one essential enzyme involved in this process.

What is nuclease? The nuclease enzyme is responsible for a number of different functions within the human body. One of its primary roles is to break the bonds between nucleotides in nucleic acids. Nucleotides represent the building blocks for a nucleic acid. Nucleotides consist of a phosphate group, a nitrogenous base, and a sugar molecule. The four nitrogenous bases in DNA include adenine, cytosine, guanine and thymine. In RNA, thymine is replaced by uracil. For RNA, the sugar molecule is ribose, while in DNA, this sugar is known as deoxyribose.

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Nuclease Function

There are a variety of nuclease functions within the human body. Perhaps its most basic role is to break the phosphodiester bonds between the sugar and phosphate groups in DNA. This function is essential for DNA replication and repair. As with all enzymes, nucleases possess active sites responsible for binding to their intended targets and for facilitating the cleavage, or removal, of a sequence of nucleotides. Nucleases typically rely upon cofactors to stabilize the intermediate products of the reaction. Some of the cofactors found in association with nucleases include magnesium, calcium, manganese, and zinc.

In order to identify the portion of DNA to remove, nuclease scans the DNA or RNA for a specific sequence or for damage to the DNA or RNA. Once a target is located, the active site of the nuclease will attach to the DNA sequence and remove the section. Using this basic function, nucleases can carry out a number of different reactions involving DNA. For example, nucleases can be used to cut out the Okazaki fragments created when DNA is replicated discontinuously on the lagging strand in order to produce a complete daughter strand.

Nucleases can also facilitate DNA repair by removing damaged sections of DNA caused by UV radiation and chemicals. Some of the repair mechanisms dependent upon nuclease activity include base excision repair, nucleotide excision repair, and mismatch repair. Sometimes, nucleases can be used to insert a specific nucleotide sequence into preexisting strands of DNA or RNA. Nucleases can also turn off, or silence, normally active genes in an organism. In recent years, this process has been increasingly used in gene editing to produce modified agricultural products and to repair gene damage in living organisms.

Nucleases can be classified in a variety of ways. DNases, for example, refers to nucleases involved with the removal of nucleotide sequences in DNA. RNases, by contrast, are nucleases that function specifically with RNA. Another broad classification for nucleases involves the locations in which these enzymes are functional. These include exonucleases and endonucleases.


Exonucleases refer to nucleases that function at the ends of RNA and DNA. Exonuclease activity involves a hydrolytic reaction that breaks the phosphodiester bonds at either the 5; or 3' end of DNA and RNA. A hydrolytic reaction occurs when water is used to break the bonds within a molecule.

With exonucleases, this results in the removal of the last nucleotide in a sequence. When the last nucleotide is removed from 3' end, the enzyme is known as a 3' exonuclease, while removal from the 5' end is associated with a 5' exonuclease. Exonucleases function by removing only a single nucleotide at a time from either end.

An example of exonuclease activity.



Endonucleases are nucleases that remove nucleotides at any location other than the ends of the DNA or RNA strand. Endonuclease activity involves the removal of a sequence of nucleotides from the internal portion of the strand. Endonucleases can either cut a strand in half or remove a specific chunk of nucleotides from within the strand. Some endonucleases are also important for immune function and are able to destroy viruses.

An example of endonuclease activity.


One special type of endonuclease is referred to as a restriction nuclease. Restriction nucleases are capable of recognizing specific groups of bases and excising these sequences from DNA strands. Restriction nucleases have become especially important in the fields of genetic cloning and the production of GMOs.

Restriction endonuclease activity.


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Frequently Asked Questions

What is the function of nuclease?

Nucleases are enzymes responsible for breaking the phosphodiester bonds between nucleotides in DNA and RNA. Nucleases work via hydrolysis, in which water is used to break the chemical bonds in a molecule.

What are examples of nucleases?

Two types of nucleases are endonuclease and exonuclease. Endonucleases remove nucleotide sequences from the internal portion of a DNA or RNA strand, while exonucleases remove a single nucleotide from the ends of DNA or RNA.

What is exonuclease activity?

Exonucleases work by removing a single nucleotide from either the 3' or 5' end of a DNA or RNA strand. This contrasts with endonuclease activity, which removes groups of nucleotides in the interior of the DNA or RNA strand.

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