Difference Between Endonuclease and Exonuclease

Key Difference – Endonuclease vs Exonuclease
 

Before looking at the difference between endonuclease and exonuclease, it is important to know what exactly a nuclease is. A nuclease is an enzyme capable of cleaving phosphodiester bonds between nucleotides in nucleic acids. Endonuclease and exonuclease are two classifications of nucleases. The key difference between endonuclease and exonuclease is that endonucleases cleave the bonds between nucleotides within the nucleic acid molecule whereas exonucleases cleave the bond between nucleotides at the 3’ or 5’ ends of the nucleic acid molecule.

CONTENTS
1. Overview and Key Difference
2. What is a Nuclease
3. What is an Endonuclease
4. What is an Exonuclease
5. Side by Side Comparison – Endonuclease vs Exonuclease
6. Summary

What is a Nuclease?

A nuclease is an enzyme which has the ability to cleave phosphodiester bonds between nucleotides in nucleic acids. It belongs to the hydrolase enzyme group since it hydrolyzes the chemical bonds between nucleotides. This enzyme is essential for natural DNA repairing mechanisms occurring in the cells and in biotechnological processes such as gene cloning, recombinant DNA technology, RFLP, AFLP, gene sequencing, gene therapy, genome mapping etc.

There are two major types of nucleases: ribonuclease and deoxyribonuclease, which act and break the chemical bonds between monomers of RNA and DNA, respectively. According to the site of action of the nucleases, they are further categorized into two groups namely endonuclease and exonuclease. Endonucleases recognize specific sequence regions of the nucleic acids and cleave the phosphodiester bonds between nucleotides which are located in the middle of the nucleic acids. Exonucleases cleave phosphodiester bonds between nucleotides which are located at the ends of the nucleic acids.

What is an Endonuclease?

Endonuclease is a type of nucleases which cleaves nucleic acids from the middle. It recognizes specific nucleotide sequences of nucleic acid and breaks the chemical bonds between nucleotides. They are also known as restriction endonucleases since they search specific restriction sites and cleave the bond and produce restriction fragments. More than 100 restriction endonucleases are identified in bacteria and archaea and are obtained for commercial purposes.

Restriction endonucleases are extensively used in biotechnology. They play a vital role in molecular cloning. Most of them are dimeric enzymes composed of two protein subunits. Two protein subunits wrap the double-stranded DNA and separately cleave both strands from both sides. There are hundreds of types of restriction endonucleases with unique recognition sites in bacteria. Due to their high specificity in restriction, they cleave only at specific sequences. Hence, they are considered as highly useful molecular tools in recombinant DNA technology. Without restriction endonucleases, the production of recombinant DNA molecule is not possible. Creation of the recombinant DNA molecule is the basic step of most molecular biological technologies.

To understand the unique sequence recognition by restriction endonucleases, following example will help the readers.

Bam HI is a restriction endonuclease which searches the following restriction site in the DNA molecule (site is shown in red letters).

Once Bam HI cleaves the nucleic acid from the restriction site, it produces the following two fragments.

EcoRI is an another restriction endonuclease highly useful in recombinant DNA technology acts on its specific restriction recognition site and cleaves DNA as shown in figure 2.

What is an Exonuclease?

Exonuclease is a nuclease enzyme which cleaves chemical bonds between nucleotides at the 3’ or 5’ ends of the nucleic acid chains. It breaks single nucleotides at the end of the chain and produces nucleosides by transferring phosphate groups to water. Exonucleases are found in archaea, bacteria, and eukaryotes. In E coli, there are 17 different exonucleases present including DNA polymeras 1, 2 and 3. Several DNA polymerases exhibit 3’ to 5’ exonuclease proofreading activity.

Exonucleases are important in DNA repairing, genetic recombination, prevention of the occurrence of mutations, genome stabilization etc.

What is the difference between Endonuclease and Exonuclease?

Endonuclease vs Exonuclease
Endonuclease is a type of nuclease enzymes which cleaves the bonds between nucleotides within the nucleic acid molecule.	Exonuclease is a type of nuclease enzymes which cleaves the bond between nucleotides at the 3’ or 5’ ends of the nucleic acid molecule.
End-Products
Endonucleases produce oligonucleotide restriction fragments	Exonucleotides produce nucleosides
Function
They break phosphodiester bonds and produce restriction fragments. But they dot remove nucleotides one by one.	They remove nucleotides one by one from the ends of the nucleic acids.
Examples
Examples include Bam HI, EcoRI, Hind III, Hpa I, Sma I,	Examples include Exonuclease I, Exonuclease III, RecBCD (Exonuclease V), RecJ exonuclease, Exonuclease VIII/RecE, Exonuclease IX, Exonuclease T, Exonuclease X etc.

Summary – Endonuclease vs Exonuclease

Nucleases are responsible for breaking phosphodiester chemical bonds between nucleotides of the nucleic acids. Nucleases can act on within or at the ends of the nucleic acid chain. According to the site of action, two main types of nucleases are found in organisms. They are endonuclease and exonuclease. Endonucleases cleave nucleotides from the middle of the chain while exonucleases cleave nucleotides from the ends of the nucleic acid chain. Endonucleases are highly important in recombinant DNA technology since they recognize specific base sequences within the nucleic acid chain and breaks bonds between nucleotides.

Reference:
1.”Restriction enzyme.” Restriction enzyme | Open Access articles | Open Access journals | Conference Proceedings | Editors | Authors | Reviewers | scientific events. N.p., n.d. Web. 11 Mar. 2017
2.Pingoud, Alfred, and Albert Jeltsch. “Structure and function of type II restriction endonucleases.” Nucleic Acids Research. Oxford University Press, 15 Sept. 2001. Web. 11 Mar. 2017
3.Lovett, Susan T. “The DNA exonucleases of Escherichia coli.” EcoSal Plus. U.S. National Library of Medicine, Dec. 2011. Web. 11 Mar. 2017

Image Courtesy:
1.”Restriction enzyme Eco RI” By Tinastella – Own work (Public Domain) via Commons Wikimedia
2.”HR RecBCD RecA”By Emw2012 – Own work (CC BY-SA 3.0) via Commons Wikimedia