What is Difference Between Restriction Endonuclease and Exonuclease

The key difference between restriction endonuclease and exonuclease is that restriction endonuclease is a nuclease enzyme that recognizes a specific DNA sequence and cleaves the DNA within or adjacent to that sequence, while exonuclease is a nuclease enzyme that cleaves the nucleotides in a polynucleotide from either 5’ end or 3’ end one at a time.

Nucleases are the enzymes that cleave phosphodiester bonds between nucleotides of nucleic acids. In living organisms, they are essential tools for many aspects of DNA repair in the cell. Defects of these enzymes can cause genetic instability and immunodeficiency. The restriction nucleases are specific nucleases whose functioning is dependent on a specific nucleotide sequence. An example is restriction endonuclease. There is a basic classification for nucleases based on the locus of activity, such as endonuclease and exonuclease. Endonuclease digests regions in the middle of the target DNA molecule. Exonuclease digests nucleic acids from the ends. Hence, restriction endonuclease and exonuclease are two types of nuclease enzymes.

CONTENTS

1. Overview and Key Difference
2. What is Restriction Endonuclease 
3. What is Exonuclease
4. Similarities – Restriction Endonuclease and Exonuclease
5. Restriction Endonuclease vs Exonuclease in Tabular Form
6. Summary – Restriction Endonuclease vs  Exonuclease

What is Restriction Endonuclease?

Restriction endonuclease is a nuclease enzyme that recognizes a specific DNA sequence and cleaves the DNA within or adjacent to that sequence. The specific DNA sequence is known as the restriction site. It is also called a restriction enzyme or restrictase. The restriction endonuclease is a very specific enzyme. It is one class of the broader endonuclease group of enzymes. Restriction endonucleases are commonly classified into five types, which differ in their structure and ability to cut the DNA substrate at the recognition site. The five types are type I, type II, type III, type IV and type V.

Restriction endonucleases are usually found in bacteria and archaea. They provide a defence mechanism for bacteria against viruses. There are more than 3600 known restriction endonucleases. They represent over 250 different specificities. Over 3000 of these have been studied in detail. Furthermore, more than 800 of these are available commercially.

What is Exonuclease?

Exonuclease is a nuclease enzyme that cleaves the nucleotides in a polynucleotide from either 5’ end or 3’ end one at a time. This occurs through a hydrolysing reaction that breaks phosphodiester bonds between the nucleotides at the end. Eukaryotes and prokaryotes have three types of exonucleases. These exonucleases are involved in the normal turnover of mRNA. They are 5’ to 3’ exonuclease (Xrn1), 3’ to 5’ exonuclease, and poly-A specific 3’ to 5’ exonuclease. 5’ to 3’ exonuclease is a dependent decapping protein. 3’ to 5’ exonuclease is an independent protein. Poly A specific 3’ to 5’ exonuclease is also known as poly-A specific ribonuclease involved in exonucleolytic degradation of poly-A tail.

In both archaea and eukaryotes, RNA degradation is performed by the multi-protein exosome complex that consists of 3’ to 5’ exoribonucleases.

What are the Similarities Between Restriction Endonuclease and Exonuclease?

• Restriction endonuclease and exonuclease are two types of nuclease enzymes.
• Both enzymes cut DNA molecules.
• These enzymes are found in prokaryotes.
• They are proteins.

What is the Difference Between Restriction Endonuclease and Exonuclease?

Restriction endonuclease is a nuclease enzyme that recognizes a specific DNA sequence and cleaves the DNA within or adjacent to that sequence, while exonuclease is a nuclease enzyme that cleaves the nucleotides in a polynucleotide from either 5’ end or 3’ end one at a time. So, this is the key difference between restriction endonuclease and exonuclease. Moreover, restriction endonuclease is only found in prokaryotes, while exonuclease is found in both prokaryotes and eukaryotes.

The following infographic lists the differences between restriction endonuclease and exonuclease in tabular form for side by side comparison.

Summary – Restriction Endonuclease vs Exonuclease

Nucleases are the enzymes that break phosphodiester bonds between nucleotides of nucleic acids. Restriction endonuclease and exonuclease are two types of nuclease enzymes. Restriction endonuclease is a nuclease enzyme that recognizes a specific DNA sequence and cleaves the DNA within or adjacent to that sequence. Exonuclease is a nuclease enzyme that cleaves the nucleotides in a polynucleotide from either their 5’ end or 3’ end one at a time. Thus, this summarizes the difference between restriction endonuclease and exonuclease.

Reference:

1. “Restriction Endonucleases.” An Overview | ScienceDirect Topics.
2. Mason, Penelope A, and Lynne S Cox. “The Role of Dna Exonucleases in Protecting Genome Stability and Their Impact on Ageing.” Age (Dordrecht, Netherlands), Springer Netherlands, Dec. 2012.

Image Courtesy:

1. “HindIII Restriction site and sticky ends vector” By Helixitta – Own work (CC BY-SA 4.0) via Commons Wikimedia
2. “Nick translation 3 — Exonuclease” By Allen Gathman (CC BY-NC-SA 2.0) via Flickr