What is the Difference Between Restriction Enzyme and Restriction Endonuclease

The main difference between the restriction enzyme and restriction endonuclease is that the restriction enzyme is a “molecular scissor” that cleaves DNA at or near specific recognition sequences known as restriction sites, whereas restriction endonuclease is one class of the endonuclease group of enzymes.

Restriction enzyme and restriction endonuclease are two names for the enzymes responsible for cleaving DNA at specific sites called restriction recognition sites.

Key Areas Covered

  1. What is Restriction Enzyme
    • Definition, Structure, Function
  2. What is Restriction Endonuclease
    • Definition, Structure, Function
  3. Similarities Between Restriction Enzyme and Restriction Endonuclease
    • Outline of Common Features
  4. Difference Between Restriction Enzyme and Restriction Endonuclease
    • Comparison with Key Differences

Key Terms

Restriction Endonuclease, Restriction Enzyme, Double-Stranded DNARestriction Enzyme vs Restriction Endonuclease

What is Restriction Enzyme

Restriction enzymes or restriction endonucleases are a broad group of endonuclease enzymes that cleave DNA in specific sites. The recognition site for cleaving in DNA is the restriction site. Moreover, there are five types of restriction enzymes: types 1, 2, 3, 4, and 5. Here, the classification is by the method of cleaving DNA substrate at their recognition site.

Restriction Enzyme Type 1

Restriction enzyme type 1 is a complex, multi-subunit enzyme with both restriction and methylase activities in combination. Furthermore, it was first identified in E. coli strains. It contains three different subunits: HsdR, HsdM, and HsdS. HsdR undergoes restriction digestion, while HsdM undergoes methylation, and HsdS is important for the recognition of both the recognition site and methylation sites. In addition, restriction enzyme 1 cleaves DNA at a site that is at a random distance of more than 1000 bp away from the restriction recognition site. This random cleavage is also followed by DNA translocation as this enzyme serves as a molecular motor. Restriction enzyme 1 genes are more common in the prokaryotic genome. Although restriction enzyme type 1 has biochemical importance, it has little practical value due to the production of discrete restriction fragments.

Compare Restriction Enzyme and Restriction Endonuclease - What's the difference?

Figure 1: Restriction Enzyme Action

Restriction Enzyme Type 2

Restriction enzyme type 2 cleaves DNA at defined positions that are either within or close to the restriction recognition site. Moreover, its recognition site is palindromic and 4-8 nucleotides in length. Generally, it is a homodimer with independent restriction and methylase activities. At the same time, it only requires magnesium as a cofactor without using ATP. Due to the production of discrete fragments by restriction digestion by cutting specifically at or close to the recognition site, restriction enzyme type 2 is more often used in laboratories for DNA analysis and cloning.

Restriction Enzyme Type 3

Restriction enzyme type 3 is the third type of restriction enzyme, recognizing two separate non-palindromic sequences, which are inversely oriented. It also cleaves DNA about 20-30 bp downstream to the recognition site. In general, restriction enzyme type 3 is a heterodimer with two different subunits. Moreover, the restriction and methylation activities occur in the same subunit of the restriction enzyme type 3. However, it rarely gives complete digestion.

Restriction Enzyme Type 4 and 5

Restriction enzyme type 4, on the other hand, targets modified DNA including methylated, hydroxymethylated, and glucosyl-hydroxymethylated DNA. Meanwhile, the restriction enzyme type 5 uses guide RNA (gRNA) as the substrate.

What is Restriction Endonuclease

Restriction endonuclease is a broad class of endonucleases. Generally, endonucleases are the enzyme that cleaves the phosphodiester bond in the polynucleotide chain. Restriction endonucleases occur in bacteria and archaea. Moreover, they protect these organisms from invading viruses. Normally, restriction endonucleases cut foreign DNA inside the prokaryote. This process is called restriction digestion. However, the modified enzymes called methyltransferase modifies host DNA by methylating DNA, blocking the cleavage of host DNA. The two processes of restriction digestion and blockage of cleaving the host DNA, are known as the restriction-modification system.

Restriction Enzyme vs Restriction Endonuclease

Figure 2: Restriction Enzyme Function

Moreover, 3 600 restriction endonucleases are there in 250 specificities. Among them, more than 800 are commercialized.

Similarities Between Restriction Enzyme and Restriction Endonuclease

  • Restriction enzyme and restriction endonuclease are two groups of enzymes that cleave DNA into pieces at or near the recognition sites.
  • They also have a role in protecting prokaryotes from invading viruses by cutting foreign DNA into pieces.
  • In addition, they play a major role in molecular biology to cut DNA for the recombination of DNA fragments.

Difference Between Restriction Enzyme and Restriction Endonuclease


Restriction enzyme refers to an enzyme produced chiefly by certain bacteria, which has the property of cleaving DNA molecules at or near a specific sequence of bases, while restriction endonuclease refers to an enzyme that cleaves DNA into fragments at or near specific recognition sites within molecules known as restriction sites.


Restriction enzymes cleave DNA at specific nucleotide sequences while restriction endonucleases cleave double-stranded DNA.


Moreover, restriction enzymes are important in biotechnology in cloning while restriction endonucleases protect the prokaryotic cell from invading pathogens.


In brief, restriction enzyme and restriction endonuclease are two types of endonucleases that cleave DNA at or near specific sequences: restriction sites. However, restriction enzymes are a group of endonucleases important in biotechnology to cleave DNA for cloning. On the other hand, restriction endonucleases are important in prokaryotes to cleave foreign DNA to protect from invading viruses. Therefore, the main difference between restriction enzyme and restriction endonuclease is their importance.

  1. Wikimedia Foundation. (2022, June 15). Restriction enzyme. Wikipedia. Retrieved August 7, 2022. 
  2. Wikimedia Foundation. (2022, April 29). Endonuclease. Wikipedia. Retrieved August 7, 2022.
Image Courtesy:
  1. HindIII Restriction site and sticky ends vector” By Helixitta – Own Work (CC BY-SA 4.0) via Commons Wikimedia
  2. Recombinant formation of plasmids” By Minestrone Soup – Own Work (CC BY-SA 3.0) via Commons Wikimedia

About the Author: Lakna

Lakna, a graduate in Molecular Biology & Biochemistry, is a Molecular Biologist and has a broad and keen interest in the discovery of nature related things

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