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Restriction Enzymes: Nature's Scissors

Restriction endonucleases – or restriction enzymes – recognize specific DNA sequences and cut them in a predictable manner. They are naturally produced by bacteria as a defense mechanism against foreign DNA. For use in botechnology, restriction enzymes are isolated from bacteria to be used a genetic tool in biotechnology.



  • Restriction enzymes are naturally produced in bacteria as a defense mechanism againt foreign DNA. 
  • Often called ‘molecular scissors’ since they can ‘cut’ DNA.
  • Each restriction enzyme cuts a specific nucleotide sequence of DNA.
  • These enzymes are now used a genetic tool for manipulating DNA and they have implications many areas of biotechnology.

Where Do Restriction Enzymes Come From?

Bacteria naturally produce restriction enzymes (also called restriction endonucleases) as a defense mechanism against foreign DNA. Just like other organisms, bacteria can be infected by viruses. However, these viruses are specific to bacteria and are called bacteriopahges. When a bacteriophage infects a bacterium, the bacteriophage injects its genetic material into the bacterium. In an attempt to defend itself, the restriction enzymes within the bacterium recognize specific DNA sequences that are unique to the viral DNA. Once the enzyme recognizes the viral DNA, it cuts them into pieces rendering harmless the bacterium.  

Bacteriophage injecting DNA into bacterium with restriction enzymes cutting viral DNA.
Title: Restriction Enzymes | Author: BiomedGuide | License: CC BY-SA 4.0 

How Do Restriction Enzymes Work?

All restriction enzymes recognize a sequence of four- to eight-nucleotides called the recognition site. The nucleotide sequence is palindromic, meaning the sequence of ATCG’s read the same forwards on one strand and ‘backwards’ on the complementary strand. Look at the image to the right, do you recognize the palindrome? You’ll notice they read the same in the 5′ to 3′ direction on one strand as they do in the 5′ to 3′ direction on the complementary strand (a).

Restriction enzyme BamHI recognition sequence and sticky ends.

On the image, you’ll notice the six-nucleotide recognition sequence (GGATCC) for the restriction enzyme BamHI. In the case of BamHI, the cut is made between the two guanines like this: G | GATCC. It is important to note that the cut is made between the two guanines for both DNA strands. This might be a little confusing since the strands go in opposite directions, but if the enzyme cuts G | GATCC on one strand, it also cuts G | GATCC on the second strand, however on the second strand we are reading the sequence backwards.

Many restriction enzymes make the staggered cuts like the one you can see in image c; where each strand of DNA is left with a short nucleotide single-stranded overhang called a “sticky end”. We call these overhangs “sticky ends” because it’s possible these overhangs can ‘stick’ back together after the’ve been cut.

Link to Learning

Restriction enzymes are named by the bacteria from which they come. For example, BamH1 is produced by the bacteria Bacillus amyloliquefaciens.

The attractive force that facilitates interactions between nucelotides is hydrogen bonding.

What Role Do Restriction Enzymes Have in Biotechnology?

These enzymes have a critical role in many important technologies in biology. In fact, many procedures that exist today would not be possible without restriction enzymes. This is because the ability of restriction enzymes to recognize and cut at specific nucleotide sequences gives us control over manipulating DNA.

DNA Fingerprinting

DNA fingerprinting is a technique used to identify unqiue patterns of DNA using a combination of polymerase chain reaction, gel electrophoresis and restriction enzymes. DNA fingerprinting has applications including identifying genetic material from crime scenes or familial relatives. Take a look at ‘Agrose Gel Electrophoresis for Dna Analysis’ for more information about DNA fringerprinting. 

Restriction Enzyme Review Questions

Conclusion Questions

    1. Where are restriction enzymes found in nature?
    2. How do restriction enzymes protect bacteria from being harmed?
    3. Can restriction enzymes be purified and used in other applications?
    4. How do restriction enzymes know where to cut DNA?
    5. What is the name for the ‘flaps’ of DNA that are left after a restriction enzyme has cut it?
    6. How are DNA fragments processed and analyzed in a gel electrophoresis experiment?

Key Words

    • Bacteriophage
    • Restriction Endonuclease
    • Sticky-ends
    • Recognition Site
  1. Clark MA, Douglas M, Choi J. “17.1 Biotechnology.” Biology 2e. OpenStax, 2018. Houston, TX. BY 4.0 | License Terms: Edited & Adapted | Access for free
  2. Fowler, Samantha, Rebecca Roush, and James Wise. “Molecular Biology.” Concepts of Biology. Houston, TX: OpenStax, 0. CC BY 4.0 License Terms: Edited & Adapted | Access for free at
  3. Helixitta. “File:HindIII Restriction site and sticky ends vector.svg.” Wikimedia Commons. 29 July 2015. CC BY 4.0