Difference Between Endonuclease and Exonuclease (With Table)

Nucleases play an indispensable role in recombinant DNA technology, genetics, and genetic engineering. Because of their ability to cut DNA segments, nucleases have various practical applications. Endonuclease and exonuclease are two such types of nucleases. Although confused as meaning the same, endonuclease and exonuclease have varying characteristics to prove that they are different.

Endonuclease vs Exonuclease

The difference between endonuclease and exonuclease is that an endonuclease is a group of enzymes that cuts DNA segments from the inner side. On the other hand, exonuclease enzymes cut DNA segments from the ends. Additionally, endonuclease enzymes have either sticky or blunt ends. In contrast, exonuclease enzymes have sticky ends. 

Endonuclease refers to the group of enzymes found within the polynucleotide chain which cleave the phosphodiester bond.  Restriction endonuclease is one of the most common types of the endonuclease. Its function is to cut the DNA segment at its recognition site. More importantly, endonuclease enzymes cut the DNA segment from the inner side. 

Exonucleases refer to the group of enzymes that function by cutting nucleotides one at a time from the Exo (end) of a polynucleotide chain. It has the potential to cut both DNA and RNA. The most vital application of exonuclease is to assist in DNA repair. More importantly, exonuclease enzymes cut DNA segments from the ends. 

Comparison Table Between Endonuclease and Exonuclease

Parameters of ComparisonEndonuclease Exonuclease 
DefinitionEndonuclease refers to the group of enzymes that cut the DNA segments from the inner side. Exonuclease refers to the group of enzymes that cut the DNA segment from the ends. 
Lag PeriodEndonucleases, like the restriction endonuclease, experience a lag period before carrying out their specific task. In exonucleases, there is an absence of lag period before the commencement of their specific task. 
Results InThe cleaving of DNA segments results in oligonucleotides. The cleaving of DNA segments results in nucleosides.  
FunctionEndonuclease enzymes play a role in defense as they prevent the entry of pathogens.Exonucleases lack any defensive functions. 
Free EndsEndonuclease enzymes don’t require free 3’ and 5’ ends to perform their functions. Exonucleases require free ends for the commencement of their specific tasks. 

What is Endonuclease?

Endonuclease refers to the group of enzymes found within the polynucleotide chain which cleave the phosphodiester bond.  Some endonuclease enzymes, for instance, deoxyribonuclease I, cut the Deoxyribonucleic acid without any regard to sequence. On the other hand, most endonuclease enzymes cleave at very specific nucleotide sequences. Additionally, they are also called restriction enzymes. 

One of the most vital groups of endonucleases is the restriction enzymes. The restriction enzymes have three categories based on their action mechanism: Type I, Type II, and Type III. One practical application of these enzymes is in genetic engineering. Moreover, restriction endonucleases are in hundreds and each one of them takes charge of attacking a specific site. 

Bacterial cells are the natural source of restriction endonuclease. Moreover, the ends of endonucleases are either blunt or sticky. An example of a famous endonuclease is Cas9. Other examples of endonucleases are BamHI, Deoxyribonuclease I, and EcoRI.

Endonucleases are vital for several reasons. However, one of the more prominent reasons is their ability to repair damaged DNA cells precisely. This, in turn, helps to avoid any further damage to the other enzymes. Apart from this, some endonuclease enzymes are defensive in function. Thus, they prevent the entry of some pathogens.

What is Exonuclease?

Exonucleases refer to the group of enzymes that function by cutting nucleotides one at a time from the Exo (end) of a polynucleotide chain. These enzymes cut the nucleotide from either the 3’ or the 5’ at one specific time. Additionally, exonuclease serves as a hydrolyzing enzyme. They consist of a large set of biochemically and structurally characterized enzymes that possess varied characteristics. 

The extensive knowledge of endonuclease enzymes is a result of a structured characterization from the bacterium E. coli. In a single E. coli cell, there are more than 20 varying activities of the exonuclease. Exonuclease is found in humans, bacteria, animals, and insects. Interestingly, the venom of lizards and snakes consists of exonuclease enzymes. 

Exonuclease enzymes play a vital role in cellular metabolism and maintenance. Moreover, they are crucial aspects of genome stability as they cut the DNA from free ends. Exonucleases may also have a part in repairing damaged DNA cells. However, they don’t have a defensive function. As a result, exonucleases may be inefficient for protection against pathogens. 

Exonucleases usually lack specific regard to sequence. Thus, they are non-specific enzymes. Some examples of exonuclease enzymes are lizard venom and Exonuclease I. In the case of exonuclease enzymes, the lag period is absent before activity. Conclusively, exonucleases are a group of enzymes serving multi-facet functions. 

Main Differences Between Endonuclease and Exonuclease

  1. Endonuclease refers to the group of enzymes that cut the DNA segments from the inner side. In contrast, exonuclease refers to the group of enzymes that cut the DNA segment from the ends.
  2. The cleaving of DNA segments by endonuclease enzymes results in oligonucleotides. On the other hand, the cleaving of DNA segments by exonucleases results in nucleosides.  
  3. While endonucleases are target-specific, exonucleases work randomly. 
  4. Endonucleases, like the restriction endonuclease, experience a lag period before carrying out their specific task. On the other hand, in exonucleases, the lag period is absent before the commencement of their specific task. 
  5. Endonuclease enzymes don’t require free 3’ and 5’ ends to perform their functions. In contrast, exonucleases require free ends for the commencement of their specific tasks. 

Conclusion

Thus, the definition, lag period, cleavage, ends, and specificity of endonuclease and exonuclease prove that they are different. Endonuclease enzymes are sequence-specific. As a result, they start their work only when they find their exact recognition site. Exonucleases, on the other hand, work randomly. Thus, they have no specific regard for sequence. 

The main function of endonuclease is to prohibit the entry of some pathogens. However, exonuclease enzymes don’t play a role in defence. Nonetheless, they play a vital role in cellular metabolism and maintenance. In conclusion, both endonuclease and exonuclease are specific in their functions, characteristics, and properties. 

References

  1. https://www.tandfonline.com/doi/abs/10.3109/10409237609105456 
  2. https://www.pnas.org/content/68/4/824.short 
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