Difference Between Endonuclease and Exonuclease

Table of Contents

Main Difference

The main difference between endonuclease and exonuclease is that endonuclease cuts nucleic acid strand at the middle, whereas exonuclease cuts nucleic acid strands from the ends.

Endonuclease vs. Exonuclease

The mechanism of endonuclease is that it cuts nucleic acids at the middle, while the exonuclease mechanism is that it cut nucleic acid at the ends. Before the activity of endonuclease, the restricted endonuclease undergoes a lag period, whereas before the activity of exonuclease it does not have a lag period. Endonuclease usually results in oligonucleotide chains after its hydrolytic activity; on the other hand, exonuclease results in single nucleosides or nucleotides after its hydrolytic reactions. Endonuclease may form either sticky ends or blunt ends, but exonuclease always forms the sticky ends. Endonuclease plays an important role in blocking the entry of pathogens; on the other hand, exonuclease does not play any significant role in blocking the entry of pathogens. Endonuclease does not require a free 3’ to 5’ end for their action; conversely, exonuclease requires a free 3’ to 5’ end for their action. The endonuclease is normally sequenced specifically; on the flip side, exonuclease is generally not- sequence-specific. Endonuclease breaks phosphodiester bonds and forms restriction fragments, but they do not eliminate nucleotides one by one, whereas exonuclease removes nucleotides one by one from the various ends of nucleic acids. Various examples of endonuclease are S1 nuclease, DNases, and restriction enzymes such as Hind ׀׀׀, Bam H1, and Eco RI; on the contrary, some examples of exonuclease are spleen Phosphodiesterase, 3’ to 5’ exonuclease domain of the DNA polymerase ׀׀׀, snake venom, 5’ to 3’ exonuclease activity, and 3’ to 5’ exonuclease domain of DNA polymerase ׀.

Comparison Chart

Endonuclease	Exonuclease
The endonuclease is a type of nucleases that nicks nucleic acids at the middle.	Exonuclease is the type of nuclease enzyme that nicks bonds or nucleic acids strands at the end.
Mechanism of Action
Cuts nucleic acids at the middle	Cuts nucleic acid at the ends
Lag Phase
Undergoes a lag period	Does not have a lag period
Results
Results in oligonucleotide chains	Results in single nucleosides or nucleotides
Blunt/Sticky Ends
May form either sticky ends or blunt ends	Always form the sticky ends
Role
Plays an important role in blocking the entry of pathogens	Does not play any significant role in blocking the entry of pathogens
Require Primers
Does not require a free 3’ to 5’ end for their action	Requires a free 3’ to 5’ end for their action
Sequence/Non-Sequence Specific
Sequence specific	Non-Sequence Specific
Examples
S1 nuclease, DNases, and restriction enzymes such as Hind ׀׀׀, Bam H1, and Eco RI	spleen Phosphodiesterase, snake venom 3’ to 5’ exonuclease domain of the DNA polymerase ׀׀׀, 5’ to 3’ exonuclease activity, and 3’ to 5’ exonuclease domain of DNA polymerase ׀

What is Endonuclease?

The endonuclease is a class of hydrolase and generally refers to an enzyme that cuts the polynucleotide chain at the middle by separating nucleotides other than two end ones. This result of endonuclease may result in two or more fragments of nucleic acids one at a time. The endonuclease is capable of acting on both RNA and DNA. Some endonucleases such as deoxyribonucleases (DNases) has non-specific cleavage. Though, many endonuclease target nucleotide sequences in a very specific manner and this is called restriction endonucleases because they are capable of recognizing the specific sequence of strands of nucleic acids. Therefore, these restricted endonucleases undergo lag periods before their action. The specific nucleotide sequence is called the restriction site.

Examples

Some examples of endonuclease are S1 nuclease, DNases, and restriction enzymes such as Hind ׀׀׀, Bam H1, and Eco RI.

What is Exonuclease?

Exonuclease is a type of hydrolases and usually refers to an enzyme that cuts the polynucleotide chain at the end of the chain by eliminating the nucleotides one at a time. Three types of exonuclease can be found in both eukaryotes and prokaryotes which are 3’ to 5’ exonuclease, 5’ to 3’ exonuclease, and poly (A)-specific 3’ to 5’ exonucleases. These all three types play a role in mRNA turnover. In E. coli, there are present 17 different types of exonucleases including DNA polymerase 1, 2, and 3. Exonuclease is very important in genetic recombination, genome stabilization, DNA repairing, prevention of the occurrence of mutations, etc.

Examples

Various examples of exonuclease are spleen Phosphodiesterase, snake venom, 3’ to 5’ exonuclease area of the DNA polymerase ׀׀׀, 5’ to 3’ exonuclease activity, and 3’ to 5’ exonuclease domain of DNA polymerase ׀.

Key Differences

The endonuclease creates a nick in between the nucleic acids, while exonuclease creates a nick at the end of the nucleic acid.

Before the action of endonuclease, the restricted endonuclease undergoes a lag period, whereas before the motion of exonuclease it does not have a lag period.

Endonuclease usually results in oligonucleotide chains after its hydrolytic activity; on the other hand, exonuclease results in single nucleosides or nucleotides after its hydrolytic reactions.

Endonuclease may form either sticky ends or blunt ends at the chains, but exonuclease always forms the sticky ends.

Endonuclease plays an important role in blocking the entry of pathogens and other chemicals; on the other hand, exonuclease does not block the entry of pathogens.

Endonuclease does not require a free 3’ to 5’ end for their act; conversely, exonuclease requires a free 3’ to 5’ end for their action.

The endonuclease is normally sequenced specifically; on the flip side, exonuclease is generally not- sequence-specific.

Endonuclease breaks phosphodiester bonds and forms restriction fragments, but they do not eliminate nucleotides one at a time, whereas exonuclease removes nucleotides one by one from the various ends of nucleic acids.

Various examples of endonuclease are S1 nuclease, DNases, and restriction enzymes such as Hind ׀׀׀, Bam H1, and Eco RI; on the contrary, some examples of exonuclease are spleen Phosphodiesterase, 3’ to 5’ exonuclease domain of the DNA polymerase ׀׀׀, snake venom, 5’ to 3’ exonuclease activity, and 3’ to 5’ exonuclease domain of DNA polymerase ׀.

Conclusion

Above discussion concludes that endonuclease cuts nucleic acid strand at the middle and it undergoes a lag period before its action, whereas exonuclease cuts nucleic acid strands from the ends and it does not undergo lag period.

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