by Microbiologist Doctor-Dr

Endonuclease Vs Exonuclease - Definition, 11 Differences and Examples

Table of Contents

1. Endonuclease Definition

2. Exonuclease Definition

3. Key Differences (Endonuclease vs Exonuclease)

·      - Basis for Comparison

·      - Endonuclease

·      - Exonuclease

4. Examples of endonucleases

·      - EcoRI

5. Examples of exonucleases

·      -  Xrn1

Endonuclease Definition

A class of enzymes known as endonucleases cleaves the phosphodiester bond found within a polynucleotide chain.

• Endonucleases have the ability to sever a chain's middle link.
• These enzymes either cleave sequences in a non-specific or specific manner. Restrictions endonucleases are endonucleases that are unique to a given sequence.
• Different bacteria and archaea produce restriction endonucleases, each of which is unique to a certain location in the polynucleotide chain.
• The DNA ligase then combines the single-stranded ends, also known as sticky ends, that were created by the cleaved sequences. Recombination is the process through which DNA is created, producing what is known as recombinant DNA.
• According to their mode of action, the restriction endonucleases, one of the most significant classes of endonucleases, can be split into three categories.
• Large multi-subunit complexes known as type I endonucleases cleave at random locations of roughly 1000 base pairs. Smaller subunits called type II endonucleases cleave the sequences when ATP is not present. Complex type III endonucleases that cleave 25 base pair sequences are also available.
• The endonuclease may cleave RNAs, single-stranded DNA, and even double-stranded DNA.
• These enzymes are essential for DNA repair because they enable accurate identification and cleavage of damaged DNA.
• This avoids pointless cleavage and further harm that could happen with other enzymes.
• It's possible for restriction endonucleases to take some time to take effect. The time needed for the individual sites to be recognised may be the cause of this delay.
• Endonuclease creates oligonucleotides by cleaving a DNA segment in the centre.
• Some endonucleases have a defence role where they can stop some viruses from entering.

Exonuclease Definition

Exonucleases are enzymes that sequentially break polynucleotide chains of DNA from either the 5' or 3' end.

• Exonuclease is a hydrolyzing enzyme that breaks the phosphodiester connection between the nucleotides, just like endonuclease does.
• The multi-protein exosome, which is made up of numerous exoribonucleases, is one of the most significant pathways for RNA breakdown in both archaea and eukaryotes.
• Exonucleases can also be discovered in the venom of lizards and snakes. These toxins function by cleaving the DNA that codes for vital proteins in the body.
• Exonulceases play a crucial role in replication because one of these enzymes works with RNA polymerase II to break down the freshly generated RNA primer on the new transcript, which is subsequently replaced by DNA nucleotides.
• Exonuclease activity is also used to modify and check DNA for mistakes.
• A decapping 5' to 3' exonuclease (Xrn1), an independent 5' to 3' exonuclease, and a polyA-specific 3' to 5' exonuclease are the three types of exonucleases found in prokaryotes and eukaryotes.
• These exonucleases are all necessary for RNA synthesis, replication, and transcription.
• Exonucleases cleave the sequences from the ends, resulting in sticky ends, unlike endonucleases which have a lag time.
• Exonucleases similarly cleave individual nucleosides from either end rather than producing oligonucleotides.
• Exonuclease lacks any protective features that would prevent the introduction of harmful bacteria.

Key Differences (Endonuclease vs Exonuclease)

Basis for Comparison	Endonuclease	Exonuclease
Definition	A class of enzymes known as endonucleases cleaves the phosphodiester bond found within a polynucleotide chain.	Exonucleases are enzymes that sequentially break polynucleotide chains of DNA from either the 5' or 3' end.
Cleavage	The centre of the nucleotide sequence is where endonucleases cleave it.	A nucleotide sequence is cut by exonulceases starting at the ends.
Lag period	There is a lag time preceding the activation of some endonucleases, such as restriction endonucleases.	Exonucleases don't have a lag time before they start working.
Results in	Oligonucleotides are produced when endonucleases cut DNA sequences.	DNA sequences are broken apart into individual nucleotides or nucleosides by exonulceases.
Ends	Endonucleases can produce either blunt or sticky ends.	The ends of exonulceases are sticky.
Specificity	There are certain endonucleases, also known as restriction endonucleases, that cleave particular places within a DNA sequence.	Exonuclease is usually non-specific.
Defensive properties	Endonucleases are able to prevent harmful bacteria from entering the system.	Exonulceases don't have any defence mechanisms.
Effect on circular DNA	A circular DNA can have particular locations cleaved by a restriction endonuclease.	Compared to linear DNA, exonulceases are less active toward circular DNA.
Inhibition	Phosphorothioate bonds must be present throughout the whole sequence in order to block endonucleases.	Five consecutive phosphorothioate links can be added to a sequence to block exonuclease.
Free ends	Endonucleases do not require free 3' or 5' ends to function.	Exonucleases should have unrestricted access to the ends.
Examples	EcoRI, BamHI, Deoxyribonulcease I are some examples of endonucleases.	Snake venom, Exonuclease I, Xrn1 are some examples of exonucleases.

Examples of endonucleases

EcoRI

• A restriction endonuclease called EcoRI breaks DNA helices at particular locations to produce pieces.
• This enzyme, which is a component of the restriction-modification system, was isolated from the E. coli species.
• The G/AATTC is broken down by EcoRI, where the "/" denotes the phosphodiester bond that the restriction enzyme is specifically designed to break down.
• It produces a sticky end with four nucleotides and a 5' overhang of AATT.
• EcoRI is a homodimer with a 31 kilodalton subunit of a globular domain with α/β architecture.
• EcoRI has been widely used for various molecular biology techniques including cloning, DNA screening, and error removal.
• DNA cleavage produces sticky ends, which boost the ligase enzyme's activity and improve the efficiency of the ligation procedure.
• EcoRI can perform non-specific cleavage when the medium's salt and enzyme concentrations are low.

Examples of exonucleases

Xrn1

• Humans have an exoribonuclease called Xrn1 that is a 5' to 3' exonuclease.
• It hydrolyzes RNAs from 5' to 3' and is encoded by the Xrn1 gene.
• Through direct interactions with the mRNA decapping protein, it contributes to the replication-dependent degradation of histone mRNA.
• In both human and yeast cells, Xrn1 is also engaged in a wide range of nuclear and cytoplasmic processes, including transcription, translation, recombination, and meiosis.
• Additionally, it starts the termination of DNA and RNA transcription to stop the overgrowth of the nucleotide chains.
• This enzyme may have a function in the production and processing of bones since mutations in this enzyme are frequently linked to osteosarcoma.

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