Endonuclease vs Exonuclease- Definition, 11 Differences, Examples

Endonucleases are a type of enzymes that can cut the phosphodiester bonds within a polynucleotide chain, such as DNA or RNA. These bonds link the nucleotides together and form the backbone of the chain. By breaking these bonds, endonucleases can split a long chain into smaller fragments.

The name endonuclease comes from the fact that these enzymes can cut the chain from the inside, rather than from the ends. This means that they can recognize and cleave specific sequences within the chain, rather than removing nucleotides one by one from the termini.

Endonucleases are classified into two main groups: restriction endonucleases and non-restriction endonucleases. Restriction endonucleases are highly specific and can only cut certain sequences that are usually four to eight nucleotides long. These sequences are called restriction sites and are often palindromic, meaning that they read the same in both directions. For example, the sequence GAATTC is a restriction site for the enzyme EcoRI, which cuts between G and A.

Non-restriction endonucleases are less specific and can cut a variety of sequences, depending on their structure and function. Some of these enzymes are involved in DNA repair, recombination, transcription, or apoptosis. For example, the enzyme T4 endonuclease V can recognize and cut DNA that has been damaged by ultraviolet light.

Endonucleases can also be categorized based on their mechanism of action. Some endonucleases cut both strands of a double-stranded DNA molecule at the same position, creating blunt ends. Others cut the strands at different positions, creating sticky ends or overhangs that can be used for ligation. Some endonucleases can also cut single-stranded DNA or RNA molecules.

Endonucleases play an important role in molecular biology and biotechnology, as they enable the manipulation and analysis of DNA and RNA molecules. For example, restriction endonucleases are widely used for cloning, mapping, sequencing, and modifying DNA. Non-restriction endonucleases are also useful for studying DNA damage and repair, gene expression, and cell death.

Restriction endonucleases are a special type of endonucleases that recognize and cleave specific DNA sequences. They are also known as restriction enzymes or molecular scissors.

Restriction endonucleases are derived from various bacteria and archaea, where they act as a defense mechanism against foreign DNA, such as viruses or plasmids. They can distinguish between the host DNA and the invading DNA by the presence or absence of specific chemical modifications, such as methylation.

Restriction endonucleases can be classified into four major types (I, II, III, and IV) based on their structure, cofactor requirements, recognition sequence, and cleavage pattern.

• Type I restriction endonucleases are large multi-subunit complexes that consist of three subunits: R (restriction), M (modification), and S (specificity). They require ATP and S-adenosyl methionine (SAM) as cofactors. They recognize asymmetric sequences of 4 to 8 base pairs and cleave at random sites about 1000 base pairs away from the recognition site. They also have methylase activity that can modify the host DNA to protect it from cleavage.
• Type II restriction endonucleases are the most widely used and studied type of restriction enzymes. They are small proteins that usually consist of a single subunit. They do not require ATP or SAM as cofactors. They recognize palindromic sequences of 4 to 8 base pairs and cleave within or near the recognition site. They produce either blunt ends or sticky ends with 5` or 3` overhangs. They do not have methylase activity and can be inhibited by methylation of the recognition site.
• Type III restriction endonucleases are also multi-subunit complexes that consist of two subunits: R (restriction) and M (modification). They require ATP and SAM as cofactors. They recognize asymmetric sequences of 5 to 7 base pairs and cleave about 25 base pairs away from the recognition site. They also have methylase activity that can modify the host DNA to protect it from cleavage.
• Type IV restriction endonucleases are less common and less well characterized than the other types. They recognize modified DNA, such as methylated or hydroxymethylated bases, and cleave at unspecified sites. They do not have methylase activity and can be inhibited by methylation of the recognition site.

Restriction endonucleases have many applications in molecular biology, such as cloning, mapping, sequencing, gene editing, and diagnostics. They can be used to cut DNA into fragments of different sizes and shapes, which can then be separated by gel electrophoresis or joined together by DNA ligase. They can also be used to introduce specific mutations or deletions into DNA by using engineered variants of restriction enzymes, such as meganucleases, zinc finger nucleases, TALENs, or CRISPR-Cas9.

Exonucleases are enzymes that cleave DNA sequences in a polynucleotide chain from either the 5’ or 3’ end one at a time. Exonuclease, like endonuclease, is a hydrolyzing enzyme that cleaves the phosphodiester bond between the nucleotides.

One of the most important routes of RNA degradation in both archaea and eukaryotes is by the multi-protein exosome, which consists of multiple exoribonucleases. Besides, exonucleases are also found in the venoms of snakes and lizards. These toxins work by the cleavage of DNA coding for essential proteins within the body.

Exonucleases are important during replication as one of these enzymes works together with RNA polymerase II degrade the newly formed RNA primer present on the new transcript which is then replaced by DNA nucleotides. Exonuclease activity is also exploited during editing and proofreading DNA for errors.

The exonuclease in prokaryotes and eukaryotes are of three types; a decapping 5’ to 3’ exonuclease (Xrn1), an independent 5’to 3’ exonuclease and a polyA-specific 3’ to 5’ exonuclease. All of these exonucleases are involved in the formation, replication, and transcription of RNAs.

Exonucleases, unlike endonucleases, do not have a lag period as they cleave the sequences from the ends, resulting in sticky ends. Similarly, exonucleases also cleave individual nucleosides from either of the ends instead of resulting in oligonucleotides. Exonuclease does not have defensive properties against the entry of pathogenic microbes.

Endonucleases and exonucleases are two types of enzymes that cleave DNA or RNA sequences in different ways. The following table summarizes some of the key differences between them:

These differences reflect the different roles and functions of endonucleases and exonucleases in various biological processes such as DNA repair, recombination, replication, transcription, and degradation.

EcoRI is a restriction endonuclease that cleaves helical structures of DNA at specific sites to form fragments. This enzyme is isolated from the E. coli species and is a part of the restriction-modification system. EcoRI cleaves the G/AATTC where the ‘/’ indicates the phosphodiester bond that is specific for the cleavage by the restriction enzyme. It results in a four nucleotide sticky end with 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. Cleavage of DNA results in sticky ends which enhances the action of ligase enzyme and makes the ligation reaction more efficient. Non-specific cleavage can be done with EcoRI when the medium has low salt and enzyme concentration.

Some other examples of endonucleases are:

• BamHI: A type II restriction endonuclease that recognizes and cleaves the GGATCC sequence, leaving a 5’ overhang of GATC.
• HindIII: A type II restriction endonuclease that recognizes and cleaves the AAGCTT sequence, leaving a 5’ overhang of AGCT.
• HaeIII: A type II restriction endonuclease that recognizes and cleaves the GGCC sequence, leaving blunt ends.
• Cas9: A CRISPR-associated endonuclease that can be programmed to target and cleave any DNA sequence by using a guide RNA molecule.

Xrn1 is a decapping 5’ to 3’ exonuclease that plays a crucial role in RNA degradation and turnover. It cleaves the RNA molecule from the 5’ end, removing the cap structure and initiating the degradation process. Xrn1 is involved in various cellular processes, including mRNA decay, RNA quality control, and RNA interference. It is highly conserved across species and is essential for maintaining RNA homeostasis.

If you want to learn more about nucleases, exonucleases, and endonucleases, you can watch this video lecture by Dhara Fatnani, a biology teacher and content creator.

In this video, she explains the following topics:

• What are nucleases and what are their functions in DNA and RNA metabolism
• What are the differences between endonucleases and exonucleases based on their mode of action, specificity, and results
• What are the types of endonucleases and exonucleases and how they are classified
• What are some examples of endonucleases and exonucleases and their roles in molecular biology techniques
• How to use endonucleases and exonucleases in DNA cloning, DNA sequencing, DNA fingerprinting, and gene editing

The video is about 15 minutes long and has clear diagrams and animations to illustrate the concepts. It also has a quiz at the end to test your understanding of the topic.

You can also subscribe to her channel for more videos on biology topics. She has videos on DNA replication, transcription, translation, gene expression, genetic engineering, biotechnology, and more.

I hope you find this video helpful and informative. If you have any questions or feedback, you can leave a comment on the video or contact her through her social media accounts. She is always happy to help and interact with her viewers.😊

Endonucleases and exonucleases are two types of enzymes that cleave the phosphodiester bonds in nucleic acids. They differ in their mode of action, specificity, results, and functions. Endonucleases cut the nucleic acid chain from the middle, whereas exonucleases cut from the ends. Endonucleases can be specific or non-specific to the sequences they cleave, whereas exonucleases are usually non-specific. Endonucleases produce oligonucleotides with sticky ends, whereas exonucleases produce mononucleotides with blunt ends. Endonucleases are involved in DNA recombination, repair, and defense, whereas exonucleases are involved in RNA degradation, replication, and editing. Both types of enzymes are essential for maintaining the integrity and stability of the genetic material. They also have various applications in molecular biology and biotechnology.

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