Difference between Restriction Endonuclease and Exonuclease

Restriction endonucleases are the important enzymes in molecular biology. The primary function of such enzymes is the cleavage of DNA at specific points. The different types and functions of restriction endonuclease enzymes, along with their examples, are important for NEET, AIIMS, Nursing and paramedical exam preparation. This topic is included in the Class 12 Biology chapter Biotechnology: Principles and Processes. This article covers the details about the restriction endonuclease, Restriction exonucleases, their differences and types of restriction endonuclease with their activity.

Latest: NEET 2024 Paper Analysis and Answer Key 

Don't Miss: Most scoring concepts for NEET | NEET papers with solutions

New: NEET Syllabus 2025 for Physics, Chemistry, Biology

NEET Important PYQ & Solutions: Physics | Chemistry | Biology | NEET PYQ's (2015-24)

This Story also Contains

1. What is Restriction Endonuclease and Restriction Exonuclease?
2. Difference between Endonuclease and Exonuclease
3. What are Nucleases?
4. Restriction Endonuclease Enzyme
5. Types of Restriction Endonuclease (Type I, II, III, and IV)
6. Function of Restriction Endonucleases
7. Example of Restriction Endonuclease
8. Application of Restriction Endonuclease
9. Restriction Exonuclease Enzyme
10. Types of Restriction exonuclease
11. Function of Restriction Exonuclease
12. Example of Restriction Exonuclease
13. Practical Applications of Restriction Endonuclease in Molecular Biology
14. Tips, Tricks, and Strategies to Prepare for the Difference between Restriction Endonuclease and Exonuclease
15. Types of Questions and Weightage of Restriction Endonuclease and Restriction Exonuclease in Exams
16. Recommended Video on the Difference between Restriction Endonuclease and Exonuclease

What is Restriction Endonuclease and Restriction Exonuclease?

Restriction endonucleases cleave DNA molecules internally at a specific site, whereas exonucleases remove nucleotides from the ends of DNA or RNA molecules and are involved in genetic engineering and molecular biology. Nucleases are therefore important in the manipulation of nucleic acids because they link the phosphodiester bonds within DNA and RNA.

Due to the considerable roles of nucleases in genetic engineering and molecular biology, it is crucial to learn about restriction endonucleases, exonucleases, and other nucleases. Among them, restriction endonucleases which cut DNA at specific sites, are essential for cloning, gene engineering and recombinant DNA technology, whereas exonucleases which remove nucleotides from the ends of DNA, are useful for DNA repair as well as replication.

The enzymes that can rather accurately and selectively cleave, splice or join nucleic acids have thoroughly changed molecular biology and encouraged the creation of techniques like CRISPR and gene therapies; the latter may be evidence of how these enzymes are valuable in research and industry.

Also Read:

• MCQ Practice on Restriction Endonuclease
• Biotechnology Principle and Process
• Restriction Enzyme
• Biotechnology and its Applications

Difference between Endonuclease and Exonuclease

Let us differentiate between restriction endonucleases and exonucleases based on features in the table below.

What are Nucleases?

Nucleases are enzymes that hydrolyze the phosphodiester bond of the nucleic acids, leading to DNA cleavage into small pieces. The enzyme mechanism involves DNA and RNA metabolism, such as DNA repair, replication, and recombination, as well as RNA decay. Nucleases can be further categorised based on their results on the nucleic acid chain, with examples being endonucleases that cut at a particular site on the chain and exonucleases that break down the DNA from the ends.

Restriction Endonuclease Enzyme

Restriction endonuclease, also called restriction enzymes, involve enzyme mechanisms that hydrolyse DNA at specific restriction sites that exist within a DNA molecule. They are widely used in genetic engineering because they cut the DNA at specific places for insertion or alteration of genes.

Restriction endonucleases were for the first time identified in the early 1960s during research on the strategies used by bacteria to fight against viral infection. Hamilton Smith and his co-workers named the first restriction enzyme discovered as HindII and it existed in the bacterium Haemophilus influenzae. This finding transformed molecular biology and was the foundational innovation for constructing genetically tailored modern technology.

Types of Restriction Endonuclease (Type I, II, III, and IV)

There are four types of restriction endonucleases:

• Type I: These enzymes only bind to some DNA sequences, but cut at any position that is arbitrary relative to the binding site.
• Type II: These enzymes can bind to the DNA sequence specific to them and cut at particular locations within or just next to the recognition sequence. REases are classified into four groups; Type I, II, III and IV, but only type II REases are widely used in molecular biology.
• Type III: These enzymes can bind with the DNA sequence, and the DNA gets cut at a fixed distance from the binding site.
• Type IV: These enzymes cut DNA at particular sites, but for this procedure, they do not need ATP hydrolysis.

Function of Restriction Endonucleases

The mechanism of action and function of restriction endonuclease are given below:

Recognition sites

Restriction endonucleases come into contact with the target DNAs by the direct complementary base interactions with the preferred, usually palindromic, nucleotide sequences. After becoming bound, the enzyme causes the breakdown of phosphodiester bonds within the DNA structure, thus, causing DNA cleavage and to be split into two sections.

Cleavage patterns

The specific sequences recognized by restriction endonucleases are normally palindromic, which simply implies that they read the same, from the 5’ to 3’ direction and in a similar sequence from the 3’ to the 5’ direction. For instance, the specific recognition site of restriction enzyme EcoRI is 5’ GAATTC 3’, it is the same for both strands of the DNA helix if read from 5 ’to 3’. The cutting patterns of restriction endonucleases differ with the enzyme under consideration as well as the particular recognition sequence. Some enzymes cut the DNA through both chains in a straight cut while others make an angular cut that gives rise to overhanging or ‘sticky’ ends.

Example of Restriction Endonuclease

Restriction Endonuclease Example:

One of the more commonly known restriction endonucleases is EcoRI, the very first restriction enzyme isolated. This cuts DNA at a specific recognition sequence - GAATTC - that allows it to be an important tool for molecular biology in dealing with DNA manipulation.

Application of Restriction Endonuclease

The application of Restriction endonuclease enzymes is given below:

Genetic engineering

Restriction endonucleases are employed to cleave the DNA at definite sites so that the foreign DNA fragments can be inserted or the unwanted sequences can be deleted.

Cloning

They are also involved in the formation of recombinant DNA molecules through their ability to make V-shaped cuts at the restriction recognition site of the vector and insert DNA.

DNA mapping

In molecular biology, methods like restriction fragment length polymorphism analysis (RFLP) and southern blotting, restriction endonuclease enzymes are employed to determine the sequence of DNA strands and variations respectively.

Restriction Endonucleases Diagram

Restriction Exonuclease Enzyme

Exonucleases are enzymes that remove nucleotides through endonucleases provided in the nucleic acids of both DNA and RNA. They have important functions related to DNA repair, replication, and RNA processing because they generate and recognise abasic sites or any nucleotide lesion.

Types of Restriction exonuclease

There are two main types of exonucleases:

5’ to 3’ exonucleases

These enzymes remove nucleotides, one at a time, from the 5’ end of the DNA or RNA strand.

3’ to 5’ exonucleases

These enzymes cut nucleotides off the 3’ end of the DNA or RNA strand in a stepwise manner.

Function of Restriction Exonuclease

The enzyme mechanism involves exonucleases participating in the breakdown of a phosphodiester bond of the nucleotide and the consequent release of nucleotides at the termini of the DNA or RNA strand. They also have polarity depending on which'' direction of the nucleic acid strand they originate from.

Example of Restriction Exonuclease

Restriction Exonuclease Example:

One of the common restriction exonucleases is ExoI. This enzyme degrades single-strand DNA from the 3' end and is implicated in DNA repair and recombination processes.

Application of Restriction Exonuclease in Molecular Biology

Exonucleases have multiple applications in molecular biology:

DNA repair

Exonucleases participate in the repair processes of DNA, which include base excision, and nucleotide excision processes for the removal of damaged, mismatched nucleotides in the DNA strands.

Degradation of RNA primers

Within the DNA replication process, RNA primers are utilised and eventually erased by exonucleases so that DNA polymerase can extend the newly created strand with DNA nucleotide.

Removal of mismatched nucleotides

Exonucleases interact with DNA mismatch repair pathways to help remove nucleotides that fail to pair with the template DNA strand in the right way thereby maintaining genome stability.

Also Read:

• NCERT Solutions for Chapter 7: Human Health and Disease
• NCERT Books for Class 12 Biology
• NCERT Syllabus for Class 12

Restriction Exonuclease Diagram

Practical Applications of Restriction Endonuclease in Molecular Biology

A few important applications of restriction endonuclease are given below:

Genetic Engineering Techniques Involving Restriction Endonucleases

Restriction endonucleases are among the requisites of genetic manipulation, as they allow for the fine control of DNA fragments. Processes like Recombinant DNA technology use restriction enzymes to cut DNA at designed positions with a view to meaningful insertions of foreign DNA segments into vector molecules. Restriction endonucleases are used in all the processes of gene cloning, gene editing and gene expression to produce genetically modified organisms and to study the function of genes.

DNA sequencing and mapping

Restriction endonucleases are widely used in DNA sequencing and mapping activities. Molecular techniques, including RFLP analysis and Southern blotting, involve the use of restriction enzymes that cut the DNA at specific sites, producing proto-typically patterns of fragments that can be used to establish a relationship between genes and chromosomes in addition to revealing genetic variations and thus studying the DNA structure and organisation.

Role Of Exonucleases in DNA Replication and Repair

Genomic exonucleases have critical functions in DNA replication and repair, protecting the integrity of the genome. During DNA replication, RNA primers are cleaved from the newly synthesised DNA chains by exonucleases and DNA polymerases, which then use DNA nucleotides to fill the gap. In DNA repair, exonucleases eradicate several nucleotides in a single type, mismatched to other nucleotides in a strand of DNA, by participating in the process of repairing errors and maintaining the integrity of genes.

Case Study: Use of Restriction Enzymes in CRISPR Technology

CRISPR, or Clustered Regularly Interspaced Short Palindromic Repeats, is a function that exploits the restriction enzymes for gene editing. CRISPR-associated (Cas) proteins are a group of proteins that function as programmable nucleases in which they are guided by short RNA sequences to the target DNA.

With the help of a guide RNA (gRNA) that complements the targeted DNA sequence, the Cas nuclease cuts the DNA at the specific site. This defined tool of gene editing has transformed molecular biology, as scientists can now work on the genes with a higher level of accuracy and speed.

Taken together, restriction endonucleases and exonucleases are rather valuable reagents in molecular biology, being used in such areas as genetic manipulation and DNA sequencing, DNA replication and DNA repair. These enzymes are still widely involved in research and development in the related area and help to elucidate the mechanisms of various molecular processes as well as create new potential for bio- and medical technologies.

NCERT Class-wise Solutions

• NCERT solutions for class 12
• NCERT solutions for class 11
• NCERT solutions for class 10
• NCERT solutions for class 9

Tips, Tricks, and Strategies to Prepare for the Difference between Restriction Endonuclease and Exonuclease

Given below are some tips and tricks to prepare for restriction endonuclease and exonuclease:

Mnemonics

Recall "RISE" regarding restriction enzyme activities: R for recognition sites, I for the ability to make internal cuts, S for specificity, and E for the enzyme activity

Study Aids

Sketch out diagrams of the sites at which restriction endonuclease cleaves DNA in order to have a good grasp of how the enzyme works to recognize and digest the DNA molecule.

Create comparison tables to highlight the distinction between restriction endonuclease and exonuclease.

Multimedia

Watch animations and videos that show how restriction endonucleases fragment DNA and how restriction endonucleases are utilized in gene cloning.

Flashcards

Prepare flashcards so you can memorize the role types and examples of Restriction Endonuclease.

Types of Questions and Weightage of Restriction Endonuclease and Restriction Exonuclease in Exams

Here are the weightage and types of questions asked in different exams about the Restriction Endonuclease and Exonuclease:

Also Read:

Recommended Video on the Difference between Restriction Endonuclease and Exonuclease