Difference Between CRISPR and Restriction Enzymes

The key difference between CRISPR and restriction enzymes is that CRISPR is a naturally occurring prokaryotic immune defense mechanism that has been recently used for eukaryotic gene editing and modification while restriction enzymes are biological scissors which cleave DNA molecules into smaller substances.

Genome editing and gene modification are interesting and innovative fields in genetics and molecular biology. Gene therapy studies widely use gene modification. Moreover, gene modification is useful in identifying the properties of the gene, functionality of the gene and how mutations in the gene could affect its function. It is important to derive efficient and reliable ways to make precise, targeted changes to the genome of living cells. CRISPR and restrictions enzymes play key roles in gene modifications. CRISPR modifies genes with high precision. Restriction enzymes work as biological scissors which cleave DNA molecules into smaller substances.

CONTENTS

1. Overview and Key Difference
2. What is CRISPR 
3. What are Restriction Enzymes
4. Similarities Between CRISPR and Restriction Enzymes
5. Side by Side Comparison – CRISPR vs Restriction Enzymes in Tabular Form
6. Summary

What is CRISPR?

The CRISPR system is a natural mechanism present in some bacteria including E. coli and Archea. It is an adaptive immune protection against foreign DNA-based invasions. Moreover, it is a sequence-specific mechanism. The CRISPR system contains several DNA repeat elements. These elements are interspersed with short “spacer” sequences derived from foreign DNA and multiple Cas genes.  Some of the Cas genes are nucleases. Thus, the complete immune system is referred to as the CRISPR/Cas system.

The CRISPR/Cas system functions in four steps:

1. The system genetically tethering invading phage and plasmid DNA segments (spacers) into CRISPR loci (called the spacer acquisition step).
2. crRNA maturation step – The host transcribes and processes CRISPR loci to generate mature CRISPR RNA (crRNA) containing both CRISPR repeat elements and the integrated spacer element.
3. The crRNA detects homologous DNA sequences by complementary base pairing. This is important when an infection is present and an infectious agent is present.
4. Target interference step – crRNA detects foreign DNA, forms a complex with the foreign DNA and protects the host against the foreign DNA.

At present, the CRISPR/Cas9 system is used to alter or modify the mammalian genome by either transcription repression or activation. The mammalian cells can respond to CRISPR/Cas9 mediated DNA breaks by adopting repair mechanism. It can either be done using non-homologous end joining method (NHEJ) or homology-directed repair (HDR). Both these repair mechanisms take place by introducing double-stranded breaks. This results in mammalian gene editing. NHEJ can lead to ablation of gene mutations and can be used to create a loss of function effects. HDR can be used for introducing specific point mutations or introducing DNA segments of varying length. At present, the CRISPR/ Cas system is used in the fields of therapeutic, biomedical, agricultural and research applications.

What are Restriction Enzymes?

A restriction enzyme, more commonly referred to as a restriction endonuclease, has the ability to cleave DNA molecules into small fragments. The cleaving process occurs near or at a special recognition site of the DNA molecule called a restriction site. A recognition site is typically composed of 4-8 base pairs. Depending on the site of cleavage, restriction enzymes can be of four (04) different types: Type I, Type II, Type III and Type IV. Other than the site of cleavage, factors such as composition, requirement of co-factors and the condition of the target sequence are taken into consideration when differentiating restriction enzymes into four groups.

During the cleavage of DNA molecules, the cleaving site can be either at the restriction site itself or at a distance from the restriction site.  Restriction enzymes create two incisions through each of the sugar-phosphate backbone in the double helix of DNA.

Restriction enzymes are mainly found in Achaea and bacteria. They utilize these enzymes as a defense mechanism against the invading viruses. The restriction enzymes cleave the foreign (pathogenic) DNA but not their own DNA. Their own DNA is protected by an enzyme known as methyltransferase, which makes modifications in the host DNA and prevents cleavage.

Type I restriction enzyme possesses a cleaving site which is away from the recognition site. Functioning of the enzyme requires ATP and the protein, S-adenosyl-L-methionine. Type I restriction enzyme is considered to be multifunctional due to the presence of both restriction and methylase activities. Type II restriction enzymes cleave within the recognition site itself or at a closer distance to it.  It only requires magnesium (Mg) for its function. Type II restriction enzymes have only one function and are independent of methylase.

What are the Similarities Between CRISPR and Restriction Enzymes?

• CRISPR and restriction enzymes are important tools in gene modification.
• Part of CRISPR or Cas9 and restriction enzymes are endonucleases.
• Both can recognize characteristic DNA sequences and cleave DNA.
• They are present in bacteria and archaea.
• Both CRISPR and restriction enzymes are sequence-specific.

What is the Difference Between CRISPR and Restriction Enzymes?

CRISPR-Cas system is a prokaryotic immune system that confers resistance to foreign genetic elements. On the other hand, restriction enzymes are endonucleases that recognize a specific sequence of nucleotides and produce a double-stranded cut in the DNA. So, this is the key difference between CRISPR and restriction enzymes.

Moreover, CRISPR- allows extremely precise cuts. In comparison to that, restriction enzyme cleavage is less precise. Furthermore, CRISPR is an advanced technique while restriction enzymes are primitive.

Below infographic summarizes the difference between CRISPR and restriction enzymes.

Summary – CRISPR vs Restriction Enzymes

CRISPR and restriction enzymes are two types of techniques used in gene modification. CRISPR is adaptive immune protection executed in some bacteria against foreign DNA based invasions. It is a natural defense mechanism. In contrast, restriction enzymes are endonucleases that cleave double-stranded DNA. Both CRISPR and restriction enzymes are able to cut DNA into small segments. However, both are sequence-specific. In comparison to CRISPR, restriction enzymes are primitive. CRISPR allows extremely precise cuts than restriction enzymes. So, this is the summary of the difference between CRISPR and restriction enzymes.

Reference:

1. “4QYZ” By Boghog – Own work (CC BY-SA 4.0) via Commons Wikimedia
2. “EcoRV Restriction Site.rsh” By Ramin Herati – Created with Inkscape (Public Domain) via Commons Wikimedia