Restriction endonucleases

Restriction Endonucleases: An Overview

Principle

Restriction endonucleases are bacterial enzymes that protect the host cell from foreign DNA, such as bacteriophage DNA, by cleaving it into smaller fragments. These enzymes recognize short, specific DNA sequences, typically 4 to 8 base pairs in length, known as recognition sites or restriction sites. Upon binding to their recognition sites, restriction endonucleases catalyze the hydrolysis of the phosphodiester bonds in the DNA backbone, resulting in double-stranded DNA breaks.

Types of Restriction Endonucleases

• Type I: These enzymes recognize specific DNA sequences but cleave the DNA at sites that are several hundred to several thousand base pairs away from the recognition site. They often require additional cofactors for activity.
• Type II: These enzymes recognize specific DNA sequences and cleave the DNA within or near the recognition site. They are commonly used in molecular biology applications and genetic engineering.
• Type III: Similar to Type I enzymes, Type III restriction endonucleases cleave DNA at sites that are several base pairs away from the recognition site. They also require additional cofactors for activity.

Nomenclature

Restriction endonucleases are named based on the genus, species, and strain of the bacterium from which they were isolated, followed by a Roman numeral to designate different enzymes from the same species. For example, EcoRI is an endonuclease isolated from Escherichia coli (strain RY13) and is the first enzyme discovered in the Eco strain.

Recognition Sites

Restriction endonucleases recognize palindromic DNA sequences, meaning that the sequence reads the same in the 5' to 3' direction on both strands. Examples of common recognition sequences include:

• EcoRI: 5'-GAATTC-3'
• HindIII: 5'-AAGCTT-3'
• BamHI: 5'-GGATCC-3'

Applications

Restriction endonucleases are used in various applications, including:

• DNA Cloning: Cleaving DNA at specific sites to generate fragments that can be ligated into vectors for cloning purposes.
• Molecular Biology Techniques: Integral to techniques such as restriction fragment length polymorphism (RFLP) analysis, Southern blotting, DNA sequencing, and site-directed mutagenesis.
• Genetic Engineering: Creating recombinant DNA molecules by cutting and splicing DNA fragments from different sources.

Restriction Modification Systems

In addition to cleaving foreign DNA, many bacteria also possess modification enzymes (methyltransferases) that methylate their own DNA at specific sites, preventing cleavage by the corresponding restriction endonuclease. The combined action of restriction endonucleases and modification enzymes constitutes a restriction modification system, which serves as a defense mechanism against foreign DNA invasion.