What Are Restriction Enzymes?

How these endonuceleases stand out

Structure of the homodimeric restriction enzyme EcoRI (cyan and green cartoon diagram) bound to double stranded DNA (brown tubes).
Credit: Boghog2/Public Domain via Wikimedia Commons

How much do you know about restriction enzymes? Get a better understanding of what they do and why they're important, with this review.

Defining Restriction Enzymes

Restriction endonucleases are a class of enzyme that cut DNA molecules. Each enzyme recognizes a unique sequence of nucleotides in the DNA strand. Such sequences are usually about 4 to 6 base-pairs long. The sequences are palindromic in that the complimentary DNA strand has the same sequence only in the reverse direction.

In other words, both strands of DNA are cut at the same location.

Where These Enzymes Are Found

Restriction enzymes are found in many different strains of bacteria where their biological role is to participate in cell defense. These enzymes “restrict” foreign (e.g. viral) DNA that enters the cell, by destroying it. The host cell has a restriction-modification system that methylates its own DNA at sites specific for its respective restriction enzymes, thereby protecting it from cleavage. More than 800 known enzymes have been discovered that recognize more than100 different nucleotide sequences.

Use in Biotechnology

Restriction enzymes are used in biotechnology to cut DNA into smaller strands in order to study fragment length differences among individuals (Restriction Fragment Length Polymophism – RFLP). They're also used for gene cloning.

RFLP techniques have been used to determine that individuals or groups of individuals have distinctive differences in gene sequences and restriction cleavage patterns in certain areas of the genome.

Knowledge of these unique areas is the basis for DNA fingerprinting. Each of these methods depends on the use of agarose gel electrophoresis for separation of the DNA fragments. TBE buffer, which is made up of Tris base, boric acid, and EDTA, is commonly used for agarose gel electrophoresis to examine DNA products.

Types of Restriction Enzymes

There are three different types of restriction enzymes. Type I cuts DNA at random locations as far as 1000 or more base-pairs from the recognition site. Type III cuts at approximately 25 base-pairs from the site. Types I and III require ATP and may be large enzymes with multiple sub-units. Type II enzymes, which are predominantly used in biotechnology, cut DNA within the recognized sequence without the need for ATP and are smaller and simpler.

Type II restriction enzymes are named according to the bacterial species from which they are isolated. For example, the enzyme EcoRI was isolated from E. coli. Most of the public is familiar with E. coli outbreaks in food.

Type II restriction enzymes can generate two different types of cuts depending on whether they cut both strands at the center of the recognition sequence or each strand closer to one end of the recognition sequence.

The former cut will generate "blunt ends" with no nucleotide overhangs. The latter generates "sticky" or "cohesive" ends because each resulting fragment of DNA has an overhang that compliments the other fragments. Both are useful in molecular genetics for making recombinant DNA and proteins.

This form of DNA stands out because it is produced by the ligation (bonding together) of two or more different strands that weren't originally linked together.