Nomenclature And Classification
Restriction enzymes are named based on the organism in which they were discovered. For example, the enzyme Hind III was isolated from Haemophilus influenzae, strain Rd. The first three letters of the name are italicized because they abbreviate the genus and species names of the organism. The fourth letter typically comes from the bacterial strain designation. The Roman numerals are used to identify specific enzymes from bacteria that contain multiple restriction enzymes. Typically, the Roman numeral indicates the order in which restriction enzymes were discovered in a particular strain.
There are three classes of restriction enzymes, labeled types I, II, and III. Type I restriction systems consist of a single enzyme that performs both modification (methylation) and restriction activities. These enzymes recognize specific DNA sequences, but cleave the DNA strand randomly, at least 1,000 base pairs (bp) away from the recognition site. Type III restriction systems have separate enzymes for restriction and methylation, but these enzymes share a common subunit. These enzymes recognize specific DNA sequences, but cleave DNA at random sequences approximately twenty-five bp from the recognition sequence. Neither type I nor type III restriction systems have found much application in recombinant DNA techniques.
Type II restriction enzymes, in contrast, are heavily used in recombinant DNA techniques. Type II enzymes consist of single, separate proteins for restriction and modification. One enzyme recognizes and cuts DNA, the other enzyme recognizes and methylates the DNA. Type II restriction enzymes cleave the DNA sequence at the same site at which they recognize it. The only exception are type IIs (shifted) restriction enzymes, which cleave DNA on one side of the recognition sequence, within twenty nucleotides of the recognition site. Type II restriction enzymes discovered to date collectively recognize over 200 different DNA sequences.
Type II restriction enzymes can cleave DNA in one of three possible ways. In one case, these enzymes cleave both DNA strands in the middle of a recognition sequence, generating blunt ends. For example:
These blunt ended fragments can be joined to any other DNA fragment with blunt ends, making these enzymes useful for certain types of DNA cloning experiments.
Type II restriction enzymes can also cleave DNA to leave a 3′ ("three prime") overhang. (An overhang means that the restriction enzyme leaves a short single-stranded "tail" of DNA at the site where the DNA was cut.) These 3′ overhanging ends can only join to another compatible 3′ overhanging end (that is, an end with the same sequence in the overhang).
In the type II restriction enzymes discovered to date, the recognition sequences range from 4 bp to 9 bp long. Cleavage will not occur unless the full length of the recognition sequence is encountered. Enzymes with a short recognition sequence cut DNA frequently; restriction enzymes with 8 or 9 bp sequences typically cut DNA very infrequently, because these longer sequences are less common in the target DNA.
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