The Naming and Characteristics of Restriction Endonucleases

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Restriction enzymes, also known as restriction endonucleases, are enzymes that can cut double-stranded DNA. Its cutting method is to cut the bond between the carbohydrate molecule and the phosphoric acid, and then create a nick on each of the two DNA strands without damaging the nucleotides and bases. There are two types of cleavage, which can produce sticky ends with protruding single-stranded DNA, and smooth ends with flat ends without protrusions. Since the broken DNA fragments can be joined by another enzyme called DNA ligase, different restriction fragments on chromosomes or DNA can be joined together through splicing.

Restriction enzymes have a wide range of applications in the fields of molecular biology and genetic engineering. Such enzymes were first discovered in certain strains of E. coli, and these strains can limit phage infection. Scientists believe that restriction enzymes are mechanisms that bacteria have evolved to fight viral infections and help remove the viral sequences that have been colonized. Daniel Nasens and Hamilton Smith of Johns Hopkins University and Warner Abel of the University of California, Berkeley, won the 1978 Nobel Prize in Physiology or Medicine for the discovery and research of restriction enzymes. One of the earliest applications of this enzyme was to transform insulin into Escherichia coli to make it capable of producing human insulin.

1. The naming and writing of restriction enzymes

Restriction endonucleases are mainly extracted from prokaryotes. The current general naming principle is: the first letter is the first letter of the bacterial genus name, the second and third letters are the first two letters of the bacterial species name, and these letters are written in italics. If the same biological species is divided into different serotypes and strains, the first letter of the strain name should be written in regular characters and placed after the third letter of the restriction enzyme name. For example, the restriction enzymes Hinc Ⅱ and Hind Ⅲ are respectively derived from Haemophilus influenza serotype c and d strains. If there are several different endonucleases in the same strain, they are represented by Roman numerals I, II, and III respectively.

2. Features of restriction endonucleases:

①Identify a specific nucleotide sequence: the sequence is generally 4-6bp in length and has a palindrome structure (palindromes, a self-complementary DNA sequence, that is, the sequence of the upper and lower strands read from the 5’→3′ direction is exactly the same).

②Have a specific restriction site: the double-stranded DNA is cut at a specific site of the recognition sequence to produce a specific restriction end. Generally, after double-stranded DNA is digested, there are three types of ends: 5’protruding sticky ends; 3’protruding sticky ends; blunt ends.

③ A binary system made up of two enzyme molecules: restriction endonuclease and methylase. The recognition sites of the two are the same, but the latter is not a cleavage, but a methylation modification to a base in the recognition sequence. The methyl group extends into the double helix, hindering the action of the restriction endonuclease, making it not cut by the corresponding restriction endonuclease.

For prokaryotes, methylases methylate their own DNA sequences to protect them from restriction enzymes. Therefore, methylases are a protective mechanism in bacteria. In other words, it is precisely because of restriction enzymes and methylases that constitute a complete immune system of prokaryotes.

Generally, different restriction enzymes have different recognition sequences, but some enzymes from different sources can recognize the same sequence. These enzymes are called isoschizomers. However, some of these enzymes have the same cut point, while some of the enzymes have different cut points. For example, Acc Ⅲ and BspEⅠ, BseAⅠ, BsiMⅠ, Bsp 13 I, Kpn21, and MroⅠ recognition sequences are all TCCGGA. Their tangent points are between T and C, that is, T/CCGGA. However, the recognition sequences of Bbe I and Kas I, Nar I, and Sfo I are all GGCGCC, but their cut points are GGCGC/C, G/GCGCC, GG/CGCC, GGC/GCC, respectively.

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