List of restriction enzyme cutting sites
Encyclopedia
A restriction enzyme
or restriction endonuclease
is a special type of biological macromolecule
that functions as part of the "immune system
" in bacteria
. One special kind of restriction enzymes is the class of "homing endonucleases", these being present in all three domains
of life, although their function seems to be very different from one domain to another.
The classical restriction enzymes cut up and hence render harmless any unknown (non-cellular
) DNA
that enters a bacterial cell as a result of a viral infection
. They recognize a specific DNA sequence, usually short (3 to 8 bp
), and cut it, producing either blunt or overhung ends, either at or nearby the recognition site
.
Restriction enzymes are very variable. An organism often has several different enzymes, each specific to a distinct DNA sequence.
The whole list contains more than 1,200 enzymes, but databases register about 4,000.
To make an accessible navigation the list has been divided in different pages and sections. Choose a letter in the next table of contents:
Databases of proteins:
Restriction enzyme
A Restriction Enzyme is an enzyme that cuts double-stranded DNA at specific recognition nucleotide sequences known as restriction sites. Such enzymes, found in bacteria and archaea, are thought to have evolved to provide a defense mechanism against invading viruses...
or restriction endonuclease
Endonuclease
Endonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain, in contrast to exonucleases, which cleave phosphodiester bonds at the end of a polynucleotide chain. Typically, a restriction site will be a palindromic sequence four to six nucleotides long. Most...
is a special type of biological macromolecule
Macromolecule
A macromolecule is a very large molecule commonly created by some form of polymerization. In biochemistry, the term is applied to the four conventional biopolymers , as well as non-polymeric molecules with large molecular mass such as macrocycles...
that functions as part of the "immune system
Immune system
An immune system is a system of biological structures and processes within an organism that protects against disease by identifying and killing pathogens and tumor cells. It detects a wide variety of agents, from viruses to parasitic worms, and needs to distinguish them from the organism's own...
" in bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
. One special kind of restriction enzymes is the class of "homing endonucleases", these being present in all three domains
Three-domain system
The three-domain system is a biological classification introduced by Carl Woese in 1977 that divides cellular life forms into archaea, bacteria, and eukaryote domains. In particular, it emphasizes the separation of prokaryotes into two groups, originally called Eubacteria and Archaebacteria...
of life, although their function seems to be very different from one domain to another.
The classical restriction enzymes cut up and hence render harmless any unknown (non-cellular
Cell (biology)
The cell is the basic structural and functional unit of all known living organisms. It is the smallest unit of life that is classified as a living thing, and is often called the building block of life. The Alberts text discusses how the "cellular building blocks" move to shape developing embryos....
) DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
that enters a bacterial cell as a result of a viral infection
Bacteriophage
A bacteriophage is any one of a number of viruses that infect bacteria. They do this by injecting genetic material, which they carry enclosed in an outer protein capsid...
. They recognize a specific DNA sequence, usually short (3 to 8 bp
Base pair
In molecular biology and genetics, the linking between two nitrogenous bases on opposite complementary DNA or certain types of RNA strands that are connected via hydrogen bonds is called a base pair...
), and cut it, producing either blunt or overhung ends, either at or nearby the recognition site
Recognition sequence
The recognition sequence, sometimes also referred to as recognition site, of any DNA-binding protein motif that exhibits binding specificity, refers to the DNA sequence , to which the domain is specific...
.
Restriction enzymes are very variable. An organism often has several different enzymes, each specific to a distinct DNA sequence.
- See the main article on restriction enzymeRestriction enzymeA Restriction Enzyme is an enzyme that cuts double-stranded DNA at specific recognition nucleotide sequences known as restriction sites. Such enzymes, found in bacteria and archaea, are thought to have evolved to provide a defense mechanism against invading viruses...
. - Further reading: Homing endonucleaseHoming endonucleaseThe homing endonucleases are a type of restriction enzymes typically encoded by introns or inteins. They act on the cellular DNA of the cells that synthesize them, in the opposite alleles of the genes that encode them.- Origin and mechanism :...
.
Restriction enzymes catalog
The list includes some of the most studied examples of restriction endoncleases. The following information is given:The whole list contains more than 1,200 enzymes, but databases register about 4,000.
To make an accessible navigation the list has been divided in different pages and sections. Choose a letter in the next table of contents:
External links
Databases and lists of restriction enzymes:- Very comprehensive database of restriction enzymes supported by New England Biolabs©. It includes all kind of biological, structural, kinetical and commercial information about thousands of enzymes. Also includes related literature for every molecule:
- Detailed information for biochemical experiments:
- Alphabetical list of enzymes and their restriction sites:
- General information about restriction sites and biochemical conditions for restriction reactions:
Databases of proteins:
- Database of structures of proteins, solved at atomic resolution:
- Databases of proteins:
See also
- List of homing endonuclease cutting sites
- Restriction enzymeRestriction enzymeA Restriction Enzyme is an enzyme that cuts double-stranded DNA at specific recognition nucleotide sequences known as restriction sites. Such enzymes, found in bacteria and archaea, are thought to have evolved to provide a defense mechanism against invading viruses...
. - IsoschizomerIsoschizomerIsoschizomers are pairs of restriction enzymes specific to the same recognition sequence. For example, Sph I and Bbu I are isoschizomers of each other. The first enzyme to recognize and cut a given sequence is known as the prototype, all subsequent enzymes that recognize and cut that sequence...
. - Detailed articles about certain restriction enzymes: EcoRIEcoRIEcoRI is an endonuclease enzyme isolated from strains of E. coli, and is part of the restriction modification system.In molecular biology it is used as a restriction enzyme. It creates sticky ends with 5' end overhangs...
, HindIIIHindIIIHindIII is a type II site-specific deoxyribonuclease restriction enzyme isolated from Haemophilus influenzae that cleaves the palindromic DNA sequence AAGCTT in the presence of the cofactor Mg2+ via hydrolysis....
, BglIIBglIIBglII is a type II restriction endonuclease enzyme isolated from certain strains of Bacillus globigii. The principal function of restriction enzymes is the protection of the host genome against foreign DNA but they may also have some involvement in recombination and transposition...
. - Homing endonucleaseHoming endonucleaseThe homing endonucleases are a type of restriction enzymes typically encoded by introns or inteins. They act on the cellular DNA of the cells that synthesize them, in the opposite alleles of the genes that encode them.- Origin and mechanism :...
. - IntronIntronAn intron is any nucleotide sequence within a gene that is removed by RNA splicing to generate the final mature RNA product of a gene. The term intron refers to both the DNA sequence within a gene, and the corresponding sequence in RNA transcripts. Sequences that are joined together in the final...
s and inteinInteinAn intein is a segment of a protein that is able to excise itself and rejoin the remaining portions with a peptide bond. Inteins have also been called "protein introns"....
s. - Intragenomic conflict: Homing endonuclease genes.
- I-CreI homing endonucleaseI-CreII-CreI is a homing endonuclease whose gene was first discovered in the chloroplast genome of Chlamydomonas reinhardtii, a species of unicellular green algae. It is named for the facts that: it resides in an Intron; it was isolated from Clamydomonas reinhardtii; it was the first such gene isolated...
.