Restriction enzymes

class of enzymes that cleaves DNA into fragments at or near specific recognition sites within the molecule known as restriction sites

EcoRI (pronounced "eco R one") is a type II restriction enzyme isolated from Escherichia coli. It cleaves DNA double helices into fragments at specific sites, and is also a part of the restriction modification system. The enzyme's name originates from the species from which it was isolated: "E" denotes generic name (Escherichia), "co" denotes species name (coli), "R" represents the strain (RY13), and the "I" denotes that it was the first enzyme isolated from this strain.

thumb|right|200px|DNA recognition sequence of EcoRV. The green line represents the cut site. thumb|right|200px|EcoRV cleaving DNA. The protein loosely binds DNA and scans for its recognition sequence. Once found, EcoRV kinks the DNA in a 50° angle and cleaves at the cognate sequence.

HindIII (pronounced "Hin D Three") is a type II site-specific deoxyribonuclease restriction enzyme isolated from Haemophilus influenzae that cleaves the DNA palindromic sequence AAGCTT in the presence of the cofactor Mg2+ via hydrolysis. thumb|HindIII restrictions process results in formation of overhanging palindromic sticky ends. The cleavage of this sequence between the AA's results in 5' overhangs on the DNA called sticky ends:

BamHI (pronounced "Bam H one") (from Bacillus amyloliquefaciens) is a type II restriction endonuclease, having the capacity for recognizing short sequences (6 bp) of DNA and specifically cleaving them at a target site. This exhibit focuses on the structure-function relations of BamHI as described by Newman, et al. (1995). BamHI binds at the recognition sequence 5'-GGATCC-3', and cleaves these sequences just after the 5'-guanine on each strand. This cleavage results in sticky ends which are 4 bp long. In its unbound form, BamHI displays a central b sheet, which resides in between α-helices.

DNA region at which restriction enzymes cleave

Isoschizomers are pairs of restriction enzymes specific to the same recognition sequence. The term is derived .

The restriction endonuclease Fok1, naturally found in Flavobacterium okeanokoites, is a bacterial type IIS restriction endonuclease consisting of an N-terminal DNA-binding domain and a non sequence-specific DNA cleavage domain at the C-terminal. Once the protein is bound to duplex DNA via its DNA-binding domain at the 5'-GGATG-3' recognition site, the DNA cleavage domain is activated and cleaves the DNA at two locations, regardless of the nucleotide sequence at the cut site. The DNA is cut 9 nucleotides downstream of the motif on the forward strand, and 13 nucleotides downstream of the motif o

type of enzyme

HaeIII is one of many restriction enzymes (endonucleases) a type of prokaryotic DNA that protects organisms from unknown, foreign DNA. It is a restriction enzyme used in molecular biology laboratories. It was the third endonuclease to be isolated from the Haemophilus aegyptius bacteria. The enzyme's recognition site—the place where it cuts DNA molecules—is the GGCC nucleotide sequence which means it cleaves DNA at the site 5′-GG/CC-3. The recognition site is usually around 4-8 bps. This enzyme's gene has been sequenced and cloned. This is done to make DNA fragments in blunt ends. H

TaqI is a restriction enzyme isolated from the bacterium Thermus aquaticus in 1978. It has a recognition sequence of

thumb|300px|BglII recognition site. The scissile bond|scissile phoshodiester bonds between the Adenine and Guanine residues of both strands are hydrolyzed within the enzyme's [[active site. Mechanism shown below. ]]

thumb|300px|Eco RII dimer based on [[Protein Data Bank|PDB ID 1NA6 ]] EcoRII (pronounced 'eco R two') is an Restriction endonuclease enzyme (REase) of the restriction modification system (RM) naturally found in Escherichia coli, a Gram-negative bacteria. Its molecular mass is 45.2 kDa, being composed of 402 amino acids.