Restriction enzymes, or restriction endonucleases, are a broad class of DNA-cutting enzymes that occur naturally in bacteria and are instrumental in its defense against viral infections (i.e. bacteriophages). Considered as nature’s molecular scissors, restriction enzymes recognize specific nucleotide sequences of DNA, called restriction sites, on which to bind and subsequently cleave into fragments via hydrolysis of the phosphodiester backbone. Restriction fragments can possess either blunt ends, which have 5'-phosphate groups that promote ligation, or sticky ends, which have 3'- or 5'-overhangs of 1 to 4 nucleotides and are more cohesive. These small stretches of single-stranded DNA can self-ligate or ligate with a complementary region on another DNA molecule. Since fragmentation occurs at or near the recognition site and transpires in a predictable manner, restriction enzymes have become essential tools in genetic engineering (e.g. DNA cloning and DNA fingerprinting).
Different bacterial species produce restriction enzymes that recognize and cut different nucleotide sequences. To this date, scientists have identified and purified hundreds of restriction enzymes, and have categorized them into four groups according to their composition, the characteristics of the cleavage site, and the enzyme cofactor requirements.
Code | Nucleotide |
A | Adenine |
C | Cytosine |
G | Guanine |
T | Thymine |
N | A, C, G or T |
M | A or C |
R | A or G |
W | A or T |
Y | C or T |
S | C or G |
K | G or T |
H | A, C or T |
B | C, G or T |
V | A, C or G |
D | A, G or T |
Enzyme | Recognition Sequence | Cut | Overhang |
---|---|---|---|
AatII | 5'- G A C G T/C -'3 3'- C/T G C A G -'5 | 5'-GACGT C-3' 3'-C TGCAG-5' | 3' ACGT |
AbaSI | 5'- C N N N N N N N N N N N/N N N N N N N N N G -'3 3'- G N N N N N N N N N/N N N N N N N N N N N C -'5 | 5'-CNNNNNNNNNNN NNNNNNNNNG-3' 3'-GNNNNNNNNN NNNNNNNNNNNC-5' | 3' NN |
Acc65I | 5'- G/G T A C C -'3 3'- C C A T G/G -'5 | 5'-G GTACC-3' 3'-CCATG G-5' | 5' GTAC |
AccI | 5'- G T/M K A C -'3 3'- C A K M/T G -'5 | 5'-GT MKAC-3' 3'-CAKM TG-5' | 5' MK |
AciI | 5'- C/C G C -'3 3'- G G C/G -'5 | 5'-C CGC-3' 3'-GGC G-5' | 5' CG |
MLA | "Quest Database™ Restriction Enzymes Cut Sites Reference Table." AAT Bioquest, Inc., 8 Oct. 2025, https://www.aatbio.com/data-sets/restriction-enzymes-cut-sites-reference-table. | |
APA | AAT Bioquest, Inc. (2025, October 8). Quest Database™ Restriction Enzymes Cut Sites Reference Table. AAT Bioquest. https://www.aatbio.com/data-sets/restriction-enzymes-cut-sites-reference-table. | |
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