Restriction Enzymes Cut Sites Table
Restriction enzymes, also called restriction endonucleases, are a group of enzymes that cut DNA and are found naturally in bacteria. They help bacteria fight off viral infections (i.e. bacteriophages). Restriction enzymes are thought of as nature’s molecular scissors because they look for specific nucleotide sequences in DNA, called “restriction sites,” that they can bind to and then cut into pieces by hydrolyzing the phosphodiester backbone. Restriction fragments can have either blunt ends, which have 5′-phosphate groups that help them stick together, or sticky ends, which have 3′- or 5′-overhangs of one to four nucleotides and are more stable. These short pieces of single-stranded DNA can connect to themselves or to another piece of DNA that has a matching area. Because fragmentation happens at or near the recognition site and in a predictable way, restriction enzymes have become important tools in genetic engineering (e.g. DNA cloning and DNA fingerprinting).
Different kinds of restriction enzymes
Different types of bacteria make restriction enzymes that cut different sequences of nucleotides. Scientists have found and cleaned up hundreds of restriction enzymes and put them into four groups based on what they are made of, what the cleavage site looks like, and what the enzyme needs as a cofactor.
- Type I restriction enzymes cut at random places about 1000 bp away from the restriction site. As cofactors for enzymes, you need ATP, AdoMet, and Mg2+. EcoK I, EcoA I, and CfrA I are all examples of Type I restriction enzymes.
- Type II restriction enzymes cut close to or right at the restriction site, and they need Mg2+ as an enzyme cofactor. EcoR I, BamH I, and Hind III are all examples of Type II restriction enzymes.
- Type III restriction enzymes cut at sites 24 to 26 bp away from the restriction site. ATP and Mg2+ are needed as cofactors for these enzymes. EcoP I, EcoP15 I, and Hinf III are all examples of Type II restriction enzymes.
- Type IV restriction enzymes cut near the restriction site or at short distances from it. They also target modified DNA such as methylated, hydroxymethylated and glucosyl-hydroxymethylated DNA.
- 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 |
AclI | 5′- A A/C G T T -‘3 3′- T T G C/A A -‘5 | 5′-AA CGTT-3′ 3′-TTGC AA-5′ | 5′ CG |
AcuI | 5′- C T G A A G N14 N N/-‘3 3′- G A C T T C N14/N N -‘5 | 5′-CTGAAGN14NN -3′ 3′-GACTTCN14 NN-5′ | 3′ NN |
AfeI | 5′- A G C/G C T -‘3 3′- T C G/C G A -‘5 | 5′-AGC GCT-3′ 3′-TCG CGA-5′ | Blunt |
AflII | 5′- C/T T A A G -‘3 3′- G A A T T/C -‘5 | 5′-C TTAAG-3′ 3′-GAATT C-5′ | 5′ TTAA |
AflIII | 5′- A/C R Y G T -‘3 3′- T G Y R C/A -‘5 | 5′-A CRYGT-3′ 3′-TGYRC A-5′ | 5′ CRYG |
AgeI | 5′- A/C C G G T -‘3 3′- T G G C C/A -‘5 | 5′-A CCGGT-3′ 3′-TGGCC A-5′ | 5′ CCGG |
AhdI | 5′- G A C N N N/N N G T C -‘3 3′- C T G N N/N N N C A G -‘5 | 5′-GACNNN NNGTC-3′ 3′-CTGNN NNNCAG-5′ | 3′ N |
AleI-v2 | 5′- C A C N N/N N G T G -‘3 3′- G T G N N/N N C A C -‘5 | 5′-CACNN NNGTG-3′ 3′-GTGNN NNCAC-5′ | Blunt |
AluI | 5′- A G/C T -‘3 3′- T C/G A -‘5 | 5′-AG CT-3′ 3′-TC GA-5′ | Blunt |
AlwI | 5′- G G A T C N4/N -‘3 3′- C C T A G N4 N/-‘5 | 5′-GGATCN4 N-3′ 3′-CCTAGN4N -5′ | 5′ N |
AlwNI | 5′- C A G N N N/C T G -‘3 3′- G T C/N N N G A C -‘5 | 5′-CAGNNN CTG-3′ 3′-GTC NNNGAC-5′ | 3′ NNN |
ApaI | 5′- G G G C C/C -‘3 3′- C/C C G G G -‘5 | 5′-GGGCC C-3′ 3′-C CCGGG-5′ | 3′ GGCC |
ApaLI | 5′- G/T G C A C -‘3 3′- C A C G T/G -‘5 | 5′-G TGCAC-3′ 3′-CACGT G-5′ | 5′ TGCA |
ApoI | 5′- R/A A T T Y -‘3 3′- Y T T A A/R -‘5 | 5′-R AATTY-3′ 3′-YTTAA R-5′ | 5′ AATT |
AscI | 5′- G G/C G C G C C -‘3 3′- C C G C G C/G G -‘5 | 5′-GG CGCGCC-3′ 3′-CCGCGC GG-5′ | 5′ CGCG |
AseI | 5′- A T/T A A T -‘3 3′- T A A T/T A -‘5 | 5′-AT TAAT-3′ 3′-TAAT TA-5′ | 5′ TA |
AsiSI | 5′- G C G A T/C G C -‘3 3′- C G C/T A G C G -‘5 | 5′-GCGAT CGC-3′ 3′-CGC TAGCG-5′ | 3′ AT |
AvaI BsoBI | 5′- C/Y C G R G -‘3 3′- G R G C Y/C -‘5 | 5′-C YCGRG-3′ 3′-GRGCY C-5′ | 5′ YCGR |
AvaII | 5′- G/G W C C -‘3 3′- C C W G/G -‘5 | 5′-G GWCC-3′ 3′-CCWG G-5′ | 5′ GWC |
AvrII | 5′- C/C T A G G -‘3 3′- G G A T C/C -‘5 | 5′-C CTAGG-3′ 3′-GGATC C-5′ | 5′ CTAG |
BaeGI | 5′- G K G C M/C -‘3 3′- C/M C G K G -‘5 | 5′-GKGCM C-3′ 3′-C MCGKG-5′ | 3′ KGCM |
BaeI | 5′- N N N N N/N10 A C N N N N G T A Y C N7 N N N N N/-‘3 3′-/N N N N N N10 T G N N N N C A T R G N7/N N N N N -‘5 | 5′-NNNNN N10ACNNNNGTAYCN7NNNNN -3′ 3′- NNNNNN10TGNNNNCATRGN7 NNNNN-5′ | 3′ NNNNN |
BamHI | 5′- G/G A T C C -‘3 3′- C C T A G/G -‘5 | 5′-G GATCC-3′ 3′-CCTAG G-5′ | 5′ GATC |
BanI | 5′- G/G Y R C C -‘3 3′- C C R Y G/G -‘5 | 5′-G GYRCC-3′ 3′-CCRYG G-5′ | 5′ GYRC |
BanII | 5′- G R G C Y/C -‘3 3′- C/Y C G R G -‘5 | 5′-GRGCY C-3′ 3′-C YCGRG-5′ | 3′ RGCY |
BbsI | 5′- G A A G A C N2/N N N N -‘3 3′- C T T C T G N2 N N N N/-‘5 | 5′-GAAGACN2 NNNN-3′ 3′-CTTCTGN2NNNN -5′ | 5′ NNNN |
BbvCI | 5′- C C/T C A G C -‘3 3′- G G A G T/C G -‘5 | 5′-CC TCAGC-3′ 3′-GGAGT CG-5′ | 5′ TCA |
BbvI | 5′- G C A G C N8/N N N N -‘3 3′- C G T C G N8 N N N N/-‘5 | 5′-GCAGCN8 NNNN-3′ 3′-CGTCGN8NNNN -5′ | 5′ NNNN |
BccI | 5′- C C A T C N4/N -‘3 3′- G G T A G N4 N/-‘5 | 5′-CCATCN4 N-3′ 3′-GGTAGN4N -5′ | 5′ N |
BceAI | 5′- A C G G C N12/N N -‘3 3′- T G C C G N12 N N/-‘5 | 5′-ACGGCN12 NN-3′ 3′-TGCCGN12NN -5′ | 5′ NN |
BcgI | 5′- N N/N10 C G A N N N N N N T G C N10 N N/-‘3 3′-/N N N10 G C T N N N N N N A C G N10/N N -‘5 | 5′-NN N10CGANNNNNNTGCN10NN -3′ 3′- NNN10GCTNNNNNNACGN10 NN-5′ | 3′ NN |
BciVI | 5′- G T A T C C N5 N/-‘3 3′- C A T A G G N5/N -‘5 | 5′-GTATCCN5N -3′ 3′-CATAGGN5 N-5′ | 3′ N |
BclI | 5′- T/G A T C A -‘3 3′- A C T A G/T -‘5 | 5′-T GATCA-3′ 3′-ACTAG T-5′ | 5′ GATC |
BfaI | 5′- C/T A G -‘3 3′- G A T/C -‘5 | 5′-C TAG-3′ 3′-GAT C-5′ | 5′ TA |
BglI | 5′- G C C N N N N/N G G C -‘3 3′- C G G N/N N N N C C G -‘5 | 5′-GCCNNNN NGGC-3′ 3′-CGGN NNNNCCG-5′ | 3′ NNN |
BglII | 5′- A/G A T C T -‘3 3′- T C T A G/A -‘5 | 5′-A GATCT-3′ 3′-TCTAG A-5′ | 5′ GATC |
BlpI | 5′- G C/T N A G C -‘3 3′- C G A N T/C G -‘5 | 5′-GC TNAGC-3′ 3′-CGANT CG-5′ | 5′ TNA |
BmgBI | 5′- C A C/G T C -‘3 3′- G T G/C A G -‘5 | 5′-CAC GTC-3′ 3′-GTG CAG-5′ | Blunt |
BmrI | 5′- A C T G G G N4 N/-‘3 3′- T G A C C C N4/N -‘5 | 5′-ACTGGGN4N -3′ 3′-TGACCCN4 N-5′ | 3′ N |
BmtI | 5′- G C T A G/C -‘3 3′- C/G A T C G -‘5 | 5′-GCTAG C-3′ 3′-C GATCG-5′ | 3′ CTAG |
BpmI | 5′- C T G G A G N14 N N/-‘3 3′- G A C C T C N14/N N -‘5 | 5′-CTGGAGN14NN -3′ 3′-GACCTCN14 NN-5′ | 3′ NN |
Bpu10I | 5′- C C/T N A G C -‘3 3′- G G A N T/C G -‘5 | 5′-CC TNAGC-3′ 3′-GGANT CG-5′ | 5′ TNA |
BpuEI | 5′- C T T G A G N14 N N/-‘3 3′- G A A C T C N14/N N -‘5 | 5′-CTTGAGN14NN -3′ 3′-GAACTCN14 NN-5′ | 3′ NN |
BsaAI | 5′- Y A C/G T R -‘3 3′- R T G/C A Y -‘5 | 5′-YAC GTR-3′ 3′-RTG CAY-5′ | Blunt |
BsaBI | 5′- G A T N N/N N A T C -‘3 3′- C T A N N/N N T A G -‘5 | 5′-GATNN NNATC-3′ 3′-CTANN NNTAG-5′ | Blunt |
BsaHI | 5′- G R/C G Y C -‘3 3′- C Y G C/R G -‘5 | 5′-GR CGYC-3′ 3′-CYGC RG-5′ | 5′ CG |
BsaI | 5′- G G T C T C N/N N N N -‘3 3′- C C A G A G N N N N N/-‘5 | 5′-GGTCTCN NNNN-3′ 3′-CCAGAGNNNNN -5′ | 5′ NNNN |
BsaJI | 5′- C/C N N G G -‘3 3′- G G N N C/C -‘5 | 5′-C CNNGG-3′ 3′-GGNNC C-5′ | 5′ CNNG |
BsaWI | 5′- W/C C G G W -‘3 3′- W G G C C/W -‘5 | 5′-W CCGGW-3′ 3′-WGGCC W-5′ | 5′ CCGG |
BsaXI | 5′- N N N/N9 A C N N N N N C T C C N7 N N N/-‘3 3′-/N N N N9 T G N N N N N G A G G N7/N N N -‘5 | 5′-NNN N9ACNNNNNCTCCN7NNN -3′ 3′- NNNN9TGNNNNNGAGGN7 NNN-5′ | 3′ NNN |
BseRI | 5′- G A G G A G N8 N N/-‘3 3′- C T C C T C N8/N N -‘5 | 5′-GAGGAGN8NN -3′ 3′-CTCCTCN8 NN-5′ | 3′ NN |
BseYI | 5′- C/C C A G C -‘3 3′- G G G T C/G -‘5 | 5′-C CCAGC-3′ 3′-GGGTC G-5′ | 5′ CCAG |
BsgI | 5′- G T G C A G N14 N N/-‘3 3′- C A C G T C N14/N N -‘5 | 5′-GTGCAGN14NN -3′ 3′-CACGTCN14 NN-5′ | 3′ NN |
BsiEI | 5′- C G R Y/C G -‘3 3′- G C/Y R G C -‘5 | 5′-CGRY CG-3′ 3′-GC YRGC-5′ | 3′ RY |
BsiHKAI | 5′- G W G C W/C -‘3 3′- C/W C G W G -‘5 | 5′-GWGCW C-3′ 3′-C WCGWG-5′ | 3′ WGCW |
BsiWI | 5′- C/G T A C G -‘3 3′- G C A T G/C -‘5 | 5′-C GTACG-3′ 3′-GCATG C-5′ | 5′ GTAC |
BslI | 5′- C C N N N N N/N N G G -‘3 3′- G G N N/N N N N N C C -‘5 | 5′-CCNNNNN NNGG-3′ 3′-GGNN NNNNNCC-5′ | 3′ NNN |
BsmAI BcoDI | 5′- G T C T C N/N N N N -‘3 3′- C A G A G N N N N N/-‘5 | 5′-GTCTCN NNNN-3′ 3′-CAGAGNNNNN -5′ | 5′ NNNN |
BsmBI-v2 | 5′- C G T C T C N/N N N N -‘3 3′- G C A G A G N N N N N/-‘5 | 5′-CGTCTCN NNNN-3′ 3′-GCAGAGNNNNN -5′ | 5′ NNNN |
BsmFI | 5′- G G G A C N10/N N N N -‘3 3′- C C C T G N10 N N N N/-‘5 | 5′-GGGACN10 NNNN-3′ 3′-CCCTGN10NNNN -5′ | 5′ NNNN |
BsmI | 5′- G A A T G C N/-‘3 3′- C T T A C/G N -‘5 | 5′-GAATGCN -3′ 3′-CTTAC GN-5′ | 3′ CN |
Bsp1286I | 5′- G D G C H/C -‘3 3′- C/H C G D G -‘5 | 5′-GDGCH C-3′ 3′-C HCGDG-5′ | 3′ DGCH |
BspCNI | 5′- C T C A G N7 N N/-‘3 3′- G A G T C N7/N N -‘5 | 5′-CTCAGN7NN -3′ 3′-GAGTCN7 NN-5′ | 3′ NN |
BspEI | 5′- T/C C G G A -‘3 3′- A G G C C/T -‘5 | 5′-T CCGGA-3′ 3′-AGGCC T-5′ | 5′ CCGG |
BspHI | 5′- T/C A T G A -‘3 3′- A G T A C/T -‘5 | 5′-T CATGA-3′ 3′-AGTAC T-5′ | 5′ CATG |
BspMI BfuAI | 5′- A C C T G C N4/N N N N -‘3 3′- T G G A C G N4 N N N N/-‘5 | 5′-ACCTGCN4 NNNN-3′ 3′-TGGACGN4NNNN -5′ | 5′ NNNN |
BsrBI | 5′- C C G/C T C -‘3 3′- G G C/G A G -‘5 | 5′-CCG CTC-3′ 3′-GGC GAG-5′ | Blunt |
BsrDI | 5′- G C A A T G N N/-‘3 3′- C G T T A C/N N -‘5 | 5′-GCAATGNN -3′ 3′-CGTTAC NN-5′ | 3′ NN |
BsrFI-v2 | 5′- R/C C G G Y -‘3 3′- Y G G C C/R -‘5 | 5′-R CCGGY-3′ 3′-YGGCC R-5′ | 5′ CCGG |
BsrGI | 5′- T/G T A C A -‘3 3′- A C A T G/T -‘5 | 5′-T GTACA-3′ 3′-ACATG T-5′ | 5′ GTAC |
BsrI | 5′- A C T G G N/-‘3 3′- T G A C/C N -‘5 | 5′-ACTGGN -3′ 3′-TGAC CN-5′ | 3′ GN |
BssHII | 5′- G/C G C G C -‘3 3′- C G C G C/G -‘5 | 5′-G CGCGC-3′ 3′-CGCGC G-5′ | 5′ CGCG |
BssSI-v2 | 5′- C/A C G A G -‘3 3′- G T G C T/C -‘5 | 5′-C ACGAG-3′ 3′-GTGCT C-5′ | 5′ ACGA |
BstAPI | 5′- G C A N N N N/N T G C -‘3 3′- C G T N/N N N N A C G -‘5 | 5′-GCANNNN NTGC-3′ 3′-CGTN NNNNACG-5′ | 3′ NNN |
BstBI | 5′- T T/C G A A -‘3 3′- A A G C/T T -‘5 | 5′-TT CGAA-3′ 3′-AAGC TT-5′ | 5′ CG |
BstEII BstEII | 5′- G/G T N A C C -‘3 3′- C C A N T G/G -‘5 | 5′-G GTNACC-3′ 3′-CCANTG G-5′ | 5′ GTNAC |
BstNI | 5′- C C/W G G -‘3 3′- G G W/C C -‘5 | 5′-CC WGG-3′ 3′-GGW CC-5′ | 5′ W |
BstUI | 5′- C G/C G -‘3 3′- G C/G C -‘5 | 5′-CG CG-3′ 3′-GC GC-5′ | Blunt |
BstXI | 5′- C C A N N N N N/N T G G -‘3 3′- G G T N/N N N N N A C C -‘5 | 5′-CCANNNNN NTGG-3′ 3′-GGTN NNNNNACC-5′ | 3′ NNNN |
BstYI | 5′- R/G A T C Y -‘3 3′- Y C T A G/R -‘5 | 5′-R GATCY-3′ 3′-YCTAG R-5′ | 5′ GATC |
BstZ17I | 5′- G T A/T A C -‘3 3′- C A T/A T G -‘5 | 5′-GTA TAC-3′ 3′-CAT ATG-5′ | Blunt |
Bsu36I | 5′- C C/T N A G G -‘3 3′- G G A N T/C C -‘5 | 5′-CC TNAGG-3′ 3′-GGANT CC-5′ | 5′ TNA |
BtgI | 5′- C/C R Y G G -‘3 3′- G G Y R C/C -‘5 | 5′-C CRYGG-3′ 3′-GGYRC C-5′ | 5′ CRYG |
BtgZI | 5′- G C G A T G N10/N N N N -‘3 3′- C G C T A C N10 N N N N/-‘5 | 5′-GCGATGN10 NNNN-3′ 3′-CGCTACN10NNNN -5′ | 5′ NNNN |
BtsCI | 5′- G G A T G N N/-‘3 3′- C C T A C/N N -‘5 | 5′-GGATGNN -3′ 3′-CCTAC NN-5′ | 3′ NN |
BtsI-v2 | 5′- G C A G T G N N/-‘3 3′- C G T C A C/N N -‘5 | 5′-GCAGTGNN -3′ 3′-CGTCAC NN-5′ | 3′ NN |
BtsIMutI | 5′- C A G T G N N/-‘3 3′- G T C A C/N N -‘5 | 5′-CAGTGNN -3′ 3′-GTCAC NN-5′ | 3′ NN |
Cac8I | 5′- G C N/N G C -‘3 3′- C G N/N C G -‘5 | 5′-GCN NGC-3′ 3′-CGN NCG-5′ | Blunt |
ClaI BspDI | 5′- A T/C G A T -‘3 3′- T A G C/T A -‘5 | 5′-AT CGAT-3′ 3′-TAGC TA-5′ | 5′ CG |
CspCI | 5′- N N/N11 C A A N N N N N G T G G N10 N N/-‘3 3′-/N N N11 G T T N N N N N C A C C N10/N N -‘5 | 5′-NN N11CAANNNNNGTGGN10NN -3′ 3′- NNN11GTTNNNNNCACCN10 NN-5′ | 3′ NN |
CviAII | 5′- C/A T G -‘3 3′- G T A/C -‘5 | 5′-C ATG-3′ 3′-GTA C-5′ | 5′ AT |
CviKI-1 | 5′- R G/C Y -‘3 3′- Y C/G R -‘5 | 5′-RG CY-3′ 3′-YC GR-5′ | Blunt |
CviQI | 5′- G/T A C -‘3 3′- C A T/G -‘5 | 5′-G TAC-3′ 3′-CAT G-5′ | 5′ TA |
DdeI | 5′- C/T N A G -‘3 3′- G A N T/C -‘5 | 5′-C TNAG-3′ 3′-GANT C-5′ | 5′ TNA |
DpnI | 5′- G A/T C -‘3 3′- C T/A G -‘5 | 5′-GA TC-3′ 3′-CT AG-5′ | Blunt |
DraI | 5′- T T T/A A A -‘3 3′- A A A/T T T -‘5 | 5′-TTT AAA-3′ 3′-AAA TTT-5′ | Blunt |
DraIII | 5′- C A C N N N/G T G -‘3 3′- G T G/N N N C A C -‘5 | 5′-CACNNN GTG-3′ 3′-GTG NNNCAC-5′ | 3′ NNN |
DrdI | 5′- G A C N N N N/N N G T C -‘3 3′- C T G N N/N N N N C A G -‘5 | 5′-GACNNNN NNGTC-3′ 3′-CTGNN NNNNCAG-5′ | 3′ NN |
EaeI | 5′- Y/G G C C R -‘3 3′- R C C G G/Y -‘5 | 5′-Y GGCCR-3′ 3′-RCCGG Y-5′ | 5′ GGCC |
EagI | 5′- C/G G C C G -‘3 3′- G C C G G/C -‘5 | 5′-C GGCCG-3′ 3′-GCCGG C-5′ | 5′ GGCC |
EarI | 5′- C T C T T C N/N N N -‘3 3′- G A G A A G N N N N/-‘5 | 5′-CTCTTCN NNN-3′ 3′-GAGAAGNNNN -5′ | 5′ NNN |
EciI | 5′- G G C G G A N9 N N/-‘3 3′- C C G C C T N9/N N -‘5 | 5′-GGCGGAN9NN -3′ 3′-CCGCCTN9 NN-5′ | 3′ NN |
Eco53kI | 5′- G A G/C T C -‘3 3′- C T C/G A G -‘5 | 5′-GAG CTC-3′ 3′-CTC GAG-5′ | Blunt |
EcoNI | 5′- C C T N N/N N N A G G -‘3 3′- G G A N N N/N N T C C -‘5 | 5′-CCTNN NNNAGG-3′ 3′-GGANNN NNTCC-5′ | 5′ N |
EcoO109I | 5′- R G/G N C C Y -‘3 3′- Y C C N G/G R -‘5 | 5′-RG GNCCY-3′ 3′-YCCNG GR-5′ | 5′ GNC |
EcoP15I | 5′- C A G C A G N25/N N -‘3 3′- G T C G T C N25 N N/-‘5 | 5′-CAGCAGN25 NN-3′ 3′-GTCGTCN25NN -5′ | 5′ NN |
EcoRI | 5′- G/A A T T C -‘3 3′- C T T A A/G -‘5 | 5′-G AATTC-3′ 3′-CTTAA G-5′ | 5′ AATT |
EcoRV | 5′- G A T/A T C -‘3 3′- C T A/T A G -‘5 | 5′-GAT ATC-3′ 3′-CTA TAG-5′ | Blunt |
Esp3I | 5′- C G T C T C N/N N N N -‘3 3′- G C A G A G N N N N N/-‘5 | 5′-CGTCTCN NNNN-3′ 3′-GCAGAGNNNNN -5′ | 5′ NNNN |
FatI | 5′-/C A T G -‘3 3′- G T A C/-‘5 | 5′- CATG-3′ 3′-GTAC -5′ | 5′ CATG |
FauI | 5′- C C C G C N4/N N -‘3 3′- G G G C G N4 N N/-‘5 | 5′-CCCGCN4 NN-3′ 3′-GGGCGN4NN -5′ | 5′ NN |
Fnu4HI | 5′- G C/N G C -‘3 3′- C G N/C G -‘5 | 5′-GC NGC-3′ 3′-CGN CG-5′ | 5′ N |
FokI | 5′- G G A T G N9/N N N N -‘3 3′- C C T A C N9 N N N N/-‘5 | 5′-GGATGN9 NNNN-3′ 3′-CCTACN9NNNN -5′ | 5′ NNNN |
FseI | 5′- G G C C G G/C C -‘3 3′- C C/G G C C G G -‘5 | 5′-GGCCGG CC-3′ 3′-CC GGCCGG-5′ | 3′ CCGG |
FspEI | 5′- C C N12/N N N N -‘3 3′- G G N12 N N N N/-‘5 | 5′-CCN12 NNNN-3′ 3′-GGN12NNNN -5′ | 5′ NNNN |
FspI | 5′- T G C/G C A -‘3 3′- A C G/C G T -‘5 | 5′-TGC GCA-3′ 3′-ACG CGT-5′ | Blunt |
HaeII | 5′- R G C G C/Y -‘3 3′- Y/C G C G R -‘5 | 5′-RGCGC Y-3′ 3′-Y CGCGR-5′ | 3′ GCGC |
HaeIII | 5′- G G/C C -‘3 3′- C C/G G -‘5 | 5′-GG CC-3′ 3′-CC GG-5′ | Blunt |
HgaI | 5′- G A C G C N5/N N N N N -‘3 3′- C T G C G N5 N N N N N/-‘5 | 5′-GACGCN5 NNNNN-3′ 3′-CTGCGN5NNNNN -5′ | 5′ NNNNN |
HhaI | 5′- G C G/C -‘3 3′- C/G C G -‘5 | 5′-GCG C-3′ 3′-C GCG-5′ | 3′ CG |
HinP1I | 5′- G/C G C -‘3 3′- C G C/G -‘5 | 5′-G CGC-3′ 3′-CGC G-5′ | 5′ CG |
HincII | 5′- G T Y/R A C -‘3 3′- C A R/Y T G -‘5 | 5′-GTY RAC-3′ 3′-CAR YTG-5′ | Blunt |
HindIII | 5′- A/A G C T T -‘3 3′- T T C G A/A -‘5 | 5′-A AGCTT-3′ 3′-TTCGA A-5′ | 5′ AGCT |
HinfI | 5′- G/A N T C -‘3 3′- C T N A/G -‘5 | 5′-G ANTC-3′ 3′-CTNA G-5′ | 5′ ANT |
HpaI | 5′- G T T/A A C -‘3 3′- C A A/T T G -‘5 | 5′-GTT AAC-3′ 3′-CAA TTG-5′ | Blunt |
HphI | 5′- G G T G A N7 N/-‘3 3′- C C A C T N7/N -‘5 | 5′-GGTGAN7N -3′ 3′-CCACTN7 N-5′ | 3′ N |
Hpy166II | 5′- G T N/N A C -‘3 3′- C A N/N T G -‘5 | 5′-GTN NAC-3′ 3′-CAN NTG-5′ | Blunt |
Hpy188I | 5′- T C N/G A -‘3 3′- A G/N C T -‘5 | 5′-TCN GA-3′ 3′-AG NCT-5′ | 3′ N |
Hpy188III | 5′- T C/N N G A -‘3 3′- A G N N/C T -‘5 | 5′-TC NNGA-3′ 3′-AGNN CT-5′ | 5′ NN |
Hpy99I | 5′- C G W C G/-‘3 3′-/G C W G C -‘5 | 5′-CGWCG -3′ 3′- GCWGC-5′ | 3′ CGWCG |
HpyAV | 5′- C C T T C N5 N/-‘3 3′- G G A A G N5/N -‘5 | 5′-CCTTCN5N -3′ 3′-GGAAGN5 N-5′ | 3′ N |
HpyCH4III | 5′- A C N/G T -‘3 3′- T G/N C A -‘5 | 5′-ACN GT-3′ 3′-TG NCA-5′ | 3′ N |
HpyCH4IV | 5′- A/C G T -‘3 3′- T G C/A -‘5 | 5′-A CGT-3′ 3′-TGC A-5′ | 5′ CG |
HpyCH4V | 5′- T G/C A -‘3 3′- A C/G T -‘5 | 5′-TG CA-3′ 3′-AC GT-5′ | Blunt |
I-CeuI | 5′- T A A C T A T A A C G G T C C T A A/G G T A G C G A A -‘3 3′- A T T G A T A T T G C C A G/G A T T C C A T C G C T T -‘5 | 5′-TAACTATAACGGTCCTAA GGTAGCGAA-3′ 3′-ATTGATATTGCCAG GATTCCATCGCTT-5′ | 3′ CTAA |
I-SceI | 5′- T A G G G A T A A/C A G G G T A A T -‘3 3′- A T C C C/T A T T G T C C C A T T A -‘5 | 5′-TAGGGATAA CAGGGTAAT-3′ 3′-ATCCC TATTGTCCCATTA-5′ | 3′ ATAA |
KasI | 5′- G/G C G C C -‘3 3′- C C G C G/G -‘5 | 5′-G GCGCC-3′ 3′-CCGCG G-5′ | 5′ GCGC |
KpnI | 5′- G G T A C/C -‘3 3′- C/C A T G G -‘5 | 5′-GGTAC C-3′ 3′-C CATGG-5′ | 3′ GTAC |
LpnPI | 5′- C C D G N10/N N N N -‘3 3′- G G H C N10 N N N N/-‘5 | 5′-CCDGN10 NNNN-3′ 3′-GGHCN10NNNN -5′ | 5′ NNNN |
MboI Sau3AI DpnII | 5′-/G A T C -‘3 3′- C T A G/-‘5 | 5′- GATC-3′ 3′-CTAG -5′ | 5′ GATC |
MboII | 5′- G A A G A N7 N/-‘3 3′- C T T C T N7/N -‘5 | 5′-GAAGAN7N -3′ 3′-CTTCTN7 N-5′ | 3′ N |
MfeI | 5′- C/A A T T G -‘3 3′- G T T A A/C -‘5 | 5′-C AATTG-3′ 3′-GTTAA C-5′ | 5′ AATT |
MluCI | 5′-/A A T T -‘3 3′- T T A A/-‘5 | 5′- AATT-3′ 3′-TTAA -5′ | 5′ AATT |
MluI | 5′- A/C G C G T -‘3 3′- T G C G C/A -‘5 | 5′-A CGCGT-3′ 3′-TGCGC A-5′ | 5′ CGCG |
MlyI | 5′- G A G T C N5/-‘3 3′- C T C A G N5/-‘5 | 5′-GAGTCN5 -3′ 3′-CTCAGN5 -5′ | Blunt |
MmeI | 5′- T C C R A C N18 N N/-‘3 3′- A G G Y T G N18/N N -‘5 | 5′-TCCRACN18NN -3′ 3′-AGGYTGN18 NN-5′ | 3′ NN |
MnlI | 5′- C C T C N6 N/-‘3 3′- G G A G N6/N -‘5 | 5′-CCTCN6N -3′ 3′-GGAGN6 N-5′ | 3′ N |
MscI | 5′- T G G/C C A -‘3 3′- A C C/G G T -‘5 | 5′-TGG CCA-3′ 3′-ACC GGT-5′ | Blunt |
MseI | 5′- T/T A A -‘3 3′- A A T/T -‘5 | 5′-T TAA-3′ 3′-AAT T-5′ | 5′ TA |
MslI | 5′- C A Y N N/N N R T G -‘3 3′- G T R N N/N N Y A C -‘5 | 5′-CAYNN NNRTG-3′ 3′-GTRNN NNYAC-5′ | Blunt |
MspA1I | 5′- C M G/C K G -‘3 3′- G K C/G M C -‘5 | 5′-CMG CKG-3′ 3′-GKC GMC-5′ | Blunt |
MspI HpaII | 5′- C/C G G -‘3 3′- G G C/C -‘5 | 5′-C CGG-3′ 3′-GGC C-5′ | 5′ CG |
MspJI | 5′- C N N R N9/N N N N -‘3 3′- G N N Y N9 N N N N/-‘5 | 5′-CNNRN9 NNNN-3′ 3′-GNNYN9NNNN -5′ | 5′ NNNN |
MwoI | 5′- G C N N N N N/N N G C -‘3 3′- C G N N/N N N N N C G -‘5 | 5′-GCNNNNN NNGC-3′ 3′-CGNN NNNNNCG-5′ | 3′ NNN |
NaeI | 5′- G C C/G G C -‘3 3′- C G G/C C G -‘5 | 5′-GCC GGC-3′ 3′-CGG CCG-5′ | Blunt |
NarI | 5′- G G/C G C C -‘3 3′- C C G C/G G -‘5 | 5′-GG CGCC-3′ 3′-CCGC GG-5′ | 5′ CG |
NciI | 5′- C C/S G G -‘3 3′- G G S/C C -‘5 | 5′-CC SGG-3′ 3′-GGS CC-5′ | 5′ S |
NcoI | 5′- C/C A T G G -‘3 3′- G G T A C/C -‘5 | 5′-C CATGG-3′ 3′-GGTAC C-5′ | 5′ CATG |
NdeI | 5′- C A/T A T G -‘3 3′- G T A T/A C -‘5 | 5′-CA TATG-3′ 3′-GTAT AC-5′ | 5′ TA |
NgoMIV | 5′- G/C C G G C -‘3 3′- C G G C C/G -‘5 | 5′-G CCGGC-3′ 3′-CGGCC G-5′ | 5′ CCGG |
NheI | 5′- G/C T A G C -‘3 3′- C G A T C/G -‘5 | 5′-G CTAGC-3′ 3′-CGATC G-5′ | 5′ CTAG |
NlaIII | 5′- C A T G/-‘3 3′-/G T A C -‘5 | 5′-CATG -3′ 3′- GTAC-5′ | 3′ CATG |
NlaIV | 5′- G G N/N C C -‘3 3′- C C N/N G G -‘5 | 5′-GGN NCC-3′ 3′-CCN NGG-5′ | Blunt |
NmeAIII | 5′- G C C G A G N19 N N/-‘3 3′- C G G C T C N19/N N -‘5 | 5′-GCCGAGN19NN -3′ 3′-CGGCTCN19 NN-5′ | 3′ NN |
NotI | 5′- G C/G G C C G C -‘3 3′- C G C C G G/C G -‘5 | 5′-GC GGCCGC-3′ 3′-CGCCGG CG-5′ | 5′ GGCC |
NruI | 5′- T C G/C G A -‘3 3′- A G C/G C T -‘5 | 5′-TCG CGA-3′ 3′-AGC GCT-5′ | Blunt |
NsiI | 5′- A T G C A/T -‘3 3′- T/A C G T A -‘5 | 5′-ATGCA T-3′ 3′-T ACGTA-5′ | 3′ TGCA |
NspI | 5′- R C A T G/Y -‘3 3′- Y/G T A C R -‘5 | 5′-RCATG Y-3′ 3′-Y GTACR-5′ | 3′ CATG |
Nt.AlwI | 5′- G G A T C N N N N/-‘3 3′-/C C T A G N N N N -‘5 | 5′-GGATCNNNN -3′ 3′- CCTAGNNNN-5′ | 3′ GGATCNNNN |
Nt.BbvCI | 5′- C C/T C A G C -‘3 3′-/G G A G T C G -‘5 | 5′-CC TCAGC-3′ 3′- GGAGTCG-5′ | 3′ CC |
Nt.BsmAI | 5′- G T C T C N/-‘3 3′-/C A G A G N -‘5 | 5′-GTCTCN -3′ 3′- CAGAGN-5′ | 3′ GTCTCN |
Nt.BspQI | 5′- G C T C T T C N/-‘3 3′-/C G A G A A G N -‘5 | 5′-GCTCTTCN -3′ 3′- CGAGAAGN-5′ | 3′ GCTCTTCN |
Nt.BstNBI | 5′- G A G T C N N N N/-‘3 3′-/C T C A G N N N N -‘5 | 5′-GAGTCNNNN -3′ 3′- CTCAGNNNN-5′ | 3′ GAGTCNNNN |
PI-PspI | 5′- T G G C A A A C A G C T A T T A T/G G G T A T T A T G G G T -‘3 3′- A C C G T T T G T C G A T/A A T A C C C A T A A T A C C C A -‘5 | 5′-TGGCAAACAGCTATTAT GGGTATTATGGGT-3′ 3′-ACCGTTTGTCGAT AATACCCATAATACCCA-5′ | 3′ TTAT |
PI-SceI | 5′- A T C T A T G T C G G G T G C/G G A G A A A G A G G T A A T -‘3 3′- T A G A T A C A G C C/C A C G C C T C T T T C T C C A T T A -‘5 | 5′-ATCTATGTCGGGTGC GGAGAAAGAGGTAAT-3′ 3′-TAGATACAGCC CACGCCTCTTTCTCCATTA-5′ | 3′ GTGC |
PacI | 5′- T T A A T/T A A -‘3 3′- A A T/T A A T T -‘5 | 5′-TTAAT TAA-3′ 3′-AAT TAATT-5′ | 3′ AT |
PciI | 5′- A/C A T G T -‘3 3′- T G T A C/A -‘5 | 5′-A CATGT-3′ 3′-TGTAC A-5′ | 5′ CATG |
PflMI | 5′- C C A N N N N/N T G G -‘3 3′- G G T N/N N N N A C C -‘5 | 5′-CCANNNN NTGG-3′ 3′-GGTN NNNNACC-5′ | 3′ NNN |
PleI | 5′- G A G T C N4/N -‘3 3′- C T C A G N4 N/-‘5 | 5′-GAGTCN4 N-3′ 3′-CTCAGN4N -5′ | 5′ N |
PluTI | 5′- G G C G C/C -‘3 3′- C/C G C G G -‘5 | 5′-GGCGC C-3′ 3′-C CGCGG-5′ | 3′ GCGC |
PmeI | 5′- G T T T/A A A C -‘3 3′- C A A A/T T T G -‘5 | 5′-GTTT AAAC-3′ 3′-CAAA TTTG-5′ | Blunt |
PmlI | 5′- C A C/G T G -‘3 3′- G T G/C A C -‘5 | 5′-CAC GTG-3′ 3′-GTG CAC-5′ | Blunt |
PpuMI | 5′- R G/G W C C Y -‘3 3′- Y C C W G/G R -‘5 | 5′-RG GWCCY-3′ 3′-YCCWG GR-5′ | 5′ GWC |
PshAI | 5′- G A C N N/N N G T C -‘3 3′- C T G N N/N N C A G -‘5 | 5′-GACNN NNGTC-3′ 3′-CTGNN NNCAG-5′ | Blunt |
PsiI-v2 | 5′- T T A/T A A -‘3 3′- A A T/A T T -‘5 | 5′-TTA TAA-3′ 3′-AAT ATT-5′ | Blunt |
PspGI | 5′-/C C W G G -‘3 3′- G G W C C/-‘5 | 5′- CCWGG-3′ 3′-GGWCC -5′ | 5′ CCWGG |
PspOMI | 5′- G/G G C C C -‘3 3′- C C C G G/G -‘5 | 5′-G GGCCC-3′ 3′-CCCGG G-5′ | 5′ GGCC |
PspXI | 5′- V C/T C G A G B -‘3 3′- B G A G C T/C V -‘5 | 5′-VC TCGAGB-3′ 3′-BGAGCT CV-5′ | 5′ TCGA |
PstI | 5′- C T G C A/G -‘3 3′- G/A C G T C -‘5 | 5′-CTGCA G-3′ 3′-G ACGTC-5′ | 3′ TGCA |
PvuI | 5′- C G A T/C G -‘3 3′- G C/T A G C -‘5 | 5′-CGAT CG-3′ 3′-GC TAGC-5′ | 3′ AT |
PvuII | 5′- C A G/C T G -‘3 3′- G T C/G A C -‘5 | 5′-CAG CTG-3′ 3′-GTC GAC-5′ | Blunt |
RsaI | 5′- G T/A C -‘3 3′- C A/T G -‘5 | 5′-GT AC-3′ 3′-CA TG-5′ | Blunt |
RsrII | 5′- C G/G W C C G -‘3 3′- G C C W G/G C -‘5 | 5′-CG GWCCG-3′ 3′-GCCWG GC-5′ | 5′ GWC |
SacI | 5′- G A G C T/C -‘3 3′- C/T C G A G -‘5 | 5′-GAGCT C-3′ 3′-C TCGAG-5′ | 3′ AGCT |
SacII | 5′- C C G C/G G -‘3 3′- G G/C G C C -‘5 | 5′-CCGC GG-3′ 3′-GG CGCC-5′ | 3′ GC |
SalI | 5′- G/T C G A C -‘3 3′- C A G C T/G -‘5 | 5′-G TCGAC-3′ 3′-CAGCT G-5′ | 5′ TCGA |
SapI BspQI | 5′- G C T C T T C N/N N N -‘3 3′- C G A G A A G N N N N/-‘5 | 5′-GCTCTTCN NNN-3′ 3′-CGAGAAGNNNN -5′ | 5′ NNN |
Sau96I | 5′- G/G N C C -‘3 3′- C C N G/G -‘5 | 5′-G GNCC-3′ 3′-CCNG G-5′ | 5′ GNC |
SbfI | 5′- C C T G C A/G G -‘3 3′- G G/A C G T C C -‘5 | 5′-CCTGCA GG-3′ 3′-GG ACGTCC-5′ | 3′ TGCA |
ScaI | 5′- A G T/A C T -‘3 3′- T C A/T G A -‘5 | 5′-AGT ACT-3′ 3′-TCA TGA-5′ | Blunt |
ScrFI | 5′- C C/N G G -‘3 3′- G G N/C C -‘5 | 5′-CC NGG-3′ 3′-GGN CC-5′ | 5′ N |
SexAI | 5′- A/C C W G G T -‘3 3′- T G G W C C/A -‘5 | 5′-A CCWGGT-3′ 3′-TGGWCC A-5′ | 5′ CCWGG |
SfaNI | 5′- G C A T C N5/N N N N -‘3 3′- C G T A G N5 N N N N/-‘5 | 5′-GCATCN5 NNNN-3′ 3′-CGTAGN5NNNN -5′ | 5′ NNNN |
SfcI | 5′- C/T R Y A G -‘3 3′- G A Y R T/C -‘5 | 5′-C TRYAG-3′ 3′-GAYRT C-5′ | 5′ TRYA |
SfiI | 5′- G G C C N N N N/N G G C C -‘3 3′- C C G G N/N N N N C C G G -‘5 | 5′-GGCCNNNN NGGCC-3′ 3′-CCGGN NNNNCCGG-5′ | 3′ NNN |
SfoI | 5′- G G C/G C C -‘3 3′- C C G/C G G -‘5 | 5′-GGC GCC-3′ 3′-CCG CGG-5′ | Blunt |
SgrAI | 5′- C R/C C G G Y G -‘3 3′- G Y G G C C/R C -‘5 | 5′-CR CCGGYG-3′ 3′-GYGGCC RC-5′ | 5′ CCGG |
SmaI | 5′- C C C/G G G -‘3 3′- G G G/C C C -‘5 | 5′-CCC GGG-3′ 3′-GGG CCC-5′ | Blunt |
SmlI | 5′- C/T Y R A G -‘3 3′- G A R Y T/C -‘5 | 5′-C TYRAG-3′ 3′-GARYT C-5′ | 5′ TYRA |
SnaBI | 5′- T A C/G T A -‘3 3′- A T G/C A T -‘5 | 5′-TAC GTA-3′ 3′-ATG CAT-5′ | Blunt |
SpeI | 5′- A/C T A G T -‘3 3′- T G A T C/A -‘5 | 5′-A CTAGT-3′ 3′-TGATC A-5′ | 5′ CTAG |
SphI | 5′- G C A T G/C -‘3 3′- C/G T A C G -‘5 | 5′-GCATG C-3′ 3′-C GTACG-5′ | 3′ CATG |
SrfI | 5′- G C C C/G G G C -‘3 3′- C G G G/C C C G -‘5 | 5′-GCCC GGGC-3′ 3′-CGGG CCCG-5′ | Blunt |
SspI | 5′- A A T/A T T -‘3 3′- T T A/T A A -‘5 | 5′-AAT ATT-3′ 3′-TTA TAA-5′ | Blunt |
StuI | 5′- A G G/C C T -‘3 3′- T C C/G G A -‘5 | 5′-AGG CCT-3′ 3′-TCC GGA-5′ | Blunt |
StyD4I | 5′-/C C N G G -‘3 3′- G G N C C/-‘5 | 5′- CCNGG-3′ 3′-GGNCC -5′ | 5′ CCNGG |
StyI | 5′- C/C W W G G -‘3 3′- G G W W C/C -‘5 | 5′-C CWWGG-3′ 3′-GGWWC C-5′ | 5′ CWWG |
SwaI | 5′- A T T T/A A A T -‘3 3′- T A A A/T T T A -‘5 | 5′-ATTT AAAT-3′ 3′-TAAA TTTA-5′ | Blunt |
TaqI-v2 | 5′- T/C G A -‘3 3′- A G C/T -‘5 | 5′-T CGA-3′ 3′-AGC T-5′ | 5′ CG |
TfiI | 5′- G/A W T C -‘3 3′- C T W A/G -‘5 | 5′-G AWTC-3′ 3′-CTWA G-5′ | 5′ AWT |
TseI ApeKI | 5′- G/C W G C -‘3 3′- C G W C/G -‘5 | 5′-G CWGC-3′ 3′-CGWC G-5′ | 5′ CWG |
Tsp45I | 5′-/G T S A C -‘3 3′- C A S T G/-‘5 | 5′- GTSAC-3′ 3′-CASTG -5′ | 5′ GTSAC |
TspRI | 5′- N N C A S T G N N/-‘3 3′-/N N G T S A C N N -‘5 | 5′-NNCASTGNN -3′ 3′- NNGTSACNN-5′ | 3′ NNCASTGNN |
Tth111I PflFI | 5′- G A C N/N N G T C -‘3 3′- C T G N N/N C A G -‘5 | 5′-GACN NNGTC-3′ 3′-CTGNN NCAG-5′ | 5′ N |
XbaI | 5′- T/C T A G A -‘3 3′- A G A T C/T -‘5 | 5′-T CTAGA-3′ 3′-AGATC T-5′ | 5′ CTAG |
XcmI | 5′- C C A N N N N N/N N N N T G G -‘3 3′- G G T N N N N/N N N N N A C C -‘5 | 5′-CCANNNNN NNNNTGG-3′ 3′-GGTNNNN NNNNNACC-5′ | 3′ N |
XhoI PaeR7I | 5′- C/T C G A G -‘3 3′- G A G C T/C -‘5 | 5′-C TCGAG-3′ 3′-GAGCT C-5′ | 5′ TCGA |
XmaI TspMI | 5′- C/C C G G G -‘3 3′- G G G C C/C -‘5 | 5′-C CCGGG-3′ 3′-GGGCC C-5′ | 5′ CCGG |
XmnI | 5′- G A A N N/N N T T C -‘3 3′- C T T N N/N N A A G -‘5 | 5′-GAANN NNTTC-3′ 3′-CTTNN NNAAG-5′ | Blunt |
ZraI | 5′- G A C/G T C -‘3 3′- C T G/C A G -‘5 | 5′-GAC GTC-3′ 3′-CTG CAG-5′ | Blunt |