Recognition Sites in Common DNA Substrates
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Industry standards for enzyme unit definitions generally use DNA substrates other than plasmid DNA. It is therefore necessary to determine how many units of enzyme will be needed in cloning experiments involving plasmid vectors. Linear DNA such as lambda can be cleaved more efficiently than closed circular plasmid DNA, and fewer units of enzyme per microgram of DNA may be required for a complete digest. The number of sites per microgram of DNA must also be considered. For example, 1µg of lambda contains 0.0317 picomoles of DNA. For a 3,000bp plasmid there are 0.5pmol DNA in 1µg. Therefore, in 1µg of lambda DNA there will be fewer cut sites to digest than in 1µg of plasmid DNA. This table provides information on the number of recognition sites for Promega's restriction enzymes in various DNA substrates.
| Enzyme | Recognition Site | Number of Sites in: | |||||
|---|---|---|---|---|---|---|---|
| lambda | Ad2 | phiX174 | pUC18 | M13mp18 | pBR322 | ||
| AgeI | A/CCGGT | 13 | 5 | 0 | 0 | 0 | 0 |
| AluI | AG/CT | 143 | 158 | 24 | 16 | 27 | 17 |
| ApaI | GGGCC/C | 1 | 12 | 0 | 0 | 0 | 0 |
| BamHI | G/GATCC | 5 | 3 | 0 | 1 | 1 | 1 |
| BclI | T/GATCA | 8 | 5 | 0 | 0 | 0 | 0 |
| BglI | GCCNNNN/NGGC | 29 | 20 | 0 | 2 | 1 | 3 |
| BglII | A/GATCT | 6 | 11 | 0 | 0 | 1 | 0 |
| CfoI | GCG/C | 215 | 375 | 18 | 17 | 26 | 31 |
| ClaI | AT/CGAT | 15 | 2 | 0 | 0 | 2 | 1 |
| DdeI | C/TNAG | 104 | 97 | 14 | 6 | 29 | 8 |
| DpnI | GmeA/TC | 116 | 87 | 0 | 15 | 7 | 22 |
| EcoRI | G/AATTC | 5 | 5 | 0 | 1 | 1 | 1 |
| EcoRV | GAT/ATC | 21 | 9 | 0 | 0 | 0 | 1 |
| HaeIII | GG/CC | 149 | 216 | 11 | 11 | 15 | 22 |
| HhaI | GCG/C | 215 | 375 | 18 | 17 | 26 | 31 |
| HindIII | A/AGCTT | 7 | 12 | 0 | 1 | 1 | 1 |
| HinfI | G/ANTC | 148 | 72 | 21 | 6 | 27 | 10 |
| HpaII | C/CGG | 328 | 171 | 5 | 13 | 18 | 26 |
| I-PpoI | CTCTCTTAA/GGTAGC | 0 | 0 | 0 | 0 | 0 | 0 |
| KpnI | GGTAC/C | 2 | 8 | 0 | 1 | 1 | 0 |
| MboI | /GATC | 116 | 87 | 0 | 15 | 7 | 22 |
| MluI | M/CGCGT | 7 | 5 | 2 | 0 | 0 | 0 |
| MspI | C/CGG | 328 | 171 | 5 | 13 | 18 | 26 |
| NcoI | C/CATGG | 4 | 20 | 0 | 0 | 0 | 0 |
| NdeI | CA/TATG | 7 | 2 | 0 | 1 | 3 | 1 |
| NheI | G/CTAGC | 1 | 4 | 0 | 0 | 0 | 1 |
| NotI | GC/GGCCGC | 0 | 7 | 0 | 0 | 0 | 0 |
| PstI | CTGCA/G | 28 | 30 | 1 | 1 | 1 | 1 |
| PvuI | CGAT/CG | 3 | 7 | 0 | 2 | 1 | 1 |
| RsaI | GT/AC | 113 | 83 | 11 | 3 | 19 | 3 |
| SacI | GAGCT/C | 2 | 16 | 0 | 1 | 1 | 0 |
| SacII | CCGC/GG | 4 | 33 | 1 | 0 | 0 | 0 |
| SalI | G/TCGAC | 2 | 3 | 0 | 1 | 1 | 1 |
| ScaI | AGT/ACT | 5 | 5 | 0 | 1 | 0 | 1 |
| SgfI | GCGAT/CGC | 0 | 1 | 0 | 0 | 0 | 0 |
| SmaI | CCC/GGG | 3 | 12 | 0 | 1 | 1 | 0 |
| SpeI | A/CTAGT | 0 | 3 | 0 | 0 | 0 | 0 |
| SphI | GCATG/C | 6 | 8 | 0 | 1 | 1 | 1 |
| TaqI | T/CGA | 121 | 50 | 10 | 4 | 13 | 7 |
| XbaI | T/CTAGA | 1 | 5 | 0 | 1 | 1 | 0 |
| XhoI | C/TCGAG | 1 | 6 | 1 | 0 | 0 | 0 |