Cleavage Specificities Generated with the use of Methylases
Specificities generated by methylation at a subset of recognition sequences of degenerate restriction endonucleases.
| Restriction Endonuclease |
Methylation | Cleavage Specificity |
| Acc I [GT(A/C)(G/T)AC] | M.Taq I [TCGmA] | GT(A/C)TAC |
| Aha II [GPuCGPyC] | M.Hha I [GmCGC] | GPuCGTC |
| Ava I [CPyCGPuG] | M.Taq I [TCGmA] | CPyCGGG |
| Ava I [CPyCGPuG] | M.Hpa II [CmCGG] | CPyCGAG |
| Ava I [CPyCGPuG] | M.Hpa II
[CmCGG] + M.Taq I [TCGmA] |
CCCGAG |
| Ban II [GPuGCPyC] | M.Alu I [AGmCT] | GPuGCCC |
| Ban II [GPuGCPyC] | M.Hae III [GGmCC] | GPuGCTC |
| Ban II [GPuGCPyC] | M.Hae III
[GGmCC] + M.Alu I [AGmCT] |
GGGCTC |
| Bsp1286 I [G(A/G/T)GC(A/C/T)C] | M.Alu I [AGmCT] | G(G/T)GC(A/C/T)C |
| Bsp1286 I [G(A/G/T)GC(A/C/T)C] | M.Hae III [GGmCC] | G(A/G/T)GC(A/T)C |
| Bsp1286 I [G(A/G/T)GC(A/C/T)C] | M.Hae III
[GGmCC] + M.Alu I [AGmCT] |
G(G/T)GC(A/T)C |
| HgiA I [G(A/T)GC(A/T)C] | M.Alu I [AGmCT] | G(A/T)GCAC |
| Hinc II [GTPyPuAC] | M.Taq I [TCGmA] | GTPyAAC |
| Sau96 I [GGNCC] | M.Hae III [GGmCC] | GGACC |
| ScrF I [CCNGG] | M.Hpa II [CmCGG] | CCAGG |
Specificities generated by methylation at the boundaries of overlapping recognition sequences of a restriction endonucleases and a methylase.
| Restriction Endonuclease |
Methylation (a) | Subset
Blocked by Methylation (b) |
| Aha II [GPuCGPyC] | M.Hpa II [CmCGG] | CCGGCGPyC |
| Alu I [AGCT] | M.Pst I [CTGCmAG] | AGCTGCAG |
| Ava II [GG(A/T)CC] | M.Hpa II [CmCGG] | CCGG(A/T)CC |
| BamH I [GGATCC] | M.Msp I [mCCGG] | CCGGATCC |
| Bgl I [GCCN5GGC] | M.Hae III [GGmCC] | GGCCN5GGC |
| BstU I [CGCG] | M.Hha I [GmCGC] | GCGCG |
| BstX I [CCAN6TGG] | M.Hae III [GGmCC] | GGCCAN5TGG |
| Cla I [ATCGAT] | dam [GmATC] | GATCGAT |
| Cla I [ATCGAT] | M.Hha I [GmCGC] | GAATCGAT |
| Dde I [CTNAG] | M.Alu I [AGmCT] | AGCTNAG |
| EcoR V [GATATC] | M.Taq I [TCGmA] | TCGATATC |
| Hinf I [GANTC] | M.Hph I [TmCACC] | GANTCACC |
| Hinf I [GANTC] | M.Mbo II [GAAGmA] (c) | GAAGANTC |
| Hinf I [GANTC] | M.Taq I [TCGmA] | TCGANTC |
| Hph I [GGTGA] | dam [GmATC] | GGTGATC |
| Mbo I [GATC] | M.Cla I [ATCGmAT] | ATCGATC |
| Mbo I [GATC] | M.Taq I [TCGmA] | TCGATC |
| Mbo I [GATC] | M.Mbo II [GAAGmA] | GAAGATC |
| Mbo II [GAAGA] | dam [GmATC] | GAAGATC |
| Msp I [CCGG] | M.BamH I [GGATmCC] | CCGGATCC |
| Msp I [CCGG] | M.Hae III [GGmCC] | GGCCGG |
| Mst I [TGCGCA] | M.H1 [GCNGC + GGmCC] (d) | GCTGCGCA |
| Nae I [GCCGGC] | M.Hae III [GGmCC] | GGCCGGC |
| Nco I [CCATGG] | M.Hae III [GGmCC] | GGCCATGG |
| Nhe I [GCTAGC] | M.Alu I [AGmCT] | AGCTAGC |
| Not I [GCGGCCGC] | M.FnuD I [mCGCG] | CGCGGCCGC |
| Nru I [TCGCGA] | dam [GmATC] | GATCGCGA |
| Pst I [CTGCAG] | M.Alu I [AGmCT] | AGCTGCAG |
| Pst I [CTGCAG] | M.H1 [GCNGC + GGmCC] |
GCTGCAG |
| Pvu II [CAGCTG] | M.H1 [GCNGC + GGmCC] |
GCAGCTG |
| Sac II [CCGCGG] | M.Hae III [GGmCC] | GGCCGCGG |
| Sau3A I [GATC] | M.Hph I [TmCACC] | GATCACC |
| Taq I [TCGA] | M.Cla I [ATCGmAT] | ATCGAT |
| Taq I [TCGA] | dam [GmATC] | GATCGA |
| Xba I [TCTAGA] | dam [GmATC] | GATCTAGA |
| Xmn I [GAAN4TTC] | M.Taq I [TCGmA] | TCGAAN4TTC |
(a) Nomenclature for methylases from: Smith, H.O. and Nathans, D. (1973) J. Mol. Biol. 81, 419. Methylase specificities from: McClelland, M. et al. (1994) Nucl. Acids Res. 22, 3640-3659.
(b) Sequences blocked by methylation are non-palindromic with only the 5´ -3´ strand written. For example, the sequence blocked by the M.Pst I-Alu I combination could also be written CTGCAGCT.
(c) McClelland, M., Nelson, M. and Cantor, C. (1985) Nucl. Acids Res. 13, 7171.
(d) M.H1 isolated from bacteriophage infected cells and methylates the sequences GCNGC and GGCC. The site of methylation within GCNGC has not been established. This methylase is similar to the Phi3T methylase [Noyer-Weider, M. et al. (1985) Gene 35, 143. Weiner, M and Nelson, M. unpublished results.