Specificities generated by methylation at a
subset of recognition sequences of degenerate restriction endonucleases.
Restriction
Endonuclease |
Methylation |
Cleavage
Specificity |
| AccI
[GT(A/C)(G/T)AC] |
M.TaqI [TCGmA] |
GT(A/C)TAC |
| AhaII
[GPuCGPyC] |
M.HhaI [GmCGC] |
GPuCGTC |
| AvaI
[CPyCGPuG] |
M.TaqI [TCGmA] |
CPyCGGG |
| AvaI
[CPyCGPuG] |
M.HpaII
[CmCGG] |
CPyCGAG |
| AvaI
[CPyCGPuG] |
M.HpaII
[CmCGG] +
M.TaqI [TCGmA] |
CCCGAG |
| BanII
[GPuGCPyC] |
M.AluI [AGmCT] |
GPuGCCC |
| BanII
[GPuGCPyC] |
M.HaeIII
[GGmCC] |
GPuGCTC |
| BanII
[GPuGCPyC] |
M.HaeIII
[GGmCC] +
M.AluI [AGmCT] |
GGGCTC |
| Bsp1286I
[G(A/G/T)GC(A/C/T)C] |
M.AluI [AGmCT] |
G(G/T)GC(A/C/T)C |
| Bsp1286I
[G(A/G/T)GC(A/C/T)C] |
M.HaeIII
[GGmCC] |
G(A/G/T)GC(A/T)C |
| Bsp1286I
[G(A/G/T)GC(A/C/T)C] |
M.HaeIII
[GGmCC] +
M.AluI [AGmCT] |
G(G/T)GC(A/T)C |
| HgiAI
[G(A/T)GC(A/T)C] |
M.AluI [AGmCT] |
G(A/T)GCAC |
| HincII
[GTPyPuAC] |
M.TaqI [TCGmA] |
GTPyAAC |
| Sau96I [GGNCC] |
M.HaeIII
[GGmCC] |
GGACC |
| ScrFI [CCNGG] |
M.HpaII
[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) |
| AhaII
[GPuCGPyC] |
M.HpaII
[CmCGG] |
CCGGCGPyC |
| AluI [AGCT] |
M.PstI
[CTGCmAG] |
AGCTGCAG |
| AvaII
[GG(A/T)CC] |
M.HpaII
[CmCGG] |
CCGG(A/T)CC |
| BamHI [GGATCC] |
M.MspI [mCCGG] |
CCGGATCC |
| BglI
[GCCN5GGC] |
M.HaeIII
[GGmCC] |
GGCCN5GGC |
| BstUI [CGCG] |
M.HhaI [GmCGC] |
GCGCG |
| BstXI
[CCAN6TGG] |
M.HaeIII
[GGmCC] |
GGCCAN5TGG |
| ClaI [ATCGAT] |
dam [GmATC] |
GATCGAT |
| ClaI [ATCGAT] |
M.HhaI [GmCGC] |
GAATCGAT |
| DdeI [CTNAG] |
M.AluI [AGmCT] |
AGCTNAG |
| EcoRV [GATATC] |
M.TaqI [TCGmA] |
TCGATATC |
| HinfI [GANTC] |
M.HphI
[TmCACC] |
GANTCACC |
| HinfI [GANTC] |
M.MboII
[GAAGmA] (c) |
GAAGANTC |
| HinfI [GANTC] |
M.TaqI [TCGmA] |
TCGANTC |
| HphI [GGTGA] |
dam [GmATC] |
GGTGATC |
| MboI [GATC] |
M.ClaI
[ATCGmAT] |
ATCGATC |
| MboI [GATC] |
M.TaqI [TCGmA] |
TCGATC |
| MboI [GATC] |
M.MboII
[GAAGmA] |
GAAGATC |
| MboII [GAAGA] |
dam [GmATC] |
GAAGATC |
| MspI [CCGG] |
M.BamHI
[GGATmCC] |
CCGGATCC |
| MspI [CCGG] |
M.HaeIII
[GGmCC] |
GGCCGG |
| MstI [TGCGCA] |
M.H1 [GCNGC +
GGmCC] (d) |
GCTGCGCA |
| NaeI [GCCGGC] |
M.HaeIII
[GGmCC] |
GGCCGGC |
| NcoI [CCATGG] |
M.HaeIII
[GGmCC] |
GGCCATGG |
| NheI [GCTAGC] |
M.AluI [AGmCT] |
AGCTAGC |
| NotI
[GCGGCCGC] |
M.FnuDI
[mCGCG] |
CGCGGCCGC |
| NruI [TCGCGA] |
dam [GmATC] |
GATCGCGA |
| PstI [CTGCAG] |
M.AluI [AGmCT] |
AGCTGCAG |
| PstI [CTGCAG] |
M.H1 [GCNGC +
GGmCC] |
GCTGCAG |
| PvuII [CAGCTG] |
M.H1 [GCNGC +
GGmCC] |
GCAGCTG |
| SacII [CCGCGG] |
M.HaeIII
[GGmCC] |
GGCCGCGG |
| Sau3AI [GATC] |
M.HphI
[TmCACC] |
GATCACC |
| TaqI [TCGA] |
M.ClaI
[ATCGmAT] |
ATCGAT |
| TaqI [TCGA] |
dam [GmATC] |
GATCGA |
| XbaI [TCTAGA] |
dam [GmATC] |
GATCTAGA |
| XmnI
[GAAN4TTC] |
M.TaqI [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-AluI 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.
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