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REBASE Methylation Sensitivity |
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Effects of methylation and other modifications on cleavage by restriction enzymes.
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Glossary of related terms: | |
| Cut | -- Not sensitive to methylation at the overlapping site. |
| Impaired | -- Rate of cleavage is lower than for unmethylated overlapping site. |
| Blocked | -- Will not cleave when overlapping site is methylated. |
| Some Blocked | -- Blocked by methylation of the overlapping site in some but not all flanking DNA contexts. |
| Variable | -- Conflicting reports of sensitivity to methylation at the overlapping site. |
| Untested | -- Effects of methylation at the overlapping site have not been tested. |
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Restriction enzymes usually have corresponding methyltransferases that
modify one or more of the bases in the recognition sequence, thereby protecting the host DNA
from the action of the restriction enzyme. The only known exceptions are PmeI and PacI. Thus all
restriction enzymes are sensitive to at least one kind of methylation, their cognate methylation. In some cases,
such as MboI and Sau3AI, the cognate methylases that protect against the action of the restriction
enzyme are different. M.MboI forms Gm6ATC, whereas M.Sau3AI forms GATm5C. The two corresponding
restriction enzymes are thus blocked by different methylations and it turns out that they can both
cut one another's DNA. This cannot be guaranteed however, and in general the methylation sensitivity of
each restriction must be tested experimentally. The results of such tests are being collected in REBASE.
This data is based on published literature references and many unpublished communications. Similar lists have been compiled previously - eg. McClelland, M., Nelson, M., Raschke, E. Nucleic Acids Res. 22: 3640-3659, 1994; and Kessler, C., Manta, V. Gene 92: 1-248, 1990. However, the results were not given in unambiguous, double-stranded form as is shown in REBASE, and many unpublished references were not thoroughly checked. In our tables, each specific data item relating to the methylation sensitivity of a restriction enzyme has been checked carefully and is both shown in full and rigorously referenced, in many cases with a comment describing how the data was generated. Many restriction enzymes are sensitive to methylation at bases other than those recognized by the cognate methylases. Sometimes, cleavage is blocked completely, but more often the rate of cleavage is affected and so depending upon the length of time of the digestion, or the amount of enzyme that is used, partial cleavage is often observed. Since rates are rarely measured and reported in the literature I have used the term "cleavage impaired" to describe these situations. It should be noted that the effects of methylation are often sequence dependent (i.e. flanking sequences can lead to large rate differences) there are many examples of apparently conflicting data in the literature. When this happens, I have tried to capture all results and provide references back to the original literature. If you come across data that is not presently included please contact us. |
Commercially available Type II restriction enzymes blocked by
| natural modifications: | ||
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2: 4: 5: 6: 8: 9: 25: 26: 30: 31: 32: |
gh m4 m5 m6 hC U fC cC Q dG 7d |
glucosylated-hydroxymethylcytosine N4-methylcytosine 5-methylcytosine 6-methyladenosine 5-hydroxymethylcytosine uracil 5-formylcytosine 5-carboxylcytosine queuosine deoxyarchaeosine 7-deazaguanine |
| synthetic modifications: | ||
|
1: 3: 7: 10: 11: 12: 13: 14: 15: 16: 17: 18: 19: 20: 21: 22: 23: 24: 27: 28: 29: |
m1 m3 hU 7Z 7E 7P 7N 8B 8M p5 EU PU NU EC PC NC zC pG VU VC VA |
1-methyadenosine 3-methylcytosine 5-hydroxymethyluracil 7-deazaadenine 7-ethynyladenine 7-phenyladenine 7-nitrophenyladenine 8-bromoadenine 8-methyladenine phosphoglucuronated 5-(4',5'-dihydroxypentyl) uracil 5-ethynyluracil 5-phenyluracil 5-(3-nitro)phenyluracil 5-ethynylcytosine 5-phenylcytosine 5-(3-nitrophenyl)cytosine 6-amino-5-nitro-3-(1'-beta-D-2'-deoxyribofuranosyl)-2(1H)-pyridone 2-amino-8-(1'-beta-D-2'-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one 5-vinyluracil 5-vinylcytosine 7-deaza-7-vinyladenine |