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Digestion of Methylated DNA:

Sensitivity to CpG Methylation

Methylated DNA substrates were prepared with SssI methyltransferase.

Enzymes which Recognition Sequences Contain CpG Inside
Single letter code:
R = G or A; 
Y = C or T; 
W = A or T; 
M = A or C; 		 K = G or T; 
S = C or G;
H = A, C or T;
V = A, C or G;		 B = C, G or T;
D = A, G or T;
N = G, A, T or C.
Enzyme Sequence Effect
AatII GACGTC blocked
AjiI CACGTC blocked
BcnI
FastDigest® NciI (BcnI)		 CCSGG impaired
Bsh1236I
FastDigest® Bsh1236I		 CGCG blocked
Bsh1285I CGRYCG blocked
BshTI
FastDigest® AgeI (BshTI)		 ACCGGT blocked
Bsp68I TCGCGA blocked
Bsp119I
FastDigest® Bsp119I		 TTCGAA blocked
Bsu15I
FastDigest® ClaI (Bsu15I)		 ATCGAT blocked
CseI GACGC blocked
Cfr9I CCCGGG impaired
Cfr10I
FastDigest® BsrFI (Cfr10I)		 RCCGGY blocked
Cfr42I CCGCGG blocked
CpoI CGGWCCG blocked
Eco47III
FastDigest® AfeI (Eco47III)		 AGCGCT blocked
Eco52I CGGCCG blocked
Eco72I CACGTG blocked
Eco88I
FastDigest® AvaI (Eco88I)		 CYCGRG impaired
Eco105I
FastDigest® SnaBI (Eco105I) 		TACGTA blocked
EheI
FastDigest® EheI		 GGCGCC blocked
Esp3I
FastDigest® BsmBI (Esp3I)		 CGTCTC blocked
FspAI
FastDigest® FspAI 		RTGCGCAY blocked
HhaI
FastDigest® HhaI		 GCGC blocked
Hin1I
FastDigest® BsaHI (Hin1I)		 GRCGYC blocked
Hin6I
FastDigest® HinP1I (Hin6I)		 GCGC blocked
HpaII
FastDigest® HpaII		 CCGG blocked
Kpn2I
FastDigest® Kpn2I		 TCCGGA blocked
MauBI CGCGCGCG blocked
MbiI GAGCGG impaired
MluI
FastDigest® MluI		 ACGCGT blocked
MreI
FastDigest® MreI		 CGCCGGCG blocked
NotI
FastDigest® NotI		 GCGGCCGC blocked
NsbI
FastDigest® FspI (NsbI)		 TGCGCA blocked
PauI GCGCGC blocked
PdiI
FastDigestŪ NaeI (PdiI)		 GCCGGC blocked
Pfl23II
FastDigestŪ BsiWI (Pfl23II)		 CGTACG blocked
Ppu21I
FastDigestŪ BsaAI (Ppu21I)		 YACGTR blocked
Psp1406I
FastDigest® AclI (Psp1406I)		 AACGTT blocked
PvuI
FastDigest® PvuI		 CGATCG blocked
SalI
FastDigest® SalI		 GTCGAC blocked
SgrDI CGTCGACG blocked
SgsI
FastDigest® AscI (SgsI)		 GGCGCGCC blocked
SfaAI
FastDigest® AsiSI (SfaAI)		 GCGATCGC blocked
SmaI
FastDigest® SmaI		 CCCGGG blocked
SmuI CCCGC blocked
SsiI
FastDigest® AciI (SsiI)		 CCGC blocked
TaiI
FastDigest® TaiI		 ACGT blocked
TaqI
FastDigest® TaqI		 TCGA not blocked
TauI GCSGC blocked
XhoI
FastDigest® XhoI		 CTCGAG impaired

Enzymes which Recognition Sequences may Overlap CpG
Single letter code:
R = G or A; 
Y = C or T; 
W = A or T; 
M = A or C; 		 K = G or T; 
S = C or G;
H = A, C or T;
V = A, C or G;		 B = C, G or T;
D = A, G or T;
N = G, A, T or C.

C = 5-methylcytosine (m5C)
Recognition sequence is indicated in bold.
Overlapping methylase sequence is green shaded.

 A   B   C D   E   G H K L   M N O   P R   S T V X

Enzyme

 Sequence  Effect
AarI 5'...CACCTGCG...3'
3'...GTGGACGC...5'		 impaired
AasI
FastDigest® DrdI (AasI)		 5'...CGAC(N)6GTC...3'
3'...GCTG(N)6CAG...5'

5'...CGAC(N)6TCCG...3'
3'...GCTG(N)6AGGC...5'

5'...GACG(N)5GTC...3'
3'...CTGC(N)5CAG...5'

5'...GACG(N)4CGTC...3'
3'...CTGC(N)4GCAG...5'

 impaired

not determined


impaired



not determined

Acc65I
FastDigest® Acc65I		 5'...GGTACCG...3'
3'...CCATGGC...5'

5'...CGGTACCG...3'
3'...GCCATGGC...5'

 impaired


blocked
AdeI
FastDigest® DraIII (AdeI)		 5'...CACGNNGTG...3'
3'...GTGCNNCAC...5'

5'...CACGNCGTG...3'
3'...GTGCNGCAC...5'

 impaired


blocked
AjuI
FastDigest® AjuI		 5'...CGAA(N)7TTGG...3'
3'...GCTT(N)7AACC...5'		 not blocked
AlfI 5'...GCA(N)6TGCG...3'
3'...CGT(N)6ACGC...5'		 not blocked
AloI 5'...CGAAC(N)6TCC...3'
3'...GCTTG(N)6AGG...5'

5'...GAAC(N)6TCCG...3'
3'...CTTG(N)6AGGC...5'

5'...GAACG(N)6TCC...3'
3'...CTTGC(N)6AGG...5'

 blocked

not blocked



not blocked
Alw21I
FastDigest® Alw21I		 5'...CGWGCWCG...3'
3'...GCWCGWGC...5'		 not blocked
Alw26I
FastDigest® Alw26I		 5'...GTCTCG...3'
3'...CAGAGC...5'

5'...CGTCTC...3'
3'...GCAGAG...5'

 not blocked


blocked
Alw44I
FastDigest® ApaLI (Alw44I)		 5'...GTGCACG...3'
3'...CACGTGC...5'		 blocked
ApaI
FastDigest® ApaI		 5'...GGGCCCG...3'
3'...CCCGGGC...5'

5'...CGGGCCCG...3'
3'...GCCCGGGC...5'

 impaired


impaired
BamHI
FastDigest® BamHI		 5'...CGGATCCG...3'
3'...GCCTAGGC...5'		 not blocked
BfuI 5'...CGTATCC...3'
3'...GCATAGG...5'

5'...GTATCCG...3'
3'...CATAGGC...5'

 not blocked


not blocked
BglI
FastDigest® BglI		 5'...GCCG(N)3CGGC...3'
3'...CGGC(N)3GCCG...5'

5'...GCC(N)5GGCG...3'
3'...CGG(N)5CCGC...5'

5'...CGCC(N)5GGCG...3'
3'...GCGG(N)5CCGC...5'

 not blocked

 

slowed


blocked
Bme1390I
FastDigest® ScrFI (Bme1390I)		 5'...CCGGG...3'
3'...GGCCC...5'		 blocked
BoxI
FastDigest® PshAI (BoxI)		 5'...GACG(N)3GTC...3'
3'...CTGC(N)3CAG...5'

5'...GACGNNCGTC...3'
3'...CTGCNNGCAG...5'

5'...GAC(N)4GTCG...3'
3'...CTG(N)4CAGC...5'

 impaired

 

blocked


not blocked
BpiI
FastDigest® BbsI (BpiI)		 5'...GAAGACG...3'
3'...CTTCTGC...5'

5'...CGAAGAC...3'
3'...GCTTCTG...5'

 not blocked


not blocked
BplI 5'...CGAG(N)5CTCG...3'
3'...GCTC(N)5GAGC...5'		 not blocked
Bpu10I 5'...CCTNAGCG...3'
3'...GGANTCGC...5'		 not blocked
Bpu1102I
FastDigest® BlpI (Bpu1102I)		 5'...CGCTNAGCG...3'
3'...GCGANTCGC...5'		 not blocked
BseDI
FastDigest® BsaJI (BseDI)		 5'...CCGCGG...3'
3'...GGCGCC...5'		 not blocked
BseGI
FastDigest® BseGI 		5'...CGGATG...3'
3'...GCCTAC...5'		 not blocked
BseJI
FastDigest® BsaBI (BseJI)		 5'...GAT(N)4ATCG...3'
3'...CTA(N)4TAGC...5'

5'...CGAT(N)4ATCG...3'
3'...GCTA(N)4TAGC...5'

 not blocked


not determined
BseLI
FastDigest® BslI (BseLI)		 5'...CCG(N)6GG...3'
3'...GGC(N)6CC...5'

5'...CCG(N)5CGG...3'
3'...GGC(N)5GCC...5'

 impaired



blocked
BseMI 5'...CGCAATG...3'
3'...GCGTTAC...5'		 not blocked
BseSI
FastDigest® BseSI		 5'...CGKGCMCG...3'
3'...GCMCGKGC...5'		 not blocked
BseXI 5'...CGCAGCG...3'
3'...GCGTCGC...5'		 not blocked
BshNI
FastDigest® BanI (BshNI)		 5'...GGYRCCG...3'
3'...CCRYGGC...5'

5'...CGGYRCCG...3'
3'...GCCRYGGC...5'

5'...GGCGCC...3'
3'...CCGCGG...5'

 impaired


blocked


impaired
Bsp120I
FastDigest® Bsp120I		 5'...GGGCCCG...3'
3'...CCCGGGC...5'		 blocked
Bsp143I 5'...GATCG...3'
3'...CTAGC...5'		 blocked
BspLI
FastDigest® NlaIV (BspLI)		 5'...GGNNCCG...3'
3'...CCNNGGC...5'

5'...CGGNNCCG...3'
3'...GCCNNGGC...5'

 not blocked


blocked
BspPI 5'...GGATCG...3'
3'...CCTAGC...5'

5'...CGGATC...3'
3'...GCCTAG...5'

 not blocked


not blocked
Bst1107I
FastDigest® BstZ17I (Bst1107I) 		5'...GTATACG...3'
3'...CATATGC...5'

5'...CGTATACG...3'
3'...GCATATGC...5'

 impaired


blocked
BsuRI
FastDigest® HaeIII (BsuRI)		 5'...CGGCCG...3'
3'...GCCGGC...5'		 not blocked
BveI 5'...ACCTGCG...3'
3'...TGGACGC...5'		 impaired
CfrI 5'...YGGCCG...3'
3'...RCCGGC...5'		 blocked
Cfr13I
FastDigest® Sau96I (Cfr13I)		 5'...GGNCCG...3'
3'...CCNGGC...5'		 blocked
Csp6I
FastDigest® Csp6I		 5'...CGTACG...3'
3'...GCATGC...5'		 not blocked
DpnI
FastDigest® DpnI		 5'...Gm6ATCG...3'
3'...CTm6AGC...5'		 not blocked
Eam1104I
FastDigest® EarI (Eam1104I)		 5'...CTCTTCG...3'
3'...GAGAAGC...5'		 not blocked
Eam1105I
FastDigest® Eam1105I		 5'...GACG(N)3CGTC...3'
3'...CTGC(N)3GCAG...5'

5'...GAC(N)5GTCG...3'
3'...CTG(N)5CAGC...5'

5'...CGAC(N)5GTCG...3'
3'...GCTG(N)5CAGC...5'

 not blocked

 

not blocked



not determined
Ecl136II
FastDigest® Ecl136II		 5'...GAGCTCG...3'
3'...CTCGAGC...5'

5'...CGAGCTCG...3'
3'...GCTCGAGC...5'

 impaired


blocked
Eco24I 5'...CGRGCYCG...3'
3'...GCYCGRGC...5'		 not blocked
Eco31I
FastDigest® Eco31I		 5'...GGTCTCG...3'
3'...CCAGAGC...5'

5'...CGGTCTC...3'
3'...GCCAGAG...5'

 not blocked


impaired
Eco32I
FastDigest® EcoRV (Eco32I)		 5'...CGATATCG...3'
3'...GCTATAGC...5'		 not blocked
Eco47I
FastDigest® AvaII (Eco47I)		 5'...GGWCCG...3'
3'...CCWGGC...5'		 blocked
Eco91I
FastDigest® Eco91I		 5'...CGGTNACCG...3'
3'...GCCANTGGC...5'		 not blocked
EcoRI
FastDigest® EcoRI		 5'...CGAATTCG...3'
3'...GCTTAAGC...5'		 impaired
FaqI 5'...GGGACG...3'
3'...CCCTGC...5'

5'...CGGGAC...3'
3'...GCCCTG...5'

 blocked


blocked
Hin4I 5'...CGAY(N)5VTC...3'
3'...GCTR(N)5BAG...5'

5'...GAY(N)5VTCG...3'
3'...CTR(N)5BAGC...5'

5'...CGAY(N)5VTCG...3'
3'...GCTR(N)5BAGC...5'		 impaired


impaired



not determined
HincII
FastDigest® HincII		 5'...GTYRACG...3'
3'...CARYTGC...5'

5'...CGTYRACG...3'
3'...GCARYTGC...5'

5'...GTCGAC...3'
3'...CAGCTG...5'

 impaired


blocked


impaired
HinfI
FastDigest® HinfI		 5'...GANTCG...3'
3'...CTNAGC...5'

5'...CGANTCG...3'
3'...GCTNAGC...5'

 impaired


impaired
HphI 5'...CGGTGA...3'
3'...GCCACT...5'		 not blocked
Hpy8I
FastDigest® Hpy8I		 5'...GTNNACG...3'
3'...CANNTGC...5'

5'...CGTNNACG...3'
3'...GCANNGGC...5'

 impaired


not determined
HpyF10VI
FastDigest® HpyF10VI 		5'...GC(N)7GCG...3'
3'...CG(N)7CGC...5'

5'...CGC(N)7GCG...3'
3'...GCG(N)7CGC...5'

5'...GCG(N)6GC...3'
3'...CGC(N)6CG...5'

5'...GCG(N)5CGC...3'
3'...CGC(N)5GCG...5'

 impaired


blocked



impaired



not determined
KpnI
FastDigest® KpnI 		5'...CGGTACCG...3'
3'...GCCATGGC...5'		 not blocked
KspAI
FastDigest® HpaI (KspAI)		 5'...GTTAACG...3'
3'...CAATTGC...5'

5'...CGTTAACG...3'
3'...GCAATTGC...5'

 impaired


blocked
Lsp1109I
FastDigest® BbvI (Lsp1109I)		 5'...CGCAGCG...3'
3'...GCGTCGC...5'		 not blocked
LweI 5'...GCATCCG...3'
3'...CGTAGGC...5'		 impaired
MbiI 5'...CGAGCGG...3'
3'...GCTCGCC...5'		 blocked
MboI
FastDigest® MboI		 5'...CGATCG...3'
3'...GCTAGC...5'		 not blocked
MboII
FastDigest® MboII		 5'...CGAAGA...3'
3'...GCTTCT...5'		 not blocked
MnlI
FastDigest® MnlI		 5'...CCTCG...3'
3'...GGAGC...5'		 not blocked
MssI
FastDigest® MssI		 5'...GTTTAAACG...3'
3'...CAAATTTGC...5'

5'...CGTTTAAACG...3'
3'...GCAAATTTGC...5'

 not blocked


not blocked
Mva1269I
FastDigest® Mva1269I		 5'...GAATGCG...3'
3'...CTTACGC...5'

5'...CGAATGC...3'
3'...GCTTACG...5'

 not blocked


not blocked
NheI
FastDigest® NheI		 5'...GCTAGCG...3'
3'...CGATCGC...5'

5'...CGCTAGCG...3'
3'...GCGATCGC...5'

 impaired


blocked
NmuCI
FastDigest® NmuCI		 5'...GTCACG...3'
3'...CATGGC...5'

5'...CGTCACG...3'
3'...GCATCGC...5'

 impaired


impaired
OliI 5'...CACGNNCGTG...3'
3'...GTGCNNGCAC...5'		 impaired
PaeI
FastDigest® SphI (PaeI)

5'...CGCATGCG...3'
3'...GCGTACGC...5'

 not blocked
PdmI
FastDigest® PdmI		 5'...GAA(N)4TTCG...3'
3'...CTT(N)4AAGC...5'

5'...CGAA(N)4TTCG...3'
3'...GCTT(N)4AAGC...5'

 impaired


blocked
PfeI 5'...GAWTCG...3'
3'...CTWAGC...5'		 blocked
PfoI
FastDigest® PfoI		 5'...TCCGGGA...3'
3'...AGGCCCT...5'		 blocked
PpiI 5'...CGAAC(N)5CTC...3'
3'...GCTTG(N)5GAG...5'

5'...GAAC(N)5CTCG...3'
3'...CTTG(N)5GAGC...5'

5'...GAACG(N)4CTC...3'
3'...CTTGC(N)4GAG...5'

 not blocked


not blocked



impaired
PsuI
FastDigest® PsuI		 5'...CGGATCCG...3'
3'...GCCTAGGC...5'		 not blocked
PsyI 5'...GACGNNGTCG...3'
3'...CTGCNNCAGC...5'		 not blocked
RsaI
FastDigest® RsaI		 5'...GTACG...3'
3'...CATGC...5'

5'...CGTACG...3'
3'...GCATGC...5'

 impaired


blocked
SacI
FastDigest® SacI		 5'...CGAGCTCG...3'
3'...GCTCGAGC...5'		 not blocked
SatI
FastDigest® Fnu4HI (SatI)		 5'...GCGGC...3'
3'...CGCCG...5'

5'...GCNGCG...3'
3'...CGNCGC...5'

 blocked


blocked
SchI 5'...GAGTCG...3'
3'...CTCAGC...5'

5'...CGAGTC...3'
3'...GCTCAG...5'

 not blocked


not blocked
SduI
FastDigest® Bsp1286I (SduI)		 5'...CGDGCHCG...3'
3'...GCHCGDGC...5'		 not blocked
FastDigest® SfaNI (BmsI) 5'...GCATCG...3'
3'...CGTAGC...5'		 impaired
SfiI 5'...CGGCC(N)5GGCCG...3'
3'...GCCGG(N)5CCGGC...5'

5'...GGCCG(N)4GGCC...3'
3'...CCGGC(N)4CCGG...5'

5'...GGCCG(N)3CGGCC...3'
3'...CCGGC(N)3GCCGG...5'

 not blocked



impaired


blocked
SmoI 5'...CTCGGT...3'
3'...GAGCCA...5'		 not blocked
TaaI
FastDigest® TaaI		 5'...ACGGT...3'
3'...TGCCA...5'		 impaired
TstI 5'...CACG(N)5TCCG...3'
3'...GTGC(N)5AGGC...5'		 not blocked
XapI
FastDigest® XapI		 5'...CGAATTCG...3'
3'...GCTTAAGC...5'		 not blocked
XceI 5'...RCATGCG...3'
3'...YGTACGC...5'

5'...CGCATGCG...3'
3'...GCGTACGC...5'

 not blocked


not determined
XmiI
FastDigest® AccI (XmiI)		 5'...GTCGAC...3'
3'...CAGCTG...5'

5'...GTMKACG...3'
3'...CAKMTGC...5'

 blocked


blocked

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Updated rugsėjo 03, 2008 15:08