List of restriction enzyme cutting sites: C–D
This article contains a list of the most studied restriction enzymes whose names start with C to D inclusive. It contains approximately 80 enzymes.
The following information is given:
Enzyme : Accepted name of the molecule , according to the internationally adopted nomenclature [ 1] [ 2] , and bibliographical references . (Further reading: see the section "Nomenclature " in the article "Restriction enzyme ".)
PDB code : Code used to identify the structure of a protein in the PDB database of protein structures. The 3D atomic structure of a protein provides highly valuable information to understand the intimate details of its mechanism of action[ 3] [ 4] .
Source : Organism that naturally produces the enzyme.
Recognition sequence : Sequence of DNA recognized by the enzyme and to which it specifically binds.
Cut : Cutting site and DNA products of the cut. The recognition sequence and the cutting site usually match, but sometimes the cutting site can be dozens of nucleotides away from the recognition site[ 5] [ 6] .
Isoschizomers and neoschizomers : An isoschizomer is an enzyme that recognizes the same sequence as another. A neoschizomer is a special type of isoschizomer that recognizes the same sequence as another, but cuts in a different manner. A maximum number of 8-10 most common isoschizomers are indicated for every enzyme but there may be many more. Neoschizomers are shown in bold and green color font (e.g.: BamHI ). When "None on date " is indicated, that means that there were no registered isoschizomers in the databases on that date with a clearly defined cutting site. Isoschizomers indicated in white font and grey background correspond to enzymes not listed in the current lists:
as in this not listed enzyme:
EcoR70I
Whole list navigation
Restriction enzymes
C
Enzyme
PDB code
Source
Recognition sequence
Cut
Isoschizomers
CacI
Clostridium acetobutylicum N1-4081
5' GATC
3' CTAG
5' --- GATC--- 3'
3' ---CTAG --- 5'
Cac8I
Clostridium acetobutylicum ABKn8
5' GCNNGC
3' CGNNCG
5' ---GCN NGC--- 3'
3' ---CGN NCG--- 5'
CaiI
Comamonas acidovarans Iti19-021
5' CAGNNNCTG
3' GTCNNNGAC
5' ---CAGNNN CTG--- 3'
3' ---GTC NNNGAC--- 5'
AlwNI
CauI
Chloroflexus aurantiacus
5' GGWCC
3' CCWGG
5' ---G GWCC--- 3'
3' ---CCWG G--- 5'
BamNxI, BcuAI, BsrAI, Eco47I, FspMSI, HgiCII, HgiJI, SmuEI
CauII
Chloroflexus aurantiacus
5' CCSGG
3' GGSCC
5' ---CC SGG--- 3'
3' ---GGS CC--- 5'
AhaI, AseII, AsuC2I, BcnI, Eco1831I , EcoHI , Kpn49kII , NciI
CauB3I
Chloroflexus aurantiacus B3
5' TCCGGA
3' AGGCCT
5' ---T CCGGA--- 3'
3' ---AGGCC T--- 5'
Aor13HI, BbvAIII, BseAI, BspEI, BspMII, Kpn2I, MroI, PtaI
CbiI
Clostridium bifermentans B-4
5' TTCGAA
3' AAGCTT
5' ---TT CGAA--- 3'
3' ---AAGC TT--- 5'
Asp10HI, Bim19I, BsiCI, BspT104I, Csp45I, LspI, NspV, SspRFI
CboI
Clostridium botulinum
5' CCGG
3' GGCC
5' ---C CGG--- 3'
3' ---GGC C--- 5'
CbrI
Citrobacter braakii 1146
5' CCWGG
3' GGWCC
5' ---CC WGG--- 3'
3' ---GGW CC--- 5'
AorI, BseBI, Bse24I, BstNI, BstOI, Bst2UI, BthDI, EcoRII , MvaI
CciNI
Curtobacterium citreus
5' GCGGCCGC
3' CGCCGGCG
5' ---GC GGCCGC--- 3'
3' ---CGCCGG CG--- 5'
CcoI
Clostridium coccoides B-2
5' GCCGGC
3' CGGCCG
5' ---GCC GGC--- 3'
3' ---CGG CCG--- 5'
CcrI
Caulobacter crescentus CB-13
5' CTCGAG
3' GAGCTC
5' ---C TCGAG--- 3'
3' ---GAGCT C--- 5'
CcuI
Chroococcidiopsis cubana
5' GGNCC
3' CCNGG
5' ---G GNCC--- 3'
3' ---CCNG G--- 5'
AsuI, Bal228I, BavBII, BsiZI, BspF4I, Cfr13I, Nsp7121I, PspPI
CcyI
Clostridium cylindrosporum
5' GATC
3' CTAG
5' --- GATC--- 3'
3' ---CTAG --- 5'
BfuCI, Bsp67I, Bst19II, CviAI, FnuCI, MboI, NmeCI, SauMI
CdiI
Citrobacter freundii RFL2
5' CATCG
3' GTAGC
5' ---CATC G--- 3'
3' ---GTAG C--- 5'
CelI
Citrobacter freundii RFL6
5' GGATCC
3' CCTAGG
5' ---G GATCC--- 3'
3' ---CCTAG G--- 5'
AliI, ApaCI, AsiI, BamHI , CelI, NspSAIV, RspLKII, SolI, Uba4009I
CelII
Coccochloris elabens 17a
5' GCTNAGC
3' CGANTCG
5' ---GC TNAGC--- 3'
3' ---CGANT CG--- 5'
CeqI
Corynebacterium equi
5' GATATC
3' CTATAG
5' ---GAT ATC--- 3'
3' ---CTA TAG--- 5'
CflI
Cellulomonas flavigena
5' CTGCAG
3' GACGTC
5' ---CTGCA G--- 3'
3' ---G ACGTC--- 5'
AjoI, BloHII, CflI, CstI, Ecl37kI, PaePI, PstI, SalPI, Srl5DI, Sst12I
CfoI
Clostridium formicoaceticum
5' GCGC
3' CGCG
5' ---GCG C--- 3'
3' ---C GCG--- 5'
AspLEI, BspLAI, BstHHI, FnuDIII, HhaI, HinP1I , HsoI , HspAI , SciNI
CfrI
Citrobacter freundii RFL2
5' YGGCCR
3' RCCGGY
5' ---Y GGCCR--- 3'
3' ---RCCGG Y--- 5'
Cfr6I
Citrobacter freundii RFL6
5' CAGCTG
3' GTCGAC
5' ---CAG CTG--- 3'
3' ---GTC GAC--- 5'
Cfr9I
Citrobacter freundii
5' CCCGGG
3' GGGCCC
5' ---C CCGGG--- 3'
3' ---GGGCC C--- 5'
AhyI, EaeAI, EclRI, Pac25I, PspAI, TspMI, XcyI, XmaI, XmaCI
Cfr10I [ 7] [ 8]
1CFR
Citrobacter freundii RFL10
5' RCCGGY
3' YGGCCR
5' ---R CCGGY--- 3'
3' ---YGGCC R--- 5'
Cfr13I
Citrobacter freundii RFL13
5' GGNCC
3' CCNGG
5' ---G GNCC--- 3'
3' ---CCNG G--- 5'
AsuI, Bal228I, BavBII, BsiZI, BspF4I, FmuI , Nsp7121I, PspPI
Cfr42I
Citrobacter freundii RFL42
5' CCGCGG
3' GGCGCC
5' ---CCGC GG--- 3'
3' ---GG CGCC--- 5'
SacII, CscI, HgaI
CfrA4I
Citrobacter freundii A4
5' CTGCAG
3' GACGTC
5' ---CTGCA G--- 3'
3' ---G ACGTC--- 5'
AjoI, BloHII, CflI, CstI, Ecl2zI, PaePI, PstI, SalPI, Srl5DI, Sst12I
CfrBI
Citrobacter freundii 4111
5' CCWWGG
3' GGWWCC
5' ---C CWWGG--- 3'
3' ---GGWWC C--- 5'
CfrJ4I
Citrobacter freundii J4
5' CCCGGG
3' GGGCCC
5' ---CCC GGG--- 3'
3' ---GGG CCC--- 5'
AhyI, CfrJ4I , EaeAI, EclRI, Pac25I, SmaI , TspMI, XcyI, XmaI
CfuI
Caulobacter fusiformis BC-25
5' GATC
3' CTAG
5' ---GA TC--- 3'
3' ---CT AG--- 5'
CfuII
Caulobacter fusiformis BC-25
5' CTGCAG
3' GACGTC
5' ---CTGCA G--- 3'
3' ---G ACGTC--- 5'
AjoI, AliAJI, CfuII, HalII, PaePI, Psp23I, PstI, SalPI, Srl5DI, YenI
ChaI
Corynebacterium halofytica
5' GATC
3' CTAG
5' ---GATC --- 3'
3' --- CTAG--- 5'
BfuCI , Bsp2095I , BspKT6I BtkII , FnuCI , MboI , NmeCI , SsiAI
CjeI
Campylobacter jejuni P37
5' CCAN6 GT
3' GGTN6 CA
5' ---CCAN6 GTN8 NNNNNNN --- 3'
3' ---GGTN6 CAN8 N NNNNNN--- 5'
— None on May 2010 —
CjePI
Campylobacter jejuni P116
5' CCAN7 TC
3' GGTN7 AG
5' ---CCAN7 TCN7 NNNNNNN --- 3'
3' ---GGTN7 AGN7 N NNNNNN--- 5'
— None on May 2010 —
ClaI
Caryophanon latum L
5' ATCGAT
3' TAGCTA
5' ---AT CGAT--- 3'
3' ---TAGC TA--- 5'
AagI, BanIII, BavCI, Bsa29I, BseCI, BspDI, Bsu15I, BsuTUI
CltI
Caryophanon latum
5' GGCC
3' CCGG
5' ---GG CC--- 3'
3' ---CC GG--- 5'
CpfI
Clostridium perfringens
5' GATC
3' CTAG
5' --- GATC--- 3'
3' ---CTAG --- 5'
AspMDI, Bsp67I, Bst19II, CcyI, FnuCI, MboI, NphI, SauMI
CpoI
Caseobacter polymorphus
5' CGGWCCG
3' GCCWGGC
5' ---CG GWCCG--- 3'
3' ---GCCWG GC--- 5'
CscI
Calothrix scopulorum
5' CCGCGG
3' GGCGCC
5' ---CCGC GG--- 3'
3' ---GG CGCC--- 5'
Cfr42I, SacII, HgaI
CsiAI
Corynebacterium sp. A
5' ACCGGT
3' TGGCCA
5' ---A CCGGT--- 3'
3' ---TGGCC A--- 5'
AgeI, AsiAI,
AsiGI,
BshTI
CspAI, PinAI
CsiBI
Corynebacterium sp. B
5' GCGGCCGC
3' CGCCGGCG
5' ---GC GGCCGC--- 3'
3' ---CGCCGG CG--- 5'
CspI
Corynebacterium sp.
5' CGGWCCG
3' GCCWGGC
5' ---CG GWCCG--- 3'
3' ---GCCWG GC--- 5'
Csp6I
Corynebacterium sp. RFL6
5' GTAC
3' CATG
5' ---G TAC--- 3'
3' ---CAT G--- 5'
AfaI , CviQI, CviRII, HpyBI , PabI, PlaAII , RsaI , RsaNI,
Csp45I
Clostridium sporogenes
5' TTCGAA
3' AAGCTT
5' ---TT CGAA--- 3'
3' ---AAGC TT--- 5'
Asp10HI, Bim19I, BsiCI, BspT104I, FspII, LspI, NspV, SspRFI
CspAI
Corynebacterium sp. 301
5' ACCGGT
3' TGGCCA
5' ---A CCGGT--- 3'
3' ---TGGCC A--- 5'
AgeI, AsiAI,
AsiGI,
BshTI
CsiAI, PinAI
CspBI
Corynebacterium sp. B
5' GCGGCCGC
3' CGCCGGCG
5' ---GC GGCCGC--- 3'
3' ---CGCCGG CG--- 5'
CspCI
Citrobacter sp. 2144
5' CAAN4 NGTGG
3' GTTN4 NCACC
5' ---CAAN5 GTGGN8 NNNN --- 3'
3' ---GTTN5 CACCN8 NN NN--- 5'
— None on May 2010 —
Csp68KI
Cyanothece sp. BH68K
5' GGWCC
3' CCWGG
5' ---G GWCC--- 3'
3' ---CCWG G--- 5'
BamNxI, BcuAI, BsrAI, Eco47I, FspMSI, HgiCII, Kzo49I, SmuEI
Csp68KII
Cyanothece sp. BH68K
5' TTCGAA
3' AAGCTT
5' ---TT CGAA--- 3'
3' ---AAGC TT--- 5'
Asp10HI, Bim19I, BsiCI, BstBI, Csp45I, LspI, PlaII, SviI
Csp68KIII
Cyanothece sp. BH68K
5' ATGCAT
3' TACGTA
5' ---ATGCA T--- 3'
3' ---T ACGTA--- 5'
BfrBI, EcoT22I, Mph1103I, NsiI, PinBI, Ppu10I, SspD5II, Zsp2I
Csp68KVI
Cyanothece sp. BH68K
5' CGCG
3' GCGC
5' ---CG CG--- 3'
3' ---GC GC--- 5'
BepI, Bpu95I, Bsp123I, BstFNI, BstUI, BtkI, FalII, SelI , ThaI
CspKVI
Cyanothece sp. BH68K
5' CGCG
3' GCGC
5' ---CG CG--- 3'
3' ---GC GC--- 5'
CstI
Clostridium sticklandii
5' CTGCAG
3' GACGTC
5' ---CTGCA G--- 3'
3' ---G ACGTC--- 5'
AjoI, AliAJI, CfrA4I, HalII, MhaAI, Pfl21I, PstI, SflI, Srl5DI, YenI
CstMI
Corynebacterium striatum M82B
5' AAGGAG
3' TTCCTC
5' ---AAGGAGN17 NNN --- 3'
3' ---TTCCTCN17 N NN--- 5'
— None on May 2010 —
CthII
Clostridium thermocellum
5' CCWGG
3' GGWCC
5' ---CC WGG--- 3'
3' ---GGW CC--- 5'
ApaORI, BseBI, Bse24I, Bst2UI, BstNI, BstM6I, EcoRII , MvaI
CviAI
Chlorella NC64A (PBCV-1)
5' GATC
3' CTAG
5' --- GATC--- 3'
3' ---CTAG --- 5'
Bme12I, Bsp67I, Bst19II, CcyI, FnuCI, MgoI, NphI, SauMI
CviAII
Chlorella NC64A (PBCV-1)
5' CATG
3' GTAC
5' ---C ATG--- 3'
3' ---GTA C--- 5'
CviBI
Chlorella NC64A (NC-1A)
5' GANTC
3' CTNAG
5' ---G ANTC--- 3'
3' ---CTNA G--- 5'
CviJI
Chlorella NC64A (IL-3A)
5' RGCY
3' YCGR
5' ---RG CY--- 3'
3' ---YC GR--- 5'
CviQI
Chlorella NC64A (NY-2A)
5' GTAC
3' CATG
5' ---G TAC--- 3'
3' ---CAT G--- 5'
AfaI , Csp6I, CviRII, HpyBI , PabI, PlaAII , RsaI , RsaNI,
CviRI
Chlorella NC64A (XZ-6E)
5' TGCA
3' ACGT
5' ---TG CA--- 3'
3' ---AC GT--- 5'
CviRII
Chlorella NC64A (XZ-6E)
5' GTAC
3' CATG
5' ---G TAC--- 3'
3' ---CAT G--- 5'
AfaI , Csp6I, CviQI, HpyBI , PabI, PlaAII , RsaI , RsaNI,
CviTI
Chlorella NC64A (CA-1A)
5' RGCY
3' YCGR
5' ---RG CY--- 3'
3' ---YC GR--- 5'
CvnI
Chromatium vinosum
5' CCTNAGG
3' GGANTCC
5' ---CC TNAGG--- 3'
3' ---GGANT CC--- 5'
AocI, AxyI, Bse21I, Bsu36I, Eco81I, MstII, SauI, SshAI
D
Enzyme
PDB code
Source
Recognition sequence
Cut
Isoschizomers
DdeI
Desulfovibrio desulfuricans
5' CTNAG
3' GANTC
5' ---C TNAG--- 3'
3' ---GANT C--- 5'
DmaI
Deleya marina
5' CAGCTG
3' GTCGAC
5' ---CAG CTG--- 3'
3' ---GTC GAC--- 5'
DpaI
Deleya pacifica
5' AGTACT
3' TCATGA
5' ---AGT ACT--- 3'
3' ---TCA TGA--- 5'
Acc113I, AssI,
BmcAI, Bpa34I,
Eco255I, RflFII, ScaI, ZrmI
DpnI
Diplococcus pneumoniae G41
5' GATC
3' CTAG
5' ---GA TC--- 3'
3' ---CT AG--- 5'
DpnII
Diplococcus pneumoniae G41
5' GATC
3' CTAG
5' --- GATC--- 3'
3' ---CTAG --- 5'
AspMDI, Bsp105I, BspFI, BstMBI, CpfI, Kzo9I, NdeII, Sth368I
DraI
Deinococcus radiophilus
5' TTTAAA
3' AAATTT
5' ---TTT AAA--- 3'
3' ---AAA TTT--- 5'
AhaIII, PauAII, SruI
DraII
Deinococcus radiophilus
5' RGGNCCY
3' YCCNGGR
5' ---RG GNCCY--- 3'
3' ---YCCNG GR--- 5'
DraIII
Deinococcus radiophilus
5' CACNNNGTG
3' GTGNNNCAC
5' ---CACNNN GTG--- 3'
3' ---GTG NNNCAC--- 5'
AdeI, BstIZ316I
DrdI
Deinococcus radiodurans
5' GACN6 GTC
3' CTGN6 CAG
5' ---GACNNNN NNGTC--- 3'
3' ---CTGNN NNNNCAG--- 5'
AasI, DseDI
DriI
Dactylococcopsis salina
5' GACN5 GTC
3' CTGN5 CAG
5' ---GACNNN NNGTC--- 3'
3' ---CTGNN NNNCAG--- 5'
AhdI, AspEI,
BmeRI,
BspOVI,
Eam1105I, EclHKI, NruGI
DsaI
Dactylococcopsis salina
5' CCRYGG
3' GGYRCC
5' ---C CRYGG--- 3'
3' ---GGYRC C--- 5'
DsaII
Dactylococcopsis salina
5' GGCC
3' CCGG
5' ---GG CC--- 3'
3' ---CC GG--- 5'
DsaIII
Dactylococcopsis salina
5' RGATCY
3' YCTAGR
5' ---R GATCY--- 3'
3' ---YCTAG R--- 5'
DsaIV
Dactylococcopsis salina
5' GGWCC
3' CCWGG
5' ---G GWCC--- 3'
3' ---CCWG G--- 5'
BamNxI, BcuAI, BsrAI, Eco47I, FspMSI, HgiEI, Kzo49I, SmuEI
DsaV
Dactylococcopsis salina
5' CCNGG
3' GGNCC
5' --- CCNGG--- 3'
3' ---GGNCC --- 5'
DseDI
Deinococcus sp. Dx
5' GACN6 GTC
3' CTGN6 CAG
5' ---GACNNNN NNGTC--- 3'
3' ---CTGNN NNNNCAG--- 5'
AasI, DrdI
Notes
^ Smith HO, Nathans D (December 1973). "Letter: A suggested nomenclature for bacterial host modification and restriction systems and their enzymes". J. Mol. Biol . 81 (3): 419– 23. doi :10.1016/0022-2836(73)90152-6 . PMID 4588280 .
^ Roberts RJ, Belfort M, Bestor T, Bhagwat AS, Bickle TA, Bitinaite J, Blumenthal RM, Degtyarev SK, Dryden DT, Dybvig K, Firman K, Gromova ES, Gumport RI, Halford SE, Hattman S, Heitman J, Hornby DP, Janulaitis A, Jeltsch A, Josephsen J, Kiss A, Klaenhammer TR, Kobayashi I, Kong H, Krüger DH, Lacks S, Marinus MG, Miyahara M, Morgan RD, Murray NE, Nagaraja V, Piekarowicz A, Pingoud A, Raleigh E, Rao DN, Reich N, Repin VE, Selker EU, Shaw PC, Stein DC, Stoddard BL, Szybalski W, Trautner TA, Van Etten JL, Vitor JM, Wilson GG, Xu SY (April 2003). "A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes" . Nucleic Acids Res . 31 (7): 1805– 12. doi :10.1093/nar/gkg274 . PMC 152790 . PMID 12654995 .
^ Jeremy MB, John LT, Lubert S (2002). "3. Protein Structure and Function" . Biochemistry . San Francisco: W. H. Freeman. ISBN 0-7167-4684-0 .
^ Anfinsen C.B. (1973). "Principles that Govern the Folding of Protein Chains". Science . 181 (4096): 223– 30. doi :10.1126/science.181.4096.223 . PMID 4124164 .
^ Kessler C, Manta V (August 1990). "Specificity of restriction endonucleases and DNA modification methyltransferases a review (Edition 3)". Gene . 92 (1– 2): 1– 248. doi :10.1016/0378-1119(90)90486-B . PMID 2172084 .
^ Pingoud A, Jeltsch A (September 2001). "Structure and function of type II restriction endonucleases" . Nucleic Acids Res . 29 (18): 3705– 27. doi :10.1093/nar/29.18.3705 . PMC 55916 . PMID 11557805 .
^ Janulaitis AA; Stakenas PS; Lebedenko EN; Berlin YuA (October 1982). "A new restriction endonuclease from Citrobacter freundii" . Nucleic Acids Res . 10 (20): 6521– 30. doi :10.1093/nar/10.20.6521 . PMC 326941 . PMID 6294607 .
^ Bozic D, Grazulis S, Siksnys V, Huber R (January 1996). "Crystal structure of Citrobacter freundii restriction endonuclease Cfr10I at 2.15 A resolution". J Mol Biol . 255 (1): 176– 86. doi :10.1006/jmbi.1996.0015 . PMID 8568865 .
Basic Concept Recognition sequence 4bp Recognition sequence 5bp Recognition sequence 6bp Recognition sequence 8bp Lists