List of restriction enzyme cutting sites: C–D

Main articles: List of restriction enzyme cutting sites and Restriction enzyme

Legend of nucleobases
Code	Nucleotide represented
A	Adenine (A)
C	Cytosine (C)
G	Guanine (G)
T	Thymine (T)
N	A, C, G or T
M	A or C
R	A or G
W	A or T
Y	C or T
S	C or G
K	G or T
H	A, C or T
B	C, G or T
V	A, C or G
D	A, G or T

This article contains a list of the most studied restriction enzymes whose names start with C to D inclusive. It contains apporoximately 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

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See also

Restriction enzymes

C

Current list/Article:

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' CCAN₆GT
3' GGTN₆CA 5' ---CCAN₆GTN₈NNNNNNN --- 3'
3' ---GGTN₆CAN₈N NNNNNN--- 5' — None on May 2010 —

CjePI Campylobacter jejuni P116 5' CCAN₇TC
3' GGTN₇AG 5' ---CCAN₇TCN₇NNNNNNN --- 3'
3' ---GGTN₇AGN₇N 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' CAAN₄NGTGG
3' GTTN₄NCACC 5' ---CAAN₅GTGGN₈NNNN --- 3'
3' ---GTTN₅CACCN₈NN 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' ---AAGGAGN₁₇NNN --- 3'
3' ---TTCCTCN₁₇N 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

This list is incomplete; you can help by expanding it.

D

Current list/Article:

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' GACN₆GTC
3' CTGN₆CAG 5' ---GACNNNN NNGTC--- 3'
3' ---CTGNN NNNNCAG--- 5' AasI, DseDI

DriI

Dactylococcopsis salina

5' GACN₅GTC
3' CTGN₅CAG

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' GACN₆GTC
3' CTGN₆CAG 5' ---GACNNNN NNGTC--- 3'
3' ---CTGNN NNNNCAG--- 5' AasI, DrdI

This list is incomplete; you can help by expanding it.

Current list/Article:

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 SKh, 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 M. Berg, John L. Tymoczko, Lubert Stryer; Web content by Neil D. Clarke (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.

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