Biology:List of restriction enzyme cutting sites: C–D

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Main pages: Biology:List of restriction enzyme cutting sites and Biology: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 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' 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

Enzyme PDB code Source Recognition sequence Cut Isoschizomers
DdeI Desulfovibrio desulfuricans 5' CTNAG
3' GANTC 		5' ---C   TNAG--- 3'
3' ---GANT   C--- 5'
BstDEI,  HpyF3I 
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.


Notes

  1. ↑ "Letter: A suggested nomenclature for bacterial host modification and restriction systems and their enzymes". J. Mol. Biol. 81 (3): 419–23. December 1973. doi:10.1016/0022-2836(73)90152-6. PMID 4588280. 
  2. ↑ "A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes". Nucleic Acids Res. 31 (7): 1805–12. April 2003. doi:10.1093/nar/gkg274. PMID 12654995. 
  3. ↑ "3. Protein Structure and Function". Biochemistry. San Francisco: W. H. Freeman. 2002. ISBN 0-7167-4684-0. https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=books&doptcmdl=GenBookHL&term=stryer%5Bbook%5D+AND+215168%5Buid%5D&rid=stryer.chapter.280. 
  4. ↑ 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. 
  5. ↑ "Specificity of restriction endonucleases and DNA modification methyltransferases a review (Edition 3)". Gene 92 (1-2): 1–248. August 1990. doi:10.1016/0378-1119(90)90486-B. PMID 2172084. 
  6. ↑ "Structure and function of type II restriction endonucleases". Nucleic Acids Res. 29 (18): 3705–27. September 2001. doi:10.1093/nar/29.18.3705. PMID 11557805. 
  7. ↑ 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. PMID 6294607. 
  8. ↑ "Crystal structure of Citrobacter freundii restriction endonuclease Cfr10I at 2.15 A resolution". J Mol Biol 255 (1): 176–86. January 1996. doi:10.1006/jmbi.1996.0015. PMID 8568865. 



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