List of homing endonuclease cutting sites

The homing endonucleases are a special type of restriction enzymes encoded by introns or inteins. They act on the cellular DNA of the cell that synthesizes them; to be precise, in the opposite allele of the gene that encode them.[1]

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

Homing endonucleases

The list includes some of the most studied examples. The following concepts have been detailed:

Enzyme SF PDB code Source D SCL Recognition sequence Cut
I-AniI[2] H1 1P8K​ Aspergillus nidulans E mito 5' TTGAGGAGGTTTCTCTGTAAATAA
3' AACTCCTCCAAAGAGACATTTATT 		5' ---TTGAGGAGGTTTC   TCTGTAAATAA--- 3'
3' ---AACTCCTCC   AAAGAGACATTTATT--- 5'
I-CeuI[3][4][5][6] H1 2EX5​ Chlamydomonas eugametos E chloro 5' TAACTATAACGGTCCTAAGGTAGCGA
3' ATTGATATTGCCAGGATTCCATCGCT 		5' ---TAACTATAACGGTCCTAA   GGTAGCGA--- 3'
3' ---ATTGATATTGCCAG   GATTCCATCGCT--- 5'
I-ChuI[7][8] H1 Q32001 Chlamydomonas humicola E chloro 5' GAAGGTTTGGCACCTCGATGTCGGCTCATC
3' CTTCCAAACCGTGGAGCTACAGCCGAGTAG		 5' ---GAAGGTTTGGCACCTCG   ATGTCGGCTCATC--- 3'
3' ---CTTCCAAACCGTG   GAGCTACAGCCGAGTAG--- 5'
I-CpaI[8][9] H1 Q39562 Chlamydomonas pallidostigmata E chloro 5' CGATCCTAAGGTAGCGAAATTCA
3' GCTAGGATTCCATCGCTTTAAGT 		5' ---CGATCCTAAGGTAGCGAA   ATTCA--- 3'
3' ---GCTAGGATTCCATC   GCTTTAAGT--- 5'
I-CpaII[10] H1 Q39559 Chlamydomonas pallidostigmata E chloro 5' CCCGGCTAACTCTGTGCCAG
3' GGGCCGATTGAGACACGGTC 		5' ---CCCGGCTAACTC   TGTGCCAG--- 3'
5' ---GGGCCGAT   TGAGACACGGTC--- 3'
I-CreI[11] H1 1BP7​ Chlamydomonas reinhardtii E chloro 5' CTGGGTTCAAAACGTCGTGAGACAGTTTGG
3' GACCCAAGTTTTGCAGCACTCTGTCAAACC 		5' ---CTGGGTTCAAAACGTCGTGA   GACAGTTTGG--- 3'
3' ---GACCCAAGTTTTGCAG   CACTCTGTCAAACC--- 5'
I-DmoI H1 1B24​ Desulfurococcus mobilis A chrm 5' ATGCCTTGCCGGGTAAGTTCCGGCGCGCAT
3' TACGGAACGGCCCATTCAAGGCCGCGCGTA 		5' ---ATGCCTTGCCGGGTAA   GTTCCGGCGCGCAT--- 3'
3' ---TACGGAACGGCC   CATTCAAGGCCGCGCGTA--- 5'
H-DreI[12] H1 1MOW​ Hybrid: I-DmoI and I-CreI AE 5' CAAAACGTCGTAAGTTCCGGCGCG
3' GTTTTGCAGCATTCAAGGCCGCGC 		5' ---CAAAACGTCGTAA   GTTCCGGCGCG--- 3'
3' ---GTTTTGCAG   CATTCAAGGCCGCGC--- 5'
I-HmuI[13][14] H3 1U3E​ Bacillus subtilis phage SP01 B phage 5' AGTAATGAGCCTAACGCTCAGCAA
3' TCATTACTCGGATTGCGAGTCGTT		   Nicking endonuclease: *
  3' ---TCATTACTCGGATTGC   GAGTCGTT--- 5'
I-HmuII[14][15] H3 Q38137 Bacillus subtilis phage SP82 B phage 5' AGTAATGAGCCTAACGCTCAACAA
3' TCATTACTCGGATTGCGAGTTGTT		   Nicking endonuclease: *
  3' ---TCATTACTCGGATTGCGAGTTGTTN35   NNNN--- 5'
I-LlaI[16][17] H3 P0A3U1 Lactococcus lactis B chrm 5' CACATCCATAACCATATCATTTTT
3' GTGTAGGTATTGGTATAGTAAAAA 		5' ---CACATCCATAA   CCATATCATTTTT--- 3'
3' ---GTGTAGGTATTGGTATAGTAA   AAA--- 5'
I-MsoI H1 1M5X​ Monomastix sp. E 5' CTGGGTTCAAAACGTCGTGAGACAGTTTGG
3' GACCCAAGTTTTGCAGCACTCTGTCAAACC 		5' ---CTGGGTTCAAAACGTCGTGA   GACAGTTTGG--- 3'
3' ---GACCCAAGTTTTGCAG   CACTCTGTCAAACC--- 5'
PI-PfuI H1 1DQ3​ Pyrococcus furiosus Vc1 A 5' GAAGATGGGAGGAGGGACCGGACTCAACTT
3' CTTCTACCCTCCTCCCTGGCCTGAGTTGAA 		5' ---GAAGATGGGAGGAGGG   ACCGGACTCAACTT--- 3'
3' ---CTTCTACCCTCC   TCCCTGGCCTGAGTTGAA--- 5'
PI-PkoII H1 2CW7​ Pyrococcus kodakarensis BAA-918 A 5' CAGTACTACGGTTAC
3' GTCATGATGCCAATG 		5' ---CAGTACTACG  GTTAC--- 3'
3' ---GTCATG  ATGCCAATG--- 5'
I-PorI[18][19] H3 Pyrobaculum organotrophum A chrm 5' GCGAGCCCGTAAGGGTGTGTACGGG
3' CGCTCGGGCATTCCCACACATGCCC 		5' ---GCGAGCCCGTAAGGGT   GTGTACGGG--- 3'
3' ---CGCTCGGGCATT   CCCACACATGCCC--- 5'
I-PpoI H4 1EVX​ Physarum polycephalum E plasmid 5' TAACTATGACTCTCTTAAGGTAGCCAAAT
3' ATTGATACTGAGAGAATTCCATCGGTTTA		 5' ---TAACTATGACTCTCTTAA   GGTAGCCAAAT--- 3'
3' ---ATTGATACTGAGAG   AATTCCATCGGTTTA--- 5'
PI-PspI H1 Q51334 Pyrococcus sp. A chrm 5' TGGCAAACAGCTATTATGGGTATTATGGGT
3' ACCGTTTGTCGATAATACCCATAATACCCA 		5' ---TGGCAAACAGCTATTAT   GGGTATTATGGGT--- 3'
3' ---ACCGTTTGTCGAT   AATACCCATAATACCCA--- 5'
I-ScaI[20][21] H1 P03873 Saccharomyces capensis E mito 5' TGTCACATTGAGGTGCACTAGTTATTAC
3' ACAGTGTAACTCCACGTGATCAATAATG 		5' ---TGTCACATTGAGGTGCACT   AGTTATTAC--- 3'
3' ---ACAGTGTAACTCCAC   GTGATCAATAATG--- 5'
I-SceI[4][5] H1 1R7M​ Saccharomyces cerevisiae E mito 5' AGTTACGCTAGGGATAACAGGGTAATATAG
3' TCAATGCGATCCCTATTGTCCCATTATATC 		5' ---AGTTACGCTAGGGATAA   CAGGGTAATATAG--- 3'
3' ---TCAATGCGATCCC   TATTGTCCCATTATATC--- 5'
PI-SceI[22][23] H1 1VDE​ Saccharomyces cerevisiae E 5' ATCTATGTCGGGTGCGGAGAAAGAGGTAATGAAATGGCA
3' TAGATACAGCCCACGCCTCTTTCTCCATTACTTTACCGT 		5' ---ATCTATGTCGGGTGC   GGAGAAAGAGGTAATGAAATGGCA--- 3'
3' ---TAGATACAGCC   CACGCCTCTTTCTCCATTACTTTACCGT--- 5'
I-SceII[24][25][26] H1 Saccharomyces cerevisiae E mito 5' TTTTGATTCTTTGGTCACCCTGAAGTATA
3' AAAACTAAGAAACCAGTGGGACTTCATAT 		5' ---TTTTGATTCTTTGGTCACCC   TGAAGTATA--- 3'
3' ---AAAACTAAGAAACCAG   TGGGACTTCATAT--- 5'
I-SecIII[24][27][28] H1 Saccharomyces cerevisiae E mito 5' ATTGGAGGTTTTGGTAACTATTTATTACC
3' TAACCTCCAAAACCATTGATAAATAATGG 		5' ---ATTGGAGGTTTTGGTAAC   TATTTATTACC--- 3'
3' ---TAACCTCCAAAACC   ATTGATAAATAATGG--- 5'
I-SceIV[24][29][30] H1 Saccharomyces cerevisiae E mito 5' TCTTTTCTCTTGATTAGCCCTAATCTACG
3' AGAAAAGAGAACTAATCGGGATTAGATGC 		5' ---TCTTTTCTCTTGATTA   GCCCTAATCTACG--- 3'
3' ---AGAAAAGAGAAC   TAATCGGGATTAGATGC--- 5'
I-SceV[24][31] H3 Saccharomyces cerevisiae E mito 5' AATAATTTTCTTCTTAGTAATGCC
3' TTATTAAAAGAAGAATCATTACGG 		5' ---AATAATTTTCT   TCTTAGTAATGCC--- 3'
3' ---TTATTAAAAGAAGAATCATTA   CGG--- 5'
I-SceVI[24][32] H3 Saccharomyces cerevisiae E mito 5' GTTATTTAATGTTTTAGTAGTTGG
3' CAATAAATTACAAAATCATCAACC 		5' ---GTTATTTAATG   TTTTAGTAGTTGG--- 3'
3' ---CAATAAATTACAAAATCATCA   ACC--- 5'
I-SceVII[20] H1 Saccharomyces cerevisiae E mito 5' TGTCACATTGAGGTGCACTAGTTATTAC
3' ACAGTGTAACTCCACGTGATCAATAATG		   Unknown **
I-Ssp6803I H5 2OST​ Synechocystis sp. PCC 6803 B 5' GTCGGGCTCATAACCCGAA
3' CAGCCCGAGTATTGGGCTT 		5' ---GTCGGGCT   CATAACCCGAA--- 3'
3' ---CAGCCCGAGTA   TTGGGCTT--- 5'
I-TevI[33][34][35] H2 1I3J​ Escherichia coli phage T4 B phage 5' AGTGGTATCAACGCTCAGTAGATG
3' TCACCATAGT TGCGAGTCATCTAC 		5' ---AGTGGTATCAAC   GCTCAGTAGATG--- 3'
3' ---TCACCATAGT   TGCGAGTCATCTAC--- 5'
I-TevII[33][36] H2 Escherichia coli phage T4 B phage 5' GCTTATGAGTATGAAGTGAACACGTTATTC
3' CGAATACTCATACTTCACTTGTGCAATAAG 		5' ---GCTTATGAGTATGAAGTGAACACGT   TATTC--- 3'
3' ---CGAATACTCATACTTCACTTGTG   CAATAAG--- 5'
I-TevIII[37] H3 Escherichia coli phage RB3 B phage 5' TATGTATCTTTTGCGTGTACCTTTAACTTC
3' ATACATAGAAAACGCACATGGAAATTGAAG 		5' ---T   ATGTATCTTTTGCGTGTACCTTTAACTTC--- 3'
3' ---AT   ACATAGAAAACGCACATGGAAATTGAAG--- 5'
PI-TliI[38][39] H1 Thermococcus litoralis A chrm 5' TAYGCNGAYACNGACGGYTTYT
3' ATRCGNCTRTGNCTGCCTAARA 		5' ---TAYGCNGAYACNGACGG   YTTYT--- 3'
3' ---ATRCGNCTRTGNC   TGCCTAARA--- 5'
PI-TliII[22][39][40] H1 Thermococcus litoralis A chrm 5' AAATTGCTTGCAAACAGCTATTACGGCTAT
3' TTTAACGAACGTTTGTCGATAATGCCGATA		   Unknown **
I-Tsp061I H1 2DCH​ Thermoproteus sp. IC-061 A 5' CTTCAGTATGCCCCGAAAC
3' GAAGTCATACGGGGCTTTG 		5' ---CTTCAGTAT   GCCCCGAAAC--- 3'
3' ---GAAGT   CATACGGGGCTTTG--- 5'
I-Vdi141I H1 3E54​ Vulcanisaeta distributa IC-141 A 5' CCTGACTCTCTTAAGGTAGCCAAA
3' GGACTGAGAGAATTCCATCGGTTT 		5' ---CCTGACTCTCTTAA   GGTAGCCAAA--- 3'
3' ---GGACTGAG   AGAATTCCATCGGTTT--- 5'

*: Nicking endonuclease: These enzymes cut only one DNA strand, leaving the other strand untouched.
**: Unknown cutting site: Researchers have not been able to determine the exact cutting site of these enzymes yet.

See also

Information sources

Databases and lists of restriction enzymes:

  • Very comprehensive database of restriction enzymes supported by New England Biolabs©. It includes all kind of biological, structural, kinetical and commercial information about thousands of enzymes. Also includes related literature for every molecule: Roberts RJ, Vincze T, Posfai J, Macelis D. "REBASE". Retrieved 2010-01-07. Restriction Enzyme Database.
  • Database of inteins, hosted by New England Biolabs©. Perler FB. "InBase". Archived from the original on 2010-08-02. Retrieved 2010-02-05. The Intein Database and Registry.[41]
  • Detailed information for biochemical experiments: "Enzyme finder". Archived from the original on 2010-01-08. Retrieved 2010-01-07. New England Biolabs© enzyme finder.
  • Alphabetical list of enzymes and their restriction sites: "GenScript© Restriction Enzyme webpage". Archived from the original on 2009-07-04. Retrieved 2010-01-07.
  • General information about restriction sites and biochemical conditions for restriction reactions: "Restriction Enzymes Resource". Archived from the original on 2002-02-03. Retrieved 2010-01-07. Promega© restriction enzymes webpage.

Databases of proteins:

  • Database of protein structures, solved at atomic resolution: "PDB". Research Collaboratory for Structural Bioinformatics (RCSB). Archived from the original on 2015-04-07. Retrieved 2010-01-25. RCSB Protein Data Bank.
  • Databases of proteins: Swiss Institute of Bioinformatics (SIB); European Bioinformatics Institute (EBI). "UniProtKB/Swiss-Prot & TrEMBL". Retrieved 2010-01-25. Swiss-Prot is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases. TrEMBL is a computer-annotated supplement of Swiss-Prot that contains all the translations of EMBL nucleotide sequence entries not yet integrated in Swiss-Prot.

Notes and references
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  4. Gauthier A, Turmel M, Lemieux C (January 1991). "A group I intron in the chloroplast large subunit rRNA gene of Chlamydomonas eugametos encodes a double-strand endonuclease that cleaves the homing site of this intron". Curr Genet. 19 (1): 43–47. doi:10.1007/BF00362086. PMID 2036685.
  5. Marshall P, Lemieux C (August 1991). "Cleavage pattern of the homing endonuclease encoded by the fifth intron in the chloroplast large subunit rRNA-encoding gene of Chlamydomonas eugametos". Gene. 104 (2): 241–5. doi:10.1016/0378-1119(91)90256-B. PMID 1916294.
  6. Turmel M, Boulanger J, Schnare MN, Gray MW, Lemieux C (March 1991). "Six group I introns and three internal transcribed spacers in the chloroplast large subunit ribosomal RNA gene of the green alga Chlamydomonas eugametos". J Mol Biol. 218 (2): 293–311. doi:10.1016/0022-2836(91)90713-G. PMID 1849178.
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