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


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

Further information: Homing endonuclease.

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] HI 1P8K Aspergillus nidulans E mito 5' TTGAGGAGGTTTCTCTGTAAATAA
3' AACTCCTCCAAAGAGACATTTATT
5' ---TTGAGGAGGTTTC   TCTGTAAATAA--- 3'
3' ---AACTCCTCC   AAAGAGACATTTATT--- 5'
I-CeuI [3][4][5][6] HI 2EX5 Chlamydomonas eugametos E chloro 5' TAACTATAACGGTCCTAAGGTAGCGA
3' ATTGATATTGCCAGGATTCCATCGCT
5' ---TAACTATAACGGTCCTAA   GGTAGCGA--- 3'
3' ---ATTGATATTGCCAG   GATTCCATCGCT--- 5'
I-ChuI [7][8] HI Chlamydomonas humicola E chloro 5' GAAGGTTTGGCACCTCGATGTCGGCTCATC
3' CTTCCAAACCGTGGAGCTACAGCCGAGTAG
5' ---GAAGGTTTGGCACCTCG   ATGTCGGCTCATC--- 3'
3' ---CTTCCAAACCGTG   GAGCTACAGCCGAGTAG--- 5'
I-CpaI [8][9] HI Chlamydomonas pallidostigmata E chloro 5' CGATCCTAAGGTAGCGAAATTCA
3' GCTAGGATTCCATCGCTTTAAGT
5' ---CGATCCTAAGGTAGCGAA   ATTCA--- 3'
3' ---GCTAGGATTCCATC   GCTTTAAGT--- 5'
I-CpaII [10] HI Chlamydomonas pallidostigmata E chloro 5' CCCGGCTAACTCTGTGCCAG
3' GGGCCGATTGAGACACGGTC
5' ---CCCGGCTAACTC   TGTGCCAG--- 3'
5' ---GGGCCGAT   TGAGACACGGTC--- 3'
I-CreI [11] HI 1BP7 Chlamydomonas reinhardtii E chloro 5' CTGGGTTCAAAACGTCGTGAGACAGTTTGG
3' GACCCAAGTTTTGCAGCACTCTGTCAAACC
5' ---CTGGGTTCAAAACGTCGTGA   GACAGTTTGG--- 3'
3' ---GACCCAAGTTTTGCAG   CACTCTGTCAAACC--- 5'
I-DmoI HI 1B24 Desulfurococcus mobilis A chrm 5' ATGCCTTGCCGGGTAAGTTCCGGCGCGCAT
3' TACGGAACGGCCCATTCAAGGCCGCGCGTA
5' ---ATGCCTTGCCGGGTAA   GTTCCGGCGCGCAT--- 3'
3' ---TACGGAACGGCC   CATTCAAGGCCGCGCGTA--- 5'
H-DreI [12] 1MOW Escherichia coli pI-DreI B 5' CAAAACGTCGTAAGTTCCGGCGCG
3' GTTTTGCAGCATTCAAGGCCGCGC
5' ---CAAAACGTCGTAA   GTTCCGGCGCG--- 3'
3' ---GTTTTGCAG   CATTCAAGGCCGCGC--- 5'
I-HmuI [13][14] HIII 1U3E Bacillus subtilis phage SPO1 B phage 5' AGTAATGAGCCTAACGCTCAGCAA
3' TCATTACTCGGATTGCGAGTCGTT
  Nicking endonuclease: *
  3' ---TCATTACTCGGATTGC   GAGTCGTT--- 5'
I-HmuII [14][15] HIII Bacillus subtilis phage SP82 B phage 5' AGTAATGAGCCTAACGCTCAACAA
3' TCATTACTCGGATTGCGAGTTGTT
  Nicking endonuclease: *
  3' ---TCATTACTCGGATTGCGAGTTGTTN35   NNNN--- 5'
I-LlaI [16][17] HIII Lactococcus lactis B chrm 5' CACATCCATAACCATATCATTTTT
3' GTGTAGGTATTGGTATAGTAAAAA
5' ---CACATCCATAA   CCATATCATTTTT--- 3'
3' ---GTGTAGGTATTGGTATAGTAA   AAA--- 5'
I-MsoI 1M5X Monomastix sp. E 5' CTGGGTTCAAAACGTCGTGAGACAGTTTGG
3' GACCCAAGTTTTGCAGCACTCTGTCAAACC
5' ---CTGGGTTCAAAACGTCGTGA   GACAGTTTGG--- 3'
3' ---GACCCAAGTTTTGCAG   CACTCTGTCAAACC--- 5'
PI-PfuI 1DQ3 Pyrococcus furiosus Vc1 A 5' GAAGATGGGAGGAGGGACCGGACTCAACTT
3' CTTCTACCCTCCTCCCTGGCCTGAGTTGAA
5' ---GAAGATGGGAGGAGGG   ACCGGACTCAACTT--- 3'
3' ---CTTCTACCCTCC   TCCCTGGCCTGAGTTGAA--- 5'
PI-PkoII 2CW7 Pyrococcus kodakaraensis KOD1 A 5' CAGTACTACGGTTAC
3' GTCATGATGCCAATG
5' ---CAGTACTACG  GTTAC--- 3'
3' ---GTCATG  ATGCCAATG--- 5'
I-PorI [18][19] HIII Pyrobaculum organotrophum A chrm 5' GCGAGCCCGTAAGGGTGTGTACGGG
3' CGCTCGGGCATTCCCACACATGCCC
5' ---GCGAGCCCGTAAGGGT   GTGTACGGG--- 3'
3' ---CGCTCGGGCATT   CCCACACATGCCC--- 5'
I-PpoI HIV 1EVX Physarum polycephalum E nuclear 5' TAACTATGACTCTCTTAAGGTAGCCAAAT
3' ATTGATACTGAGAGAATTCCATCGGTTTA
5' ---TAACTATGACTCTCTTAA   GGTAGCCAAAT--- 3'
3' ---ATTGATACTGAGAG   AATTCCATCGGTTTA--- 5'
PI-PspI HI Pyrococcus sp. A chrm 5' TGGCAAACAGCTATTATGGGTATTATGGGT
3' ACCGTTTGTCGATAATACCCATAATACCCA
5' ---TGGCAAACAGCTATTAT   GGGTATTATGGGT--- 3'
3' ---ACCGTTTGTCGAT   AATACCCATAATACCCA--- 5'
I-ScaI [20][21] HI Saccharomyces capensis E mito 5' TGTCACATTGAGGTGCACTAGTTATTAC
3' ACAGTGTAACTCCACGTGATCAATAATG
5' ---TGTCACATTGAGGTGCACT   AGTTATTAC--- 3'
3' ---ACAGTGTAACTCCAC   GTGATCAATAATG--- 5'
I-SceI [4][5] HI 1R7M Saccharomyces cerevisiae E mito 5' AGTTACGCTAGGGATAACAGGGTAATATAG
3' TCAATGCGATCCCTATTGTCCCATTATATC
5' ---AGTTACGCTAGGGATAA   CAGGGTAATATAG--- 3'
3' ---TCAATGCGATCCC   TATTGTCCCATTATATC--- 5'
PI-SceI [22][23] HI 1VDE Saccharomyces cerevisiae E 5' ATCTATGTCGGGTGCGGAGAAAGAGGTAATGAAATGGCA
3' TAGATACAGCCCACGCCTCTTTCTCCATTACTTTACCGT
5' ---ATCTATGTCGGGTGC   GGAGAAAGAGGTAATGAAATGGCA--- 3'
3' ---TAGATACAGCC   CACGCCTCTTTCTCCATTACTTTACCGT--- 5'
I-SceII [24][25][26] HI Saccharomyces cerevisiae E mito 5' TTTTGATTCTTTGGTCACCCTGAAGTATA
3' AAAACTAAGAAACCAGTGGGACTTCATAT
5' ---TTTTGATTCTTTGGTCACCC   TGAAGTATA--- 3'
3' ---AAAACTAAGAAACCAG   TGGGACTTCATAT--- 5'
I-SecIII [24][27][28] HI Saccharomyces cerevisiae E mito 5' ATTGGAGGTTTTGGTAACTATTTATTACC
3' TAACCTCCAAAACCATTGATAAATAATGG
5' ---ATTGGAGGTTTTGGTAAC   TATTTATTACC--- 3'
3' ---TAACCTCCAAAACC   ATTGATAAATAATGG--- 5'
I-SceIV [24][29][30] HI Saccharomyces cerevisiae E mito 5' TCTTTTCTCTTGATTAGCCCTAATCTACG
3' AGAAAAGAGAACTAATCGGGATTAGATGC
5' ---TCTTTTCTCTTGATTA   GCCCTAATCTACG--- 3'
3' ---AGAAAAGAGAAC   TAATCGGGATTAGATGC--- 5'
I-SceV [24][31] HIII Saccharomyces cerevisiae E mito 5' AATAATTTTCTTCTTAGTAATGCC
3' TTATTAAAAGAAGAATCATTACGG
5' ---AATAATTTTCT   TCTTAGTAATGCC--- 3'
3' ---TTATTAAAAGAAGAATCATTA   CGG--- 5'
I-SceVI [24][32] HIII Saccharomyces cerevisiae E mito 5' GTTATTTAATGTTTTAGTAGTTGG
3' CAATAAATTACAAAATCATCAACC
5' ---GTTATTTAATG   TTTTAGTAGTTGG--- 3'
3' ---CAATAAATTACAAAATCATCA   ACC--- 5'
I-SceVII [20] HI Saccharomyces cerevisiae E mito 5' TGTCACATTGAGGTGCACTAGTTATTAC
3' ACAGTGTAACTCCACGTGATCAATAATG
  Unknown **
I-Ssp6803I 2OST Synechocystis sp. PCC 6803 B 5' GTCGGGCTCATAACCCGAA
3' CAGCCCGAGTATTGGGCTT
5' ---GTCGGGCT   CATAACCCGAA--- 3'
3' ---CAGCCCGAGTA   TTGGGCTT--- 5'
I-TevI [33][34][35] HII 1I3J Escherichia coli phage T4 B phage 5' AGTGGTATCAACGCTCAGTAGATG
3' TCACCATAGT TGCGAGTCATCTAC
5' ---AGTGGTATCAAC   GCTCAGTAGATG--- 3'
3' ---TCACCATAGT   TGCGAGTCATCTAC--- 5'
I-TevII [33][36] HII Escherichia coli phage T4 B phage 5' GCTTATGAGTATGAAGTGAACACGTTATTC
3' CGAATACTCATACTTCACTTGTGCAATAAG
5' ---GCTTATGAGTATGAAGTGAACACGT   TATTC--- 3'
3' ---CGAATACTCATACTTCACTTGTG   CAATAAG--- 5'
I-TevIII [37] HIII Escherichia coli phage RB3 B phage 5' TATGTATCTTTTGCGTGTACCTTTAACTTC
3' ATACATAGAAAACGCACATGGAAATTGAAG
5' ---T   ATGTATCTTTTGCGTGTACCTTTAACTTC--- 3'
3' ---AT   ACATAGAAAACGCACATGGAAATTGAAG--- 5'
PI-TliI [38][39] HI Thermococcus litoralis A chrm 5' TAYGCNGAYACNGACGGYTTYT
3' ATRCGNCTRTGNCTGCCTAARA
5' ---TAYGCNGAYACNGACGG   YTTYT--- 3'
3' ---ATRCGNCTRTGNC   TGCCTAARA--- 5'
PI-TliII [22][39][40] HI Thermococcus litoralis A chrm 5' AAATTGCTTGCAAACAGCTATTACGGCTAT
3' TTTAACGAACGTTTGTCGATAATGCCGATA
  Unknown **
I-Tsp061I 2DCH Thermoproteus sp. IC-061 A 5' CTTCAGTATGCCCCGAAAC
3' GAAGTCATACGGGGCTTTG
5' ---CTTCAGTAT   GCCCCGAAAC--- 3'
3' ---GAAGT   CATACGGGGCTTTG--- 5'
I-Vdi141I 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". Retrieved 2010-02-05. The Intein Database and Registry .[41]
  • Detailed information for biochemical experiments: "Enzyme finder". Retrieved 2010-01-07. New England Biolabs© enzyme finder. 
  • Alphabetical list of enzymes and their restriction sites: "GenScript© Restriction Enzyme webpage". Retrieved 2010-01-07. 
  • General information about restriction sites and biochemical conditions for restriction reactions: "Restriction Enzymes Resource". 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). Retrieved 2010-01-25. RCSB Protein Data Bank. 
  • Databases of proteins:  

Notes and references

  1. ^ Lambowitz AM, Belfort M (1993). "Introns as mobile genetic elements". Annu Rev Biochem. 62: 587–622.  
  2. ^ Naito T, Kusano K, Kobayashi I (February 1995). "Selfish behavior of restriction-modification systems". Science 267 (5199): 897–99.  
  3. ^ Jacquier A, Dujon B (June 1985). "An intron-encoded protein is active in a gene conversion process that spreads an intron into a mitochondrial gene". Cell 42 (2): 383–94.  
  4. ^ a b 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.  
  5. ^ a b 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.  
  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.  
  7. ^ Côté V, Mercier JP, Lemieux C, Turmel M (July 1993). "The single group-I intron in the chloroplast rrnL gene of Chlamydomonas humicola encodes a site-specific DNA endonuclease (I-ChuI)". Gene 129 (1): 69–76.  
  8. ^ a b Turmel M, Gutell RR, Mercier JP, Otis C, Lemieux C (July 1993). "Analysis of the chloroplast large subunit ribosomal RNA gene from 17 Chlamydomonas taxa. Three internal transcribed spacers and 12 group I intron insertion sites". J Mol Biol 232 (2): 446–67.  
  9. ^ Turmel M, Côté V, Otis C, Mercier JP, Gray MW, Lonergan KM, Lemieux C (July 1995). "Evolutionary transfer of ORF-containing group I introns between different subcellular compartments (chloroplast and mitochondrion)". Mol Biol Evol 12 (4): 533–45.  
  10. ^ Turmel M, Mercier JP, Côté V, Otis C, Lemieux C (July 1995). "The site-specific DNA endonuclease encoded by a group I intron in the Chlamydomonas pallidostigmatica chloroplast small subunit rRNA gene introduces a single-strand break at low concentrations of Mg2+". Nucleic Acids Res 23 (13): 2519–25.  
  11. ^ Jurica MS, Monnat RJ, Stoddard BL (October 1998). "DNA recognition and cleavage by the LAGLIDADG homing endonuclease I-CreI". Mol. Cell 2 (4): 469–76.  
  12. ^ Chevalier BS, Kortemme T, Chadsey MS, Baker D, Monnat RJ, Stoddard BL (October 2002). "Design, activity, and structure of a highly specific artificial endonuclease". Mol. Cell 10 (4): 895–905.  
  13. ^ Goodrich-Blair H, Scarlato V, Gott JM, Xu M, Shub DA (October 1990). "A self-splicing group I intron in the DNA polymerase gene of Bacillus subtilis bacteriophage SPO1". Cell 63 (2): 417–24.  
  14. ^ a b Goodrich-Blair H, Shub DA (January 1996). "Beyond homing: competition between intron endonucleases confers a selective advantage on flanking genetic markers". Cell 84 (2): 211–21.  
  15. ^ Goodrich-Blair H, Shub DA (September 1994). "The DNA polymerase genes of several HMU-bacteriophages have similar group I introns with highly divergent open reading frames". Nucleic Acids Res 22 (18): 3715–21.  
  16. ^ Shearman C, Godon JJ, Gasson M (July 1996). "Splicing of a group II intron in a functional transfer gene of Lactococcus lactis". Mol Microbiol 21 (1): 45–53.  
  17. ^ Mills DA, McKay LL, Dunny GM (June 1996). "Splicing of a group II intron involved in the conjugative transfer of pRS01 in lactococci". J Bacteriol 178 (12): 3531–8.  
  18. ^ Lykke-Andersen J, Thi-Ngoc HP, Garrett RA (November 1994). "DNA substrate specificity and cleavage kinetics of an archaeal homing-type endonuclease from Pyrobaculum organotrophum". Nucleic Acids Res 22 (22): 4583–90.  
  19. ^ Dalgaard JZ, Garrett RA (November 1992). "Protein-coding introns from the 23S rRNA-encoding gene form stable circles in the hyperthermophilic archaeon Pyrobaculum organotrophum". Gene 121 (1): 103–10.  
  20. ^ a b Szczepanek T, Lazowska J (July 1996). "Replacement of two non-adjacent amino acids in the S.cerevisiae bi2 intron-encoded RNA maturase is sufficient to gain a homing-endonuclease activity". EMBO J 15 (14): 3758–67.  
  21. ^ Lazowska J, Szczepanek T, Macadre C, Dokova M (1992). "Two homologous mitochondrial introns from closely related Saccharomyces species differ by only a few amino acid replacements in their Open Reading Frames: one is mobile, the other is not". C R Acad Sci Paris 315 (2): 37–41.  
  22. ^ a b Kane PM, Yamashiro CT, Wolczyk DF, Neff N, Goebl M, Stevens TH (November 1990). "Protein splicing converts the yeast TFP1 gene product to the 69-kD subunit of the vacuolar H(+)-adenosine triphosphatase". Science 250 (4981): 651–7.  
  23. ^ Gimble FS, Thorner J (May 1992). "Homing of a DNA endonuclease gene by meiotic gene conversion in Saccharomyces cerevisiae". Nature 357 (6376): 301–6.  
  24. ^ a b c d e Bonitz SG, Coruzzi G, Thalenfeld BE, Tzagoloff A, Macino G (December 1980). "Assembly of the mitochondrial membrane system. Structure and nucleotide sequence of the gene coding for subunit 1 of yeast cytochrme oxidase". J Biol Chem 255 (24): 11927–41.  
  25. ^ Hanson DK, Lamb MR, Mahler HR, Perlman PS (March 1982). "Evidence for translated intervening sequences in the mitochondrial genome of Saccharomyces cerevisiae". J Biol Chem 257 (6): 3218–24.  
  26. ^ Delahodde A, Goguel V, Becam AM, Creusot F, Perea J, Banroques J, Jacq C (February 1989). "Site-specific DNA endonuclease and RNA maturase activities of two homologous intron-encoded proteins from yeast mitochondria". Cell 56 (3): 431–41.  
  27. ^ Sargueil B, Delahodde A, Hatat D, Tian GL, Lazowska J, Jacq C (February 1991). "A new specific DNA endonuclease activity in yeast mitochondria". Mol Gen Genet 225 (2): 340–1.  
  28. ^ Perea J, Desdouets C, Schapria M, Jacq C (January 1993). "I-Sce III: a novel group I intron-encoded endonuclease from the yeast mitochondria". Nucleic Acids Res 21 (2): 358.  
  29. ^ Moran JV, Wernette CM, Mecklenburg KL, Butow RA, Perlman PS (August 1992). "Intron 5 alpha of the COXI gene of yeast mitochondrial DNA is a mobile group I intron". Nucleic Acids Res 20 (15): 4069–76.  
  30. ^ Seraphin B, Faye G, Hatat D, Jacq C (April 1992). "The yeast mitochondrial intron aI5 alpha: associated endonuclease activity and in vivo mobility". Gene 113 (1): 1–8.  
  31. ^ Liang F, Romanienko PJ, Weaver DT, Jeggo PA, Jasin M (August 1996). "Chromosomal double-strand break repair in Ku80-deficient cells". PNAS 93 (17): 8929–33.  
  32. ^ Yang J, Zimmerly S, Perlman PS, Lambowitz AM (May 1996). "Efficient integration of an intron RNA into double-stranded DNA by reverse splicing". Nature 381 (6580): 332–5.  
  33. ^ a b Bell-Pedersen D, Quirk S, Clyman J, Belfort M (July 1990). "Intron mobility in phage T4 is dependent upon a distinctive class of endonucleases and independent of DNA sequences encoding the intron core: mechanistic and evolutionary implications". Nucleic Acids Res 18 (13): 3763–70.  
  34. ^ Chu FK, Maley G, Pedersen-Lane J, Wang AM, Maley F (May 1990). "Characterization of the restriction site of a prokaryotic intron-encoded endonuclease". PNAS 87 (9): 3574–8.  
  35. ^ Bell-Pedersen D, Quirk SM, Aubrey M, Belfort M (October 1989). "A site-specific endonuclease and co-conversion of flanking exons associated with the mobile td intron of phage T4". Gene 82 (1): 119–26.  
  36. ^ Shub DA, Gott JM, Xu MQ, Lang BF, Michel F, Tomaschewski J, Pedersen-Lane J, Belfort M (February 1988). "Structural conservation among three homologous introns of bacteriophage T4 and the group I introns of eukaryotes". PNAS 85 (4): 1151–5.  
  37. ^ Eddy SR, Gold L (June 1991). "The phage T4 nrdB intron: a deletion mutant of a version found in the wild". Genes Dev 5 (6): 1032–41.  
  38. ^ Xu M, Southworth MW, Mersha FB, Hornstra LJ, Perler FB (December 1993). "In vitro protein splicing of purified precursor and the identification of a branched intermediate". Cell 75 (7): 1371–7.  
  39. ^ a b Perler FB, Comb DG, Jack WE, Moran LS, Qiang B, Kucera RB, Benner J, Slatko BE, Nwankwo DO, Hempstead SK, Carlow CKS, Jannasch H (June 1992). "Intervening sequences in an Archaea DNA polymerase gene". PNAS 89 (12): 5577–81.  
  40. ^ Hirata R, Ohsumk Y, Nakano A, Kawasaki H, Suzuki K, Anraku Y (April 1990). "Molecular structure of a gene, VMA1, encoding the catalytic subunit of H(+)-translocating adenosine triphosphatase from vacuolar membranes of Saccharomyces cerevisiae". J Biol Chem 265 (12): 6726–33.  
  41. ^ Perler FB (January 2002). "InBase: the Intein Database". Nucleic Acids Res 30 (1): 383–4.