Nucleic Acids Research, 2003, Vol. 31, No. 7 1805-1812
© 2003 Oxford University Press
A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes
New England Biolabs, Beverly, MA 01915, USA, 1 Molecular Genetics Program, New York State Department of Health, Albany, NY 12201-2002, USA, 2 Genetics and Development, Columbia University, New York, NY 10032, USA, 3 Department of Chemistry, Wayne State University, Detroit, MI 48202, USA, 4 Department of Microbiology, Biozentrum, Universitat Basel, CH-4056 Basel, Switzerland, 5 Program in Bioinformatics and Proteomics/Genomics, Medical College of Ohio, Toledo, OH 43699-0008, USA, 6 SibEnzyme, 630090 Novosibirsk, Russia, 7 School of Chemistry, University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JJ, UK, 8 Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA, 9 Biophysics Laboratories, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DT, UK, 10 A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia, 11 The University of Illinois College of Medicine, Urbana, IL 61801-3602, USA, 12 Department of Biochemistry, University of Bristol Medical School, Bristol BS8 1TD, UK, 13 Department of Biology, University of Rochester, Rochester, NY 14627-0211, USA, 14 Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA, 15 Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK, 16 Institute of Biotechnology, LT-2028 Vilnius, Lithuania, 17 Institut für Biochemie, Justus-Liebig-Universität, D-35392 Giessen, Germany, 18 Department of Dairy and Food Science, Royal Veterinary and Agricultural University, DK-1958 Frederiksberg C, Denmark, 19 Institute of Biochemistry, BRC, H-6701 Szeged, Hungary, 20 Departments of Food Science and Microbiology, North Carolina State University, Raleigh, NC 27695-7624, USA, 21 Department of Molecular Biology, Institute of Medical Science, University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan, 22 Institut für Virologie-Charite, Humboldt Universitat, D-10098 Berlin, Germany, 23 Brookhaven National Laboratory, Upton, NY 11973-5000, USA, 24 Department of Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA, 25 National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan, 26 Institute of Cell and Molecular Biology, University of Edinburgh, The King’s Buildings, Edinburgh EH9 3JR, UK, 27 Department of Microbiology and Cell Biology, Indian Institute of Science, IN-560012 Bangalore, India, 28 Institute of Microbiology, Warsaw University, Miecznikowa 1, 02-096 Warsaw, Poland, 29 University of California, Santa Barbara, Santa Barbara, CA 93106-0001, USA, 30 State Research Center of Virology and Biotechnology ‘Vektor’, Koltsovo, Novosibirsk region 633059, Russia, 31 Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA, 32 Department of Biochemistry, The Chinese University of Hong Kong, Hong Kong, 33 Department of Microbiology, University of Maryland, College Park, MD 20742, USA, 34 Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, 35 McArdle Laboratory, University of Wisconsin, Madison, WI 53706, USA, 36 MPI für Molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany, 37 Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA and 38 Faculdade de Farmacia de Lisboa, 1600-083 Lisbon, Portugal
*To whom correspondence should be addressed. Tel: +1 978 927 3382; Fax: +1 978 921 1527; Email: roberts{at}neb.com
A nomenclature is described for restriction endonucleases, DNA methyltransferases, homing endonucleases and related genes and gene products. It provides explicit categories for the many different Type II enzymes now identified and provides a system for naming the putative genes found by sequence analysis of microbial genomes.
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|
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|
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|
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|
|
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|
|
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|
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|
|
|
|
|
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|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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