July 19

Endonuclease Entry Help

Four distinct categories of LHEs can be entered into the database:

  1. Wild-type enzymes with validated, known DNA cleavage activity and a corresponding target site sequence.
  2. Engineered endonucleases, corresponding to mutated variants of a previously entered wild-type endonuclease.
  3. 'Chimeric’ endonucleases, corresponding to combinations of N- and C-terminal domains, subunits, or DNA-contacting surfaces from two different LHEs.
  4. ‘Pseudo-endonucleases’, corresponding to wild-type LHE sequences found in genomic sequence databases that are dysfunctional in terms of expression, folding or activity.

Please ensure that your HE entry, regardless of its origin, meets established criteria for endonuclease naming. Please see Roberts et al. (2003) Nucleic Acids Research 31 (7): 1805 - 18172 for additional details.

  1. Wild type LAGLIDADG homing endonucleases (LHEs) should have a prefix corresponding to "I-" if they are intron-encoded; "PI-" if they are intein-encoded, and "F-" if they are encoded by free-standing genes.
  2. This prefix is then followed by a three letter code corresponding to the genus and species of the host organism (for example 'Sce' for Saccharomyces cerevisiae or 'Ppo' for Physarum polycephalum). If the endonuclease is encoded by a unique strain, the identifier number can also be added to the name: for example 'I-Ssp6803I' for a homing endonuclease from Synechocystis PCC6803. The final Roman numeral corresponds to the order of discovery of HEs from that given organism.
  3. BEFORE ASSIGNING A NEW ENDONUCLEASE NAME, PLEASE CONSULT 'REBASE' (http://rebase.neb.com/rebase/rebase.html) and be sure that the acronym that you have chosen for your enzyme is not already in use for a different enzyme. If it is, you can add a unique character or strain designator to distinguish your enzyme. Our recommendation for homing endonucleases is to add an "M" for those that are encoded in a mitochondrial genome, or a "C" for those encoded in a chloroplast genome (for example, I-CpaMI for the LHE encoded in the mitochondrial genome in Cordyceps kanzashiana).
  4. Additional conventions for non-natural (i.e. engineered) endonucleases:
    • Hybrid fusions of individual N- and C-terminal domains: Simply use the entry tool to create a chimeric name such as "I-AniI/I-OnuI".
    • Single chain versions of naturally homodimeric enzymes: Add "(m)" after wild-type name (i.e. "I-CreI(m)") to denote the monomerization of the enzyme.
    • Engineered or selected enzymes with altered properties: Add parenthetical text (such as "I-OnuI(E2)" and cite appropriate study or notes of explanation.

Once novel endonucleases have been entered in the database, additional entry tools can be subsequently be employed to enter information for that enzyme regarding its Position Weight Matrix (PWM), modules of amino acids that surround individual clusters of DNA base pairs in the target site, and/or mutations in the endonuclease that are known to alter specificity at one or more DNA basepairs.

Detailed additional directions and information regarding data entry for LHEs, as listed above, is linked directly on each entry page.