Homing endonuclease structure and function

  title={Homing endonuclease structure and function},
  author={Barry L. Stoddard},
  journal={Quarterly Reviews of Biophysics},
  pages={49 - 95}
  • B. Stoddard
  • Published 1 February 2005
  • Biology
  • Quarterly Reviews of Biophysics
Homing endonucleases are encoded by open reading frames that are embedded within group I, group II and archael introns, as well as inteins (intervening sequences that are spliced and excised post-translationally). These enzymes initiate transfer of those elements (and themselves) by generating strand breaks in cognate alleles that lack the intervening sequence, as well as in additional ectopic sites that broaden the range of intron and intein mobility. Homing endonucleases can be divided into… 

Homing endonucleases: DNA scissors on a mission.

This review examines the categories of homing endonucleases that have been described so far and their possible applications to biotechnology and strategies to engineer homingendon nucleases to alter target site specificities will be addressed.

Homing endonuclease I-TevIII: dimerization as a means to a double-strand break

I-TevIII, the H–N–H endonuclease encoded by the RB3 nrdB intron, is described, which makes a double-strand break on the DNA homing site by acting as a dimer, and through deletion analysis, the dimerization interface was mapped to the DNA-binding domain.

Evolutionary Relationships, Design, and Biochemical Characterization of Homing Endonucleases

In these experiments, crystal structures uncovered unexpected shifts in the DNA backbone relative to the wild type endonucleases and have thus been informative in the redesign process of homing endonuclease variants.

Coevolution of a homing endonuclease and its host target sequence.

Insertion of Group II Intron-Based Ribozyme Switches into Homing Endonuclease Genes.

Fungal mitochondrial genomes act as "reservoirs" for homing endonucleases. These enzymes with their DNA site-specific cleavage activities are attractive tools for genome editing, targeted mutagenesis

Homing endonucleases: from basics to therapeutic applications

The use of tailored HEs opens up new possibilities for gene therapy in patients with monogenic diseases that can be treated ex vivo, and several members of this enzyme family have been used as templates to engineer tools to cleave DNA sequences that differ from their original wild-type targets.

A group II intron encodes a functional LAGLIDADG homing endonuclease and self-splices under moderate temperature and ionic conditions.

In vitro splicing assays indicate that the protein does not enhance intron splicing, and RNA-binding assays show that theprotein does not appear to bind to the intron RNA precursor transcript, which raises intriguing questions concerning the functional and evolutionary relationships of the two components of this unique composite element.

Fellowships, Grants, & Awards

An insertion of the Green Fluorescence Protein (GFP) into a loop which is located between the endonuclease and splicing domains of the Sce VMA1 intein is described.

Inteins, introns, and homing endonucleases: recent revelations about the life cycle of parasitic genetic elements

Two outstanding publications on the amoeba Naegleria group I intron and the PRP8 inteins in ascomycetes provide important stepping stones towards integrated studies on how these parasitic elements evolve through time together with, or despite, their hosts.



A family of nuclear homing endonucleases.

Homing endonucleases from archaea introns, protein insertions, and the mobile group I introns from organelles share a common motif, the LAGLI-DADG motif, which makes them attractive tools for mapping of large genomes.

DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI

The structure of the I-PpoI homing endonuclease bound to homing-site DNA determined to 1.8 Å resolution is reported, which shows an elongated fold of dimensions 25 × 35 × 80‬, with mixed α/β topology.

Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility.

The current understanding of homing endonucleases is reviewed, including their diversity and evolution, DNA-binding and catalytic mechanisms, and attempts to engineer them to bind novel DNA substrates.

Crystal structure of an archaeal intein-encoded homing endonuclease PI-PfuI.

It is suggested that the cleavage of each strand is catalyzed by each of the two non-equivalent active sites of PI-PfuI.

Isolation and characterization of new homing endonuclease specificities at individual target site positions.

Homing endonucleases: keeping the house in order.

The evolution of homing endonucleases is considered, both at the structure-function level and in terms of their persistence in widely divergent biological systems.

Degenerate DNA recognition by I-PpoI endonuclease.

Related homing endonucleases I-BmoI and I-TevI use different strategies to cleave homologous recognition sites

  • D. R. EdgellD. Shub
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 2001
The results suggest that each endonuclease has independently evolved the ability to distinguish intron-containing from intronless alleles while maintaining the same conserved recognition sequence centered on DNA-encoding active site residues of TS.

Interaction of the intron-encoded mobility endonuclease I-PpoI with its target site

The endonuclease protected most of the purines found in both the major and minor grooves of the DNA helix from modification by dimethyl sulfate (DMS), however, the reactivity to DMS was enhanced at some purines, suggesting that binding leads to a conformational change in the DNA.