Oligonucleotide-directed gene-editing technology: mechanisms and future prospects

Expert Opin Biol Ther. 2012 Mar;12(3):329-42. doi: 10.1517/14712598.2012.660522. Epub 2012 Feb 10.


Introduction: Gene editing, as defined here, uses short synthetic oligonucleotides to introduce small, site-specific changes into mammalian genomes, including repair of genetic point mutations. Early RNA-DNA oligonucleotides (chimeraplasts) were problematic, but application of single-stranded all-DNA molecules (ssODNs) has matured the technology into a reproducible tool with therapeutic potential.

Areas covered: The review illustrates how gene-editing mechanisms are linked to DNA repair systems and DNA replication, and explains that while homologous recombination (HR) and nucleotide excision repair (NER) are implicated, the mismatch repair (MMR) system is inhibitory. Although edited cells often arrest in late S-phase or G2-phase, alternative ssODN chemistries can improve editing efficiency and cell viability. The final section focuses on the exciting tandem use of ssODNs with zinc finger nucleases to achieve high frequency genome editing.

Expert opinion: For a decade, changing the genetic code of cells via ssODNs was largely done in reporter gene systems to optimize methods and as proof-of-principle. Today, editing endogenous genes is advancing, driven by a clearer understanding of mechanisms, by effective ssODN designs and by combination with engineered endonuclease technologies. Success is becoming routine in vitro and ex vivo, which includes editing embryonic stem (ES) and induced pluripotent stem (iPS) cells, suggesting that in vivo organ gene editing is a future option.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Animals
  • DNA Replication*
  • Gene Targeting*
  • Genetic Engineering*
  • Genetic Therapy*
  • Humans
  • Oligonucleotides / pharmacology*


  • Oligonucleotides