Gene editing using ssODNs with engineered endonucleases

Methods Mol Biol. 2015:1239:251-65. doi: 10.1007/978-1-4939-1862-1_14.

Abstract

Gene editing using engineered endonucleases, such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 nucleases, requires the creation of a targeted, chromosomal DNA double-stranded break (DSB). In mammalian cells, these DSBs are typically repaired by one of the two major DNA repair pathways: nonhomologous end joining (NHEJ) or homology-directed repair (HDR). NHEJ is an error-prone repair process that can result in a wide range of end-joining events that leads to somewhat random mutations at the site of DSB. HDR is a precise repair pathway that can utilize either an endogenous or exogenous piece of homologous DNA as a template or "donor" for repair. Traditional gene editing via HDR has relied on the co-delivery of a targeted, engineered endonuclease and a circular plasmid donor construct. More recently, it has been shown that single-stranded oligodeoxynucleotides (ssODNs) can also serve as DNA donors and thus obviate the more laborious and time-consuming plasmid vector construction process. Here we describe the use of ssODNs for making defined genome modifications in combination with engineered endonucleases.

MeSH terms

  • Cloning, Molecular / methods
  • DNA Breaks, Double-Stranded
  • DNA End-Joining Repair
  • DNA, Single-Stranded*
  • Endonucleases / genetics*
  • Flow Cytometry / methods
  • Gene Expression
  • Gene Targeting / methods
  • Genetic Engineering / methods*
  • Genetic Load
  • Genetic Vectors / genetics
  • Mutagenesis, Insertional
  • Oligodeoxyribonucleotides*
  • Ribosomal Protein S6 Kinases, 90-kDa / genetics
  • Single-Cell Analysis / methods
  • Transfection

Substances

  • DNA, Single-Stranded
  • Oligodeoxyribonucleotides
  • Ribosomal Protein S6 Kinases, 90-kDa
  • ribosomal protein S6 kinase, 90kDa, polypeptide 3
  • Endonucleases