Free Access
Environ. Biosafety Res.
Volume 8, Number 2, April-June 2009
Page(s) 57 - 64
Published online 10 July 2009
  • Aarts M, Dekker M, de Vries S, van der Wal A, te Riele H (2006) Generation of a mouse mutant by oligonucleotide-mediated gene modification in ES cells. Nucleic Acids Res. 34: e147 [Google Scholar]
  • Agarwal S, Gamper HB, Kmiec EB (2003) Nucleotide replacement at two sites can be directed by modified single-stranded oligonucleotides in vitro and in vivo. Biomol Eng. 20: 7–20 [CrossRef] [PubMed] [Google Scholar]
  • Alexeev V, Igoucheva O, Yoon K (2002) Simultaneous targeted alteration of the tyrosinase and c-kit genes by single-stranded oligonucleotides. Gene Ther. 9: 1667–1675 [CrossRef] [PubMed] [Google Scholar]
  • Andersen MS, Sorensen CB, Bolund L, Jensen TG (2002) Mechanisms underlying targeted gene correction using chimeric RNA/DNA and single-stranded DNA oligonucleotides. J. Mol. Med. 80: 770–781 [CrossRef] [PubMed] [Google Scholar]
  • BAC (2007) Advice of the Belgian Biosafety Advisory Council on the use of “Targeted Gene Repair” as a strategy to develop novel organisms (ref. WIV-ISP/BAC/2007_SC_529). Belgian Biosafety Advisory Council. (accessed March 3rd, 2009) [Google Scholar]
  • BASF (2009) BASF and Cibus achieve development milestone in CLEARFIELD® Production System. (accessed March 3rd, 2009) [Google Scholar]
  • Beetham PR, Kipp PB, Sawycky XL, Arntzen CJ, May GD (1999) A tool for functional plant genomics: chimeric RNA/DNA oligonucleotides cause in vivo gene-specific mutations. Proc. Natl. Acad. Sci. USA 96: 8774–8778 [CrossRef] [Google Scholar]
  • Bertoni C, Morris GE, Rando TA (2005) Strand bias in oligonucleotide-mediated dystrophin gene editing. Hum. Mol. Genet. 14: 221–233 [CrossRef] [PubMed] [Google Scholar]
  • Campbell CR, Keown W, Lowe L, Kirschling D, Kucherlapati R (1989) Homologous recombination involving small single-stranded oligonucleotides in human cells. New Biol. 1: 223–227 [PubMed] [Google Scholar]
  • Christensen LA, Finch RA, Booker AJ, Vasquez KM (2006) Targeting oncogenes to improve breast cancer chemotherapy. Cancer Res. 66: 4089–4094 [CrossRef] [PubMed] [Google Scholar]
  • COGEM (2005) Toepassingen van oligonucleotiden. Effecten en potentiële genoomveranderingen (Advies CGM/050707-02). Commissie Genetische Modificatie, The Netherlands. (accessed March 3rd, 2009) [Google Scholar]
  • COGEM (2006) New techniques in plant biotechnology (COGEM Report CGM/061024-02). Commissie Genetische Modificatie, The Netherlands. (accessed March 3rd, 2009) [Google Scholar]
  • Cole-Strauss A, Gamper H, Holloman WK, Muñoz M, Cheng N, Kmiec EB (1999) Targeted gene repair directed by the chimeric RNA/DNA oligonucleotide in a mammalian cell-free extract. Nucleic Acids Res. 27: 1323–1330 [CrossRef] [PubMed] [Google Scholar]
  • Davis BR, Brown DB, Carsrud ND, inventors. February 5, 2004. Single-stranded end-capped oligonucleotide mediated targeted gene repair and modification and uses thereof. United States Patent Application No. 20040023903 [Google Scholar]
  • De Meyer SF, Pareyn I, Baert J, Deckmyn H, Vanhoorelbeke K (2007) False positive results in chimeraplasty for von Willebrand Disease. Thromb Res. 119: 93–104 [CrossRef] [PubMed] [Google Scholar]
  • de Semir D, Aran JM (2006) Targeted gene repair: the ups and downs of a promising gene therapy approach. Curr. Gene Ther. 6: 481–504 [CrossRef] [PubMed] [Google Scholar]
  • Dong C, Beetham P, Vincent K, Sharp P (2006) Oligonucleotide-directed gene repair in wheat using a transient plasmid gene repair assay system. Plant Cell Rep. 25: 457–465 [CrossRef] [PubMed] [Google Scholar]
  • EC (1990) Council Directive 90/219/EEC of 23 April 1990, on the contained use of genetically modified micro-organisms. Off. J. Eur. Union L 117: 1–14 [Google Scholar]
  • EC (1998) Council Directive 98/81/EC of 26 October 1998 amending Directive 90/219/EEC on the contained use of genetically modified micro-organisms. Off. J. Eur. Union L 330: 13–31 [Google Scholar]
  • EC (2001) Directive 2001/18/EC of the European Parliament and of the Council of 12 March 2001 on the deliberate release into the environment of genetically modified organisms and repealing Council Directive 90/220/EEC. Off. J. Eur. Union L 106: 1–38 [Google Scholar]
  • EC (2003) Regulation (EC) No 1830/2003 of the European Parliament and of the Council of 22 September 2003 concerning the traceability and labelling of genetically modified organisms and the traceability of food and feed products produced from genetically modified organisms and amending Directive 2001/18/EC. Off. J. Eur. Union L 268: 24–28 [Google Scholar]
  • Engstrom JU, Kmiec EB (2008) DNA replication, cell cycle progression and the targeted gene repair reaction. Cell Cycle 15: 1402–1414 [CrossRef] [Google Scholar]
  • Gamper HB, Parekh H, Rice MC, Bruner M, Youkey H, Kmiec EB (2000) The DNA strand of chimeric RNA/DNA oligonucleotides can direct gene repair/conversion activity in mammalian and plant cell-free extracts. Nucleic Acids Res. 28: 4332–4339 [CrossRef] [PubMed] [Google Scholar]
  • Grabowski P (2008) Failure to repair the c.338C>T mutation in carnitine palmitoyl transferase 2 deficient skin fibroblasts using chimeraplasty. Mol. Genet. Metabol. 93: 347–349 [CrossRef] [Google Scholar]
  • Hohn B, Puchta H (1999) Gene therapy in plants. Proc. Natl. Acad. Sci. 96: 8321–8323 [CrossRef] [Google Scholar]
  • Huen MS, Li XT, Lu LY, Watt RM, Liu DP, Huang JD (2006) The involvement of replication in single stranded oligonucleotide-mediated gene repair. Nucleic Acids Res. 34: 6183–6194 [CrossRef] [PubMed] [Google Scholar]
  • Igoucheva O, Alexeev V, Yoon K (2004a) Oligonucleotide-directed mutagenesis and targeted gene correction: a mechanistic point of view. Curr. Mol. Med. 4: 445–463 [CrossRef] [PubMed] [Google Scholar]
  • Igoucheva O, Alexeev V, Yoon K (2004b) Mechanism of gene repair open for discussion. Oligonucleotides 14: 311–321 [CrossRef] [PubMed] [Google Scholar]
  • Igoucheva O, Alexeev V, Scharer O, Yoon K (2006) Involvement of ERCC1/XPF and XPG in oligodeoxynucleotide-directed gene modification. Oligonucleotides 16: 94–104 [CrossRef] [PubMed] [Google Scholar]
  • Iida S, Terada R (2005) Modification of endogeneous natural genes by gene targeting in rice and other higher plants. Plant Mol. Biol. 59: 205–219 [CrossRef] [PubMed] [Google Scholar]
  • Jacobsen E, Schouten HJ (2008) Cisgenesis, a new tool for traditional plant breeding, should be exempted from the regulation on genetically modified organisms in a step by step approach. Potato Res. 51: 75–88 [CrossRef] [Google Scholar]
  • Kalish JM, Glazer PM (2005) Targeted genome modification via triple helix formation. Ann. N. Y. Acad. Sci. 1058: 151–161 [CrossRef] [PubMed] [Google Scholar]
  • Kmiec EB (2003) Targeted gene repair – in the arena. J. Clin. Invest. 112: 632–636 [PubMed] [Google Scholar]
  • Kochevenko A, Willmitzer L (2003) Chimeric RNA/DNA oligonucleotide-based site-specific modification of the tobacco acetolactate syntase gene. Plant Physiol. 132: 174–184 [CrossRef] [PubMed] [Google Scholar]
  • Laible G, Wagner S, Alderson J (2006) Oligonucleotide-mediated gene modification and its promise for animal agriculture. Gene 366: 17–26 [CrossRef] [PubMed] [Google Scholar]
  • Li XT, Costantino N, Lu LY, Liu DP, Watt RM, Cheah KS, Court DL, Huang JD (2003) Identification of factors influencing strand bias in oligonucleotide-mediated recombination in Escherichia coli. Nucleic Acids Res. 31: 6674–6687 [CrossRef] [PubMed] [Google Scholar]
  • Li J, Hsia AP, Schnable PS (2007) Recent advances in plant recombination. Curr. Opin. Plant Biol. 10: 131–135 [CrossRef] [PubMed] [Google Scholar]
  • Liu L, Rice MC, Kmiec EB (2001) In vivo gene repair of point and frameshift mutations directed by chimeric RNA/DNA oligonucleotides and modified single-stranded oligonucleotides. Nucleic Acids Res. 29: 4238–4250 [CrossRef] [PubMed] [Google Scholar]
  • Liu L, Rice MC, Drury M, Cheng S, Gamper H, Kmiec EB (2002) Strand bias in targeted gene repair is influenced by transcriptional activity. Mol. Cell. Biol. 22: 3852–3863 [CrossRef] [PubMed] [Google Scholar]
  • May GD, Kmiec EB, Rice MC, inventors. November 22, 2001. Plant gene targeting using oligonucleotides. World Intellectual Property Organization No. WO/2001/087914 [Google Scholar]
  • Murphy BR, Moayedpardazi HS, Gewirtz AM, Diamond SL, Pierce EA (2007) Delivery and mechanistic considerations for the production of knock-in mice by single-stranded oligonucleotide gene targeting. Gene Ther. 14: 304–315 [CrossRef] [PubMed] [Google Scholar]
  • Nielsen KM (2003) Transgenic organisms – time for conceptual diversification? Nat. Biotechnol. 21: 227–228 [CrossRef] [PubMed] [Google Scholar]
  • Okuzaki A, Toriyama K (2004) Chimeric RNA/DNA oligonucleotide-directed gene targeting in rice. Plant Cell Rep. 22: 509–512 [CrossRef] [PubMed] [Google Scholar]
  • Parekh-Olmedo H, Kmiec EB (2007) Progress and prospects: targeted gene alteration (TGA). Gene Ther. 14: 1675–1680 [CrossRef] [PubMed] [Google Scholar]
  • Parekh-Olmedo H, Ferrara L, Brachman E, Kmiec EB (2005) Gene therapy progress and prospects: targeted gene repair. Gene Ther. 12: 639–646 [CrossRef] [PubMed] [Google Scholar]
  • Radecke S, Radecke F, Peter I, Schwarz K (2006) Physical incorporation of a single-stranded oligodeoxynucleotide during targeted repair of a human chromosomal locus. J. Gene Med. 8: 217–228 [CrossRef] [PubMed] [Google Scholar]
  • Rando TA (2002) Oligonucleotide-mediated gene therapy for muscular dystrophies. Neuromuscul. Disord. Suppl 1: S55–S60 [Google Scholar]
  • Reiss B (2003) Homologous recombination and gene targeting in plant cells. Int. Rev. Cytol. 228: 85–139 [CrossRef] [PubMed] [Google Scholar]
  • Ruiter R, van den Brande I, Stals E, Delauré S, Cornelissen M, D'Halluin K (2003) Spontaneous mutation frequency in plants obscures the effect of chimeraplasty. Plant Mol. Biol. 53: 675–689 [CrossRef] [PubMed] [Google Scholar]
  • Simon P, Cannata F, Concordet JP, Giovannangeli C (2008) Targeting DNA with triplex-forming oligonucleotides to modify gene sequence. Biochimie 90: 1109–1116 [CrossRef] [PubMed] [Google Scholar]
  • Sørensen CB, Krogsdam AM, Andersen MS, Kristiansen K, Bolund L, Jensen TG (2005) Site-specific strand bias in gene correction using single-stranded oligonucleotides. J. Mol. Med. 83: 39–49 [CrossRef] [PubMed] [Google Scholar]
  • Storici F (2008) RNA-mediated DNA modifications and RNA-templated DNA repair. Curr. Opin. Mol. Ther. 10: 224–230 [PubMed] [Google Scholar]
  • Suzuki T (2008) Targeted gene modification by oligonucleotides and small DNA fragments in eukaryotes. Front. Biosci. 13: 737–744 [CrossRef] [PubMed] [Google Scholar]
  • Wright DA, Townsend JA, Winfrey RJ Jr, Irwin PA, Rajagopal J, Lonosky PM, Hall BD, Jondle MD, Voytas DF (2005) High-frequency homologous recombination in plants mediated by zinc-finger nucleases. Plant J. 44: 693–705 [CrossRef] [PubMed] [Google Scholar]
  • Wu XS, Liu DP, Liang CC (2001) Prospects of chimeric RNA-DNA oligonucleotides in gene therapy. J. Biomed. Sci. 8: 439–445 [CrossRef] [PubMed] [Google Scholar]
  • Yin W, Kren BT, Steer CJ (2005) Site-specific base changes in the coding or promoter region of the human beta- and gamma-globin genes by single-stranded oligonucleotides. Biochem. J. 390: 253–261 [CrossRef] [PubMed] [Google Scholar]
  • Zhang Z, Eriksson M, Falk G, Graff C, Presnell SC, Read MS, Nichols TC, Blombäck M, Anvret M (1998) Failure to achieve gene conversion with chimeric circular oligonucleotides: potentially misleading PCR artifacts observed. Antisense Nucleic Acid Drug Dev. 8: 531–536 [CrossRef] [PubMed] [Google Scholar]
  • Zhu T, Peterson DJ, Tagliani L, St Clair G, Baszczynski CL, Bowen B (1999) Targeted manipulation of maize genes in vivo using chimeric RNA/DNA oligonucleotides. Proc. Natl. Acad. Sci. USA 96: 8768–8773 [CrossRef] [Google Scholar]
  • Zhu T, Mettenburg K, Peterson DJ, Tagliani L, Baszczynski CL (2000) Engineering herbicide-resistant maize using chimeric RNA/DNA oligonucleotides. Nature Biotech. 18: 555–558 [CrossRef] [Google Scholar]