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

Bibliography

• Parekh-Olmedo H, Kmiec EB. Progress and prospects: targeted gene alteration (TGA). Gene Ther 2007;14:1675-80
   PubMed Web of Science ®Google Scholar
• Yoon K, Cole-Strauss A, Kmiec EB. Targeted gene correction of episomal DNA in mammalian cells mediated by a chimeric RNA-DNA oligonucleotide. Proc Natl Acad Sci USA 1996;93:2071-6
   PubMed Web of Science ®Google Scholar
• Cole-Strauss A, Yoon K, Xiang Y, Correction of the mutation responsible for sickle cell anemia by an RNA-DNA oligonucleotide. Science 1996;273:1386-9
   PubMed Web of Science ®Google Scholar
• Tagalakis AD, Graham IR, Riddell DR, Gene correction of the apolipoprotein (Apo) E2 phenotype to wild-type ApoE3 by in situ chimeraplasty. J Biol Chem 2001;276:13226-30
   PubMed Web of Science ®Google Scholar
• Zhang Z, Eriksson M, Falk G, Failure to achieve gene conversion with chimeric circular oligonucleotides: potentially misleading PCR artifacts observed. Antisense Nucleic Acid Drug Dev 1998;8:531-6
   PubMedGoogle Scholar
• van der Steege G, Schuilenga-Hut PH, Buys CH, Persistent failures in gene repair. Nat Biotechnol 2001;19:305-6
   PubMed Web of Science ®Google Scholar
• Manzano A, Mohri Z, Sperber G, Failure to generate atheroprotective apolipoprotein AI phenotypes using synthetic RNA/DNA oligonucleotides (chimeraplasts). J Gene Med 2003;5:795-802
   PubMed Web of Science ®Google Scholar
• Moerschell RP, Tsunasawa S, Sherman F. Transformation of yeast with synthetic oligonucleotides. Proc Natl Acad Sci USA 1988;85:524-8
   PubMed Web of Science ®Google Scholar
• Campbell CR, Keown W, Lowe L, Homologous recombination involving small single-stranded oligonucleotides in human cells. New Biol 1989;1:223-7
   PubMedGoogle Scholar
• Gamper HB, Parekh H, Rice MC, The DNA strand of chimeric RNA/DNA oligonucleotides can direct gene repair/conversion activity in mammalian and plant cell-free extracts. Nucleic Acids Res 2000;28:4332-9
   PubMed Web of Science ®Google Scholar
• Pierce EA, Liu Q, Igoucheva O, Oligonucleotide-directed single-base DNA alterations in mouse embryonic stem cells. Gene Ther 2003;10:24-33
   PubMed Web of Science ®Google Scholar
• Dekker M, Brouwers C, te Riele H. Targeted gene modification in mismatch-repair-deficient embryonic stem cells by single-stranded DNA oligonucleotides. Nucleic Acids Res 2003;31:e27
   PubMed Web of Science ®Google Scholar
• Nickerson HD, Colledge WH. A LacZ-based transgenic mouse for detection of somatic gene repair events in vivo. Gene Ther 2004;11:1351-7
   PubMed Web of Science ®Google Scholar
• Olsen PA, Randøl M, Luna L, Genomic sequence correction by single-stranded DNA oligonucleotides: role of DNA synthesis and chemical modifications of the oligonucleotide ends. J Gene Med 2005;7:1534-44
   PubMed Web of Science ®Google Scholar
• Aarts M, Dekker M, de Vries S, Generation of a mouse mutant by oligonucleotide-mediated gene modification in ES cells. Nucleic Acids Res 2006;34:e147
   PubMed Web of Science ®Google Scholar
• Radecke S, Radecke F, Peter I, Schwarz K. Physical incorporation of a single-stranded oligodeoxynucleotide during targeted repair of a human chromosomal locus. J Gene Med 2006;8:217-28
   PubMed Web of Science ®Google Scholar
• Morozov V, Wawrousek EF. Single-strand DNA-mediated targeted mutagenesis of genomic DNA in early mouse embryos is stimulated by Rad51/54 and by Ku70/86 inhibition. Gene Ther 2007;15:468-72
   PubMed Web of Science ®Google Scholar
• Igoucheva O, Alexeev V, Anni H, Rubin E. Oligonucleotide-mediated gene targeting in human hepatocytes: implications of mismatch repair. Oligonucleotides 2008;18:111-22
   PubMed Web of Science ®Google Scholar
• Disterer P, Simons JP, Owen JS. Validation of oligonucleotide-mediated gene editing. Gene Ther 2009;16:824-6
   PubMed Web of Science ®Google Scholar
• Papaioannou I, Disterer P, Owen JS. Use of internally nuclease-protected single-strand DNA oligonucleotides and silencing the mismatch repair protein, MSH2, enhance replication of corrected cells following gene editing. J Gene Med 2009;11:267-74
   PubMed Web of Science ®Google Scholar
• Bertoni C, Morris GE, Rando TA. Strand bias in oligonucleotide-mediated dystrophin gene editing. Hum Mol Genet 2005;14:221-33
   PubMed Web of Science ®Google Scholar
• Andrieu-Soler C, Halhal M, Boatright JH, Single-stranded oligonucleotide-mediated in vivo gene repair in the rd1 retina. Mol Vis 2007;13:692-706
   PubMed Web of Science ®Google Scholar
• Olsen PA, Randol M, Krauss S. Implications of cell cycle progression on functional sequence correction by short single-stranded DNA oligonucleotides. Gene Ther 2005;12:546-51
   PubMed Web of Science ®Google Scholar
• Ferrara L, Kmiec EB. Targeted gene repair activates Chk1 and Chk2 and stalls replication in corrected cells. DNA Repair (Amst) 2006;5:422-31
   PubMed Web of Science ®Google Scholar
• Gamper HB Jr, Cole-Strauss A, Metz R, A plausible mechanism for gene correction by chimeric oligonucleotides. Biochemistry 2000;39:5808-16
   PubMed Web of Science ®Google Scholar
• Drury MD, Kmiec EB. Double displacement loops (double d-loops) are templates for oligonucleotide-directed mutagenesis and gene repair. Oligonucleotides 2004;14:274-86
   PubMed Web of Science ®Google Scholar
• Igoucheva O, Alexeev V, Yoon K. Mechanism of gene repair open for discussion. Oligonucleotides 2004;14:311-21
   PubMed Web of Science ®Google Scholar
• Aarts M, te Riele H. Subtle gene modification in mouse ES cells: evidence for incorporation of unmodified oligonucleotides without induction of DNA damage. Nucleic Acids Res 2010;38:6956-67
   PubMed Web of Science ®Google Scholar
• Moynahan ME, Jasin M. Mitotic homologous recombination maintains genomic stability and suppresses tumorigenesis. Nat Rev Mol Cell Biol 2010;11:196-207
   PubMed Web of Science ®Google Scholar
• Rauth S, Song KY, Ayares D, Transfection and homologous recombination involving single-stranded DNA substrates in mammalian cells and nuclear extracts. Proc Natl Acad Sci USA 1986;83:5587-91
   PubMed Web of Science ®Google Scholar
• Alexeev V, Igoucheva O, Yoon K. Simultaneous targeted alteration of the tyrosinase and c-kit genes by single-stranded oligonucleotides. Gene Ther 2002;9:1667-75
   PubMed Web of Science ®Google Scholar
• Radecke F, Radecke S, Schwarz K. Unmodified oligodeoxynucleotides require single-strandedness to induce targeted repair of a chromosomal EGFP gene. J Gene Med 2004;6:1257-71
   PubMed Web of Science ®Google Scholar
• Ferrara L, Engstrom JU, Schwartz T, Recovery of cell cycle delay following targeted gene repair by oligonucleotides. DNA Repair (Amst) 2007;6:1529-35
   PubMed Web of Science ®Google Scholar
• Igoucheva O, Alexeev V, Yoon K. Differential cellular responses to exogenous DNA in mammalian cells and its effect on oligonucleotide-directed gene modification. Gene Ther 2006;13:266-75
   PubMed Web of Science ®Google Scholar
• Olsen PA, Solhaug A, Booth JA, Cellular responses to targeted genomic sequence modification using single-stranded oligonucleotides and zinc-finger nucleases. DNA Repair (Amst) 2009;8:298-308
   PubMedGoogle Scholar
• Bonner M, Kmiec EB. DNA breakage associated with targeted gene alteration directed by DNA oligonucleotides. Mutat Res 2009;669:85-94
   PubMed Web of Science ®Google Scholar
• Disterer P, Papaioannou I, Evans VC, Oligonucleotide-mediated gene editing is underestimated in cells expressing mutated GFP, and is positively associated with target protein expression. J Gene Med 2012;14:109-119
   PubMed Web of Science ®Google Scholar
• Jensen NM, Dalsgaard T, Jakobsen M, An update on targeted gene repair in mammalian cells: methods and mechanisms. J Biomed Sci 2011;18:10
   PubMed Web of Science ®Google Scholar
• Storici F, Snipe JR, Chan GK, Conservative repair of a chromosomal double-strand break by single-strand DNA through two steps of annealing. Mol Cell Biol 2006;26:7645-57
   PubMed Web of Science ®Google Scholar
• Liu J, Majumdar A, Liu J, Sequence conversion by single strand oligonucleotide donors via non-homologous end joining in mammalian cells. J Biol Chem 2010;285:23198-207
   PubMed Web of Science ®Google Scholar
• Paques F, Haber JE. Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 1999;63:349-404
   PubMed Web of Science ®Google Scholar
• Wang Z, Zhou ZJ, Liu DP, Huang JD. Single-stranded oligonucleotide-mediated gene repair in mammalian cells has a mechanism distinct from homologous recombination repair. Biochem Biophys Res Commun 2006;350:568-73
   PubMed Web of Science ®Google Scholar
• Rodriguez-Bravo V, Guaita-Esteruelas S, Salvador N, Different S/M checkpoint responses of tumor and non tumor cell lines to DNA replication inhibition. Cancer Res 2007;67:11648-56
   PubMed Web of Science ®Google Scholar
• Modrich P. Mechanisms in eukaryotic mismatch repair. J Biol Chem 2006;281:30305-9
   PubMed Web of Science ®Google Scholar
• Evans E, Alani E. Roles for mismatch repair factors in regulating genetic recombination. Mol Cell Biol 2000;20:7839-44
   PubMed Web of Science ®Google Scholar
• Sugawara N, Goldfarb T, Studamire B, Heteroduplex rejection during single-strand annealing requires Sgs1 helicase and mismatch repair proteins Msh2 and Msh6 but not Pms1. Proc Natl Acad Sci USA 2004;101:9315-20
   PubMed Web of Science ®Google Scholar
• Dekker M, Brouwers C, Aarts M, Effective oligonucleotide-mediated gene disruption in ES cells lacking the mismatch repair protein MSH3. Gene Ther 2006;13:686-94
   PubMed Web of Science ®Google Scholar
• Adamson AW, Beardsley DI, Kim WJ, Methylator-induced, mismatch repair-dependent G2 arrest is activated through Chk1 and Chk2. Mol Biol Cell 2005;16:1513-26
   PubMed Web of Science ®Google Scholar
• O'Brien V, Brown R. Signalling cell cycle arrest and cell death through the MMR System. Carcinogenesis 2006;27:682-92
   PubMed Web of Science ®Google Scholar
• Wielders EA, Dekker RJ, Holt I, Characterization of MSH2 variants by endogenous gene modification in mouse embryonic stem cells. Hum Mutat 2011;32:389-96
   PubMed Web of Science ®Google Scholar
• Dekker M, de Vries S, Aarts M, Transient suppression of MLH1 allows effective single-nucleotide substitution by single-stranded DNA oligonucleotides. Mutat Res 2011;715:52-60
   PubMed Web of Science ®Google Scholar
• Sancar A. DNA excision repair. Annu Rev Biochem 1996;65:43-81
   PubMed Web of Science ®Google Scholar
• Igoucheva O, Alexeev V, Scharer O, Yoon K. Involvement of ERCC1/XPF and XPG in oligodeoxynucleotide-directed gene modification. Oligonucleotides 2006;16:94-104
   PubMed Web of Science ®Google Scholar
• Aarts M, te Riele H. Progress and prospects: oligonucleotide-directed gene modification in mouse embryonic stem cells: a route to therapeutic application. Gene Ther 2011;18:213-19
   PubMed Web of Science ®Google Scholar
• Bertoni C, Rustagi A, Rando TA. Enhanced gene repair mediated by methyl-CpG-modified single-stranded oligonucleotides. Nucleic Acids Res 2009;37:7468-82
   PubMed Web of Science ®Google Scholar
• Andrieu-Soler C, Casas M, Faussat AM, Stable transmission of targeted gene modification using single-stranded oligonucleotides with flanking LNAs. Nucleic Acids Res 2005;33:3733-42
   PubMed Web of Science ®Google Scholar
• Wuepping M, Kenner O, Hegele H, Higher efficiency of thymine-adenine clamp-modified single-stranded oligonucleotides in targeted nucleotide sequence correction is not correlated with lower intracellular degradation. Hum Gene Ther 2009;20:283-7
   PubMed Web of Science ®Google Scholar
• Zendegui JG, Vasquez KM, Tinsley JH, In vivo stability and kinetics of absorption and disposition of 3' phosphopropyl amine oligonucleotides. Nucleic Acids Res 1992;20:307-14
   PubMed Web of Science ®Google Scholar
• Vasquez KM, Narayanan L, Glazer PM. Specific mutations induced by triplex-forming oligonucleotides in mice. Science 2000;290:530-3
   PubMed Web of Science ®Google Scholar
• Burgin AB Jr, Huizenga BN, Nash HA. A novel suicide substrate for DNA topoisomerases and site-specific recombinases. Nucleic Acids Res 1995;23:2973-9
   PubMed Web of Science ®Google Scholar
• Kayali R, Bury F, Ballard M, Bertoni C. Site-directed gene repair of the dystrophin gene mediated by PNA-ssODNs. Hum Mol Genet 2010;19:3266-81
   PubMed Web of Science ®Google Scholar
• Porteus MH, Carroll D. Gene targeting using zinc finger nucleases. Nat Biotechnol 2005;23:967-73
   PubMed Web of Science ®Google Scholar
• Porteus MH. Mammalian gene targeting with designed zinc finger nucleases. Mol Ther 2006;13:438-46
   PubMed Web of Science ®Google Scholar
• Maeder ML, Thibodeau-Beganny S, Osiak A, Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification. Mol Cell 2008;31:294-301
   PubMed Web of Science ®Google Scholar
• Lombardo A, Genovese P, Beausejour CM, Gene editing in human stem cells using zinc finger nucleases and integrase-defective lentiviral vector delivery. Nat Biotechnol 2007;25:1298-306
   PubMed Web of Science ®Google Scholar
• Geurts AM, Cost GJ, Freyvert Y, Knockout rats via embryo microinjection of zinc-finger nucleases. Science 2009;325:433
   PubMed Web of Science ®Google Scholar
• Osiak A, Radecke F, Guhl E, Selection-independent generation of gene knockout mouse embryonic stem cells using zinc-finger nucleases. PLoS One 2011;6:e28911
   PubMed Web of Science ®Google Scholar
• Hockemeyer D, Soldner F, Beard C, Efficient targeting of expressed and silent genes in human ESCs and iPSCs using zinc-finger nucleases. Nat Biotechnol 2009;27:851-7
   PubMed Web of Science ®Google Scholar
• Mussolino C, Cathomen T. On target? Tracing zinc-finger-nuclease specificity. Nat Methods 2011;8:725-6
   PubMed Web of Science ®Google Scholar
• Isalan M. Zinc-finger nucleases: how to play two good hands. Nat Methods 2012;9:32-4
   Google Scholar
• Pruett-Miller SM, Reading DW, Porter SN, Porteus MH. Attenuation of zinc finger nuclease toxicity by small-molecule regulation of protein levels. PLoS Genet 2009;5:e1000376
   PubMed Web of Science ®Google Scholar
• Zou J, Maeder ML, Mali P, Gene targeting of a disease-related gene in human induced pluripotent stem and embryonic stem cells. Cell Stem Cell 2009;5:97-110
   PubMed Web of Science ®Google Scholar
• Sander JD, Dahlborg EJ, Goodwin MJ, Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA). Nat Methods 2011;8:67-9
   PubMed Web of Science ®Google Scholar
• Kim S, Lee MJ, Kim H, Preassembled zinc-finger arrays for rapid construction of ZFNs. Nat Methods 2011;8:7
   PubMed Web of Science ®Google Scholar
• Radecke F, Peter I, Radecke S, Targeted chromosomal gene modification in human cells by single-stranded oligodeoxynucleotides in the presence of a DNA double-strand break. Mol Ther 2006;14:798-808
   PubMed Web of Science ®Google Scholar
• Wang Z, Zhou ZJ, Liu DP, Huang JD. Double-stranded break can be repaired by single-stranded oligonucleotides via the ATM/ATR pathway in mammalian cells. Oligonucleotides 2008;18:21-32
   PubMed Web of Science ®Google Scholar
• Radecke S, Radecke F, Cathomen T, Schwarz K. Zinc-finger nuclease-induced gene repair with oligodeoxynucleotides: wanted and unwanted target locus modifications. Mol Ther 2010;18:743-53
   PubMed Web of Science ®Google Scholar
• Chen F, Pruett-Miller SM, Huang Y, High-frequency genome editing using ssDNA oligonucleotides with zinc-finger nucleases. Nat Methods 2011;8:753-5
   PubMed Web of Science ®Google Scholar
• Li T, Huang S, Zhao X, Modularly assembled designer TAL effector nucleases for targeted gene knockout and gene replacement in eukaryotes. Nucleic Acids Res 2011;39:6315-25
   PubMed Web of Science ®Google Scholar
• Mussolini C, Morbitzer R, Lutge F, A novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity. Nucleic Acids Res 2011;39:9283-93
   PubMed Web of Science ®Google Scholar
• Silva G, Poirot L, Galetto R, Meganucleases and other tools for targeted genome engineering: perspectives and challenges for gene therapy. Curr Gene Ther 2011;11:11-27
   PubMed Web of Science ®Google Scholar
• Soldner F, Laganiere J, Cheng AW, Generation of isogenic pluripotent stem cells differing exclusively at two early onset Parkinson point mutations. Cell 2011;146:318-31
   PubMed Web of Science ®Google Scholar
• Li H, Haurigot V, Doyon Y, In vivo genome editing restores haemostasis in a mouse model of haemophilia. Nature 2011;475:217-21
   PubMed Web of Science ®Google Scholar