Triplex-Stimulated Intermolecular Recombination at a Single-Copy Genomic Target

Molecular Therapy

Volumn 14, Issue 3, 2006, Pages 392-400

  Knauert, Melissa P ^a   Kalish, Jennifer M ^a   Hegan, Denise C ^a   Glazer, Peter M ^a  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

firefly luciferase; gene correction; homologous recombination; oligonucleotide; phosphoramidate; triplex forming oligonucleotide

Indexed keywords

FIREFLY LUCIFERASE; OLIGONUCLEOTIDE; SINGLE STRANDED DNA;

ANIMAL CELL; ARTICLE; CONTROLLED STUDY; GENE LOCUS; GENE TARGETING; GENE THERAPY; GENETIC TRANSFECTION; HOMOLOGOUS RECOMBINATION; MAMMAL CELL; NONHUMAN; REPORTER GENE; TRIPLE HELIX;

ANIMALS; CELL LINE; CHO CELLS; CRICETINAE; CRICETULUS; DNA; DNA, SINGLE-STRANDED; GENE TARGETING; GENE THERAPY; GENES, REPORTER; HUMANS; LUCIFERASES, FIREFLY; OLIGONUCLEOTIDES; RECOMBINATION, GENETIC; TRANSFECTION;

MAMMALIA;

EID: 33746923523     PISSN: 15250016     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ymthe.2006.03.020     Document Type: Article

References (38)

1. Capecchi M.R. Altering the genome by homologous recombination. Science 244 (1989) 1288-1292
2. Doetschman T., Maeda N., and Smithies O. Targeted mutation of the Hprt gene in mouse embryonic stem cells. Proc. Natl. Acad. Sci. USA 85 (1988) 8583-8587
3. Hendrie P.C., Hirata R.K., and Russell D.W. Chromosomal integration and homologous gene targeting by replication-incompetent vectors based on the autonomous parvovirus minute virus of mice. J. Virol. 77 (2003) 13136-13145
4. Chamberlain J.R., et al. Gene targeting in stem cells from individuals with osteogenesis imperfecta. Science 303 (2004) 1198-1201
5. Vasquez K.M., Marburger K., Intody Z., and Wilson J.H. Manipulating the mammalian genome by homologous recombination. Proc. Natl. Acad. Sci. USA 98 (2001) 8403-8410
6. Jasin M. Genetic manipulation of genomes with rare-cutting endonucleases. Trends Genet. 12 (1996) 224-228
7. Waldman A.S. Targeted homologous recombination in mammalian cells. Crit. Rev. Oncol. Hematol. 12 (1992) 49-64
8. Taghian D.G., and Nickoloff J.A. Chromosomal double-strand breaks induce gene conversion at high frequency in mammalian cells. Mol. Cell. Biol. 17 (1997) 6386-6393
9. Donoho G., Jasin M., and Berg P. Analysis of gene targeting and intrachromosomal homologous recombination stimulated by genomic double-strand breaks in mouse embryonic stem cells. Mol. Cell. Biol. 18 (1998) 4070-4078
10. Lukacsovich T., Yang D., and Waldman A.S. Repair of a specific double-strand break generated within a mammalian chromosome by yeast endonuclease I-SceI. Nucleic Acids Res. 22 (1994) 5649-5657
11. Datta H.J., Chan P.P., Vasquez K.M., Gupta R.C., and Glazer P.M. Triplex-induced recombination in human cell-free extracts. dependence on xpa and hsrad51. J. Biol. Chem. 276 (2001) 18018-18023
12. Porteus M.H., Cathomen T., Weitzman M.D., and Baltimore D. Efficient gene targeting mediated by adeno-associated virus and DNA double-strand breaks. Mol. Cell. Biol. 23 (2003) 3558-3565
13. Porteus M.H., and Baltimore D. Chimeric nucleases stimulate gene targeting in human cells. Science 300 (2003) 763
14. Bibikova M., Beumer K., Trautman J.K., and Carroll D. Enhancing gene targeting with designed zinc finger nucleases. Science 300 (2003) 764
15. Urnov F.D., et al. Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 435 (2005) 646-651
16. Broitman S.L., Im D.D., and Fresco J.R. Formation of the triple-stranded polynucleotide helix, poly(A.A.U). Proc. Natl. Acad. Sci. USA 84 (1987) 5120-5124
17. Le Doan T., et al. Sequence-specific recognition, photocrosslinking and cleavage of the DNA double helix by an oligo-[alpha]-thymidylate covalently linked to an azidoproflavine derivative. Nucleic Acids Res. 15 (1987) 7749-7760
18. Moser H.E., and Dervan P.B. Sequence-specific cleavage of double helical DNA by triple helix formation. Science 238 (1987) 645-650
19. Letai A.G., Palladino M.A., Fromm E., Rizzo V., and Fresco J.R. Specificity in formation of triple-stranded nucleic acid helical complexes: studies with agarose-linked polyribonucleotide affinity columns. Biochemistry 27 (1988) 9108-9112
20. Kohwi Y., and Kohwi-Shigematsu T. Magnesium ion-dependent triple-helix structure formed by homopurine-homopyrimidine sequences in supercoiled plasmid DNA. Proc. Natl. Acad. Sci. USA 85 (1988) 3781-3785
21. Pilch D.S., Levenson C., and Shafer R.H. Structure, stability, and thermodynamics of a short intermolecular purine-purine-pyrimidine triple helix. Biochemistry 30 (1991) 6081-6088
22. Beal P.A., and Dervan P.B. Second structural motif for recognition of DNA by oligonucleotide-directed triple-helix formation. Science 251 (1991) 1360-1363
23. Postel E.H., Flint S.J., Kessler D.J., and Hogan M.E. Evidence that a triplex-forming oligodeoxyribonucleotide binds to the c-myc promoter in HeLa cells, thereby reducing c-myc mRNA levels. Proc. Natl. Acad. Sci. USA 88 (1991) 8227-8231
24. Kohwi Y., Malkhosyan S.R., and Kohwi-Shigematsu T. Intramolecular dG.dG.dC triplex detected in Escherichia coli cells. J. Mol. Biol. 223 (1992) 817-822
25. Faruqi A.F., Seidman M.M., Segal D.J., Carroll D., and Glazer P.M. Recombination induced by triple helix-targeted DNA damage in mammalian cells. Mol. Cell. Biol. 16 (1996) 6820-6828
26. Wang G., Seidman M.M., and Glazer P.M. Mutagenesis in mammalian cells induced by triple helix formation and transcription-coupled repair. Science 271 (1996) 802-805
27. Faruqi A.F., Datta H.J., Carroll D., Seidman M.M., and Glazer P.M. Triple-helix formation induces recombination in mammalian cells via a nucleotide excision repair-dependent pathway. Mol. Cell. Biol. 20 (2000) 990-1000
28. Knauert M.P., et al. Distance and affinity dependence of triplex-induced recombination. Biochemistry 44 (2005) 3856-3864
29. Wang G., and Glazer P.M. Altered repair of targeted psoralen photoadducts in the context of an oligonucleotide-mediated triple helix. J. Biol. Chem. 270 (1995) 22595-22601
30. Luo Z., Macris M.A., Faruqi A.F., and Glazer P.M. High-frequency intrachromosomal gene conversion induced by triplex-forming oligonucleotides microinjected into mouse cells. Proc. Natl. Acad. Sci. USA 97 (2000) 9003-9008
31. Kalish J.M., Seidman M.M., Weeks D.L., and Glazer P.M. Triplex-induced recombination and repair in the pyrimidine motif. Nucleic Acids Res. 33 (2005) 3492-3502
32. Sorensen C.B., et al. Site-specific strand bias in gene correction using single-stranded oligonucleotides. J. Mol. Med. 83 (2005) 39-49
33. Olsen P.A., Randol M., and Krauss S. Implications of cell cycle progression on functional sequence correction by short single-stranded DNA oligonucleotides. Gene Ther. 12 (2005) 546-551
34. Asensio J.L., Carr R., Brown T., and Lane A.N. Conformational and thermodynamic properties of parallel intramolecular triple helices containing a DNA, RNA, or 2′-OMeDNA third strand. J. Am. Chem. Soc. 121 (1999) 11063-11070
35. Chan P.P., et al. Targeted correction of an episomal gene in mammalian cells by a short DNA fragment tethered to a triplex-forming oligonucleotide. J. Biol. Chem. 274 (1999) 11541-11548
36. Kahan B.D., et al. Phase I and phase II safety and efficacy trial of intercellular adhesion molecule-1 antisense oligodeoxynucleotide (ISIS 2302) for the prevention of acute allograft rejection. Transplantation 78 (2004) 858-863
37. Miller D.G., Petek L.M., and Russell D.W. Human gene targeting by adeno-associated virus vectors is enhanced by DNA double-strand breaks. Mol. Cell. Biol. 23 (2003) 3550-3557
38. Southern E.M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J. Mol. Biol. 98 (1975) 503-517