Abstract
Gene therapy has been hindered by the low frequency of homologous recombination in mammalian cells. To stimulate recombination, we investigated the use of triple-helix-forming oligonucleotides (TFOs) to target DNA damage to a selected site within cells. By treating cells with TFOs linked to psoralen, recombination was induced within a simian virus 40 vector carrying two mutant copies of the supF tRNA reporter gene. Gene conversion events, as well as mutations at the target site, were also observed. The variety of products suggests that multiple cellular pathways can act on the targeted damage, and data showing that the triple helix can influence these pathways are presented. The ability to specifically induce recombination or gene conversion within mammalian cells by using TFOs may provide a new research tool and may eventually lead to novel applications in gene therapy.
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- Beal P. A., Dervan P. B. Second structural motif for recognition of DNA by oligonucleotide-directed triple-helix formation. Science. 1991 Mar 15;251(4999):1360–1363. doi: 10.1126/science.2003222. [DOI] [PubMed] [Google Scholar]
- Bollag R. J., Waldman A. S., Liskay R. M. Homologous recombination in mammalian cells. Annu Rev Genet. 1989;23:199–225. doi: 10.1146/annurev.ge.23.120189.001215. [DOI] [PubMed] [Google Scholar]
- Cheng S., Sancar A., Hearst J. E. RecA-dependent incision of psoralen-crosslinked DNA by (A)BC excinuclease. Nucleic Acids Res. 1991 Feb 11;19(3):657–663. doi: 10.1093/nar/19.3.657. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Cheng S., Van Houten B., Gamper H. B., Sancar A., Hearst J. E. Use of psoralen-modified oligonucleotides to trap three-stranded RecA-DNA complexes and repair of these cross-linked complexes by ABC excinuclease. J Biol Chem. 1988 Oct 15;263(29):15110–15117. [PubMed] [Google Scholar]
- Choulika A., Perrin A., Dujon B., Nicolas J. F. Induction of homologous recombination in mammalian chromosomes by using the I-SceI system of Saccharomyces cerevisiae. Mol Cell Biol. 1995 Apr;15(4):1968–1973. doi: 10.1128/mcb.15.4.1968. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Cimino G. D., Gamper H. B., Isaacs S. T., Hearst J. E. Psoralens as photoactive probes of nucleic acid structure and function: organic chemistry, photochemistry, and biochemistry. Annu Rev Biochem. 1985;54:1151–1193. doi: 10.1146/annurev.bi.54.070185.005443. [DOI] [PubMed] [Google Scholar]
- Cole R. S. Repair of DNA containing interstrand crosslinks in Escherichia coli: sequential excision and recombination. Proc Natl Acad Sci U S A. 1973 Apr;70(4):1064–1068. doi: 10.1073/pnas.70.4.1064. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Cooney M., Czernuszewicz G., Postel E. H., Flint S. J., Hogan M. E. Site-specific oligonucleotide binding represses transcription of the human c-myc gene in vitro. Science. 1988 Jul 22;241(4864):456–459. doi: 10.1126/science.3293213. [DOI] [PubMed] [Google Scholar]
- Dardalhon M., Averbeck D. Pulsed-field gel electrophoresis analysis of the repair of psoralen plus UVA induced DNA photoadducts in Saccharomyces cerevisiae. Mutat Res. 1995 Jan;336(1):49–60. doi: 10.1016/0921-8777(94)00037-7. [DOI] [PubMed] [Google Scholar]
- Deng W. P., Nickoloff J. A. Mismatch repair of heteroduplex DNA intermediates of extrachromosomal recombination in mammalian cells. Mol Cell Biol. 1994 Jan;14(1):400–406. doi: 10.1128/mcb.14.1.400. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Desautels L., Brouillette S., Wallenburg J., Belmaaza A., Gusew N., Trudel P., Chartrand P. Characterization of nonconservative homologous junctions in mammalian cells. Mol Cell Biol. 1990 Dec;10(12):6613–6618. doi: 10.1128/mcb.10.12.6613. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Duval-Valentin G., Thuong N. T., Hélène C. Specific inhibition of transcription by triple helix-forming oligonucleotides. Proc Natl Acad Sci U S A. 1992 Jan 15;89(2):504–508. doi: 10.1073/pnas.89.2.504. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gasparro F. P., Havre P. A., Olack G. A., Gunther E. J., Glazer P. M. Site-specific targeting of psoralen photoadducts with a triple helix-forming oligonucleotide: characterization of psoralen monoadduct and crosslink formation. Nucleic Acids Res. 1994 Jul 25;22(14):2845–2852. doi: 10.1093/nar/22.14.2845. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Grigoriev M., Praseuth D., Guieysse A. L., Robin P., Thuong N. T., Hélène C., Harel-Bellan A. Inhibition of gene expression by triple helix-directed DNA cross-linking at specific sites. Proc Natl Acad Sci U S A. 1993 Apr 15;90(8):3501–3505. doi: 10.1073/pnas.90.8.3501. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hanson K. D., Sedivy J. M. Analysis of biological selections for high-efficiency gene targeting. Mol Cell Biol. 1995 Jan;15(1):45–51. doi: 10.1128/mcb.15.1.45. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hasty P., Rivera-Pérez J., Bradley A. The role and fate of DNA ends for homologous recombination in embryonic stem cells. Mol Cell Biol. 1992 Jun;12(6):2464–2474. doi: 10.1128/mcb.12.6.2464. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Havre P. A., Glazer P. M. Targeted mutagenesis of simian virus 40 DNA mediated by a triple helix-forming oligonucleotide. J Virol. 1993 Dec;67(12):7324–7331. doi: 10.1128/jvi.67.12.7324-7331.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Havre P. A., Gunther E. J., Gasparro F. P., Glazer P. M. Targeted mutagenesis of DNA using triple helix-forming oligonucleotides linked to psoralen. Proc Natl Acad Sci U S A. 1993 Aug 15;90(16):7879–7883. doi: 10.1073/pnas.90.16.7879. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Huang J. C., Svoboda D. L., Reardon J. T., Sancar A. Human nucleotide excision nuclease removes thymine dimers from DNA by incising the 22nd phosphodiester bond 5' and the 6th phosphodiester bond 3' to the photodimer. Proc Natl Acad Sci U S A. 1992 Apr 15;89(8):3664–3668. doi: 10.1073/pnas.89.8.3664. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ing N. H., Beekman J. M., Kessler D. J., Murphy M., Jayaraman K., Zendegui J. G., Hogan M. E., O'Malley B. W., Tsai M. J. In vivo transcription of a progesterone-responsive gene is specifically inhibited by a triplex-forming oligonucleotide. Nucleic Acids Res. 1993 Jun 25;21(12):2789–2796. doi: 10.1093/nar/21.12.2789. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Jachymczyk W. J., von Borstel R. C., Mowat M. R., Hastings P. J. Repair of interstrand cross-links in DNA of Saccharomyces cerevisiae requires two systems for DNA repair: the RAD3 system and the RAD51 system. Mol Gen Genet. 1981;182(2):196–205. doi: 10.1007/BF00269658. [DOI] [PubMed] [Google Scholar]
- Kucherlapati R. S., Eves E. M., Song K. Y., Morse B. S., Smithies O. Homologous recombination between plasmids in mammalian cells can be enhanced by treatment of input DNA. Proc Natl Acad Sci U S A. 1984 May;81(10):3153–3157. doi: 10.1073/pnas.81.10.3153. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Letai A. G., Palladino M. A., Fromm E., Rizzo V., Fresco J. R. Specificity in formation of triple-stranded nucleic acid helical complexes: studies with agarose-linked polyribonucleotide affinity columns. Biochemistry. 1988 Dec 27;27(26):9108–9112. doi: 10.1021/bi00426a007. [DOI] [PubMed] [Google Scholar]
- Lin F. L., Sperle K., Sternberg N. Intermolecular recombination between DNAs introduced into mouse L cells is mediated by a nonconservative pathway that leads to crossover products. Mol Cell Biol. 1990 Jan;10(1):103–112. doi: 10.1128/mcb.10.1.103. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lin P. F., Bardwell E., Howard-Flanders P. Initiation of genetic exchanges in lambda phage--prophage crosses. Proc Natl Acad Sci U S A. 1977 Jan;74(1):291–295. doi: 10.1073/pnas.74.1.291. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Maher L. J., 3rd, Wold B., Dervan P. B. Inhibition of DNA binding proteins by oligonucleotide-directed triple helix formation. Science. 1989 Aug 18;245(4919):725–730. doi: 10.1126/science.2549631. [DOI] [PubMed] [Google Scholar]
- Mansour S. L., Thomas K. R., Capecchi M. R. Disruption of the proto-oncogene int-2 in mouse embryo-derived stem cells: a general strategy for targeting mutations to non-selectable genes. Nature. 1988 Nov 24;336(6197):348–352. doi: 10.1038/336348a0. [DOI] [PubMed] [Google Scholar]
- Maryon E., Carroll D. Involvement of single-stranded tails in homologous recombination of DNA injected into Xenopus laevis oocyte nuclei. Mol Cell Biol. 1991 Jun;11(6):3268–3277. doi: 10.1128/mcb.11.6.3268. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Moser H. E., Dervan P. B. Sequence-specific cleavage of double helical DNA by triple helix formation. Science. 1987 Oct 30;238(4827):645–650. doi: 10.1126/science.3118463. [DOI] [PubMed] [Google Scholar]
- Parris C. N., Seidman M. M. A signature element distinguishes sibling and independent mutations in a shuttle vector plasmid. Gene. 1992 Aug 1;117(1):1–5. doi: 10.1016/0378-1119(92)90482-5. [DOI] [PubMed] [Google Scholar]
- Perrouault L., Asseline U., Rivalle C., Thuong N. T., Bisagni E., Giovannangeli C., Le Doan T., Hélène C. Sequence-specific artificial photo-induced endonucleases based on triple helix-forming oligonucleotides. Nature. 1990 Mar 22;344(6264):358–360. doi: 10.1038/344358a0. [DOI] [PubMed] [Google Scholar]
- Postel E. H., Flint S. J., Kessler D. J., 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 U S A. 1991 Sep 15;88(18):8227–8231. doi: 10.1073/pnas.88.18.8227. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Praseuth D., Perrouault L., Le Doan T., Chassignol M., Thuong N., Hélène C. Sequence-specific binding and photocrosslinking of alpha and beta oligodeoxynucleotides to the major groove of DNA via triple-helix formation. Proc Natl Acad Sci U S A. 1988 Mar;85(5):1349–1353. doi: 10.1073/pnas.85.5.1349. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Raha M., Wang G., Seidman M. M., Glazer P. M. Mutagenesis by third-strand-directed psoralen adducts in repair-deficient human cells: high frequency and altered spectrum in a xeroderma pigmentosum variant. Proc Natl Acad Sci U S A. 1996 Apr 2;93(7):2941–2946. doi: 10.1073/pnas.93.7.2941. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Reardon J. T., Spielmann P., Huang J. C., Sastry S., Sancar A., Hearst J. E. Removal of psoralen monoadducts and crosslinks by human cell free extracts. Nucleic Acids Res. 1991 Sep 11;19(17):4623–4629. doi: 10.1093/nar/19.17.4623. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Rouet P., Smih F., Jasin M. Expression of a site-specific endonuclease stimulates homologous recombination in mammalian cells. Proc Natl Acad Sci U S A. 1994 Jun 21;91(13):6064–6068. doi: 10.1073/pnas.91.13.6064. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Saffran W. A., Cantor C. R., Smith E. D., Magdi M. Psoralen damage-induced plasmid recombination in Saccharomyces cerevisiae: dependence on RAD1 and RAD52. Mutat Res. 1992 Jun;274(1):1–9. doi: 10.1016/0921-8777(92)90038-5. [DOI] [PubMed] [Google Scholar]
- Sandor Z., Bredberg A. Triple helix directed psoralen adducts induce a low frequency of recombination in an SV40 shuttle vector. Biochim Biophys Acta. 1995 Sep 19;1263(3):235–240. doi: 10.1016/0167-4781(95)00109-t. [DOI] [PubMed] [Google Scholar]
- Segal D. J., Carroll D. Endonuclease-induced, targeted homologous extrachromosomal recombination in Xenopus oocytes. Proc Natl Acad Sci U S A. 1995 Jan 31;92(3):806–810. doi: 10.1073/pnas.92.3.806. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sladek F. M., Melian A., Howard-Flanders P. Incision by UvrABC excinuclease is a step in the path to mutagenesis by psoralen crosslinks in Escherichia coli. Proc Natl Acad Sci U S A. 1989 Jun;86(11):3982–3986. doi: 10.1073/pnas.86.11.3982. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sladek F. M., Munn M. M., Rupp W. D., Howard-Flanders P. In vitro repair of psoralen-DNA cross-links by RecA, UvrABC, and the 5'-exonuclease of DNA polymerase I. J Biol Chem. 1989 Apr 25;264(12):6755–6765. [PubMed] [Google Scholar]
- Strobel S. A., Doucette-Stamm L. A., Riba L., Housman D. E., Dervan P. B. Site-specific cleavage of human chromosome 4 mediated by triple-helix formation. Science. 1991 Dec 13;254(5038):1639–1642. doi: 10.1126/science.1836279. [DOI] [PubMed] [Google Scholar]
- Thomas K. R., Folger K. R., Capecchi M. R. High frequency targeting of genes to specific sites in the mammalian genome. Cell. 1986 Feb 14;44(3):419–428. doi: 10.1016/0092-8674(86)90463-0. [DOI] [PubMed] [Google Scholar]
- Tsujimura T., Maher V. M., Godwin A. R., Liskay R. M., McCormick J. J. Frequency of intrachromosomal homologous recombination induced by UV radiation in normally repairing and excision repair-deficient human cells. Proc Natl Acad Sci U S A. 1990 Feb;87(4):1566–1570. doi: 10.1073/pnas.87.4.1566. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Van Houten B., Gamper H., Hearst J. E., Sancar A. Analysis of sequential steps of nucleotide excision repair in Escherichia coli using synthetic substrates containing single psoralen adducts. J Biol Chem. 1988 Nov 15;263(32):16553–16560. [PubMed] [Google Scholar]
- Van Houten B., Gamper H., Holbrook S. R., Hearst J. E., Sancar A. Action mechanism of ABC excision nuclease on a DNA substrate containing a psoralen crosslink at a defined position. Proc Natl Acad Sci U S A. 1986 Nov;83(21):8077–8081. doi: 10.1073/pnas.83.21.8077. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Vos J. M., Hanawalt P. C. DNA interstrand cross-links promote chromosomal integration of a selected gene in human cells. Mol Cell Biol. 1989 Jul;9(7):2897–2905. doi: 10.1128/mcb.9.7.2897. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wang G., Glazer P. M. Altered repair of targeted psoralen photoadducts in the context of an oligonucleotide-mediated triple helix. J Biol Chem. 1995 Sep 22;270(38):22595–22601. doi: 10.1074/jbc.270.38.22595. [DOI] [PubMed] [Google Scholar]
- Wang G., Levy D. D., Seidman M. M., Glazer P. M. Targeted mutagenesis in mammalian cells mediated by intracellular triple helix formation. Mol Cell Biol. 1995 Mar;15(3):1759–1768. doi: 10.1128/mcb.15.3.1759. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wang G., Seidman M. M., Glazer P. M. Mutagenesis in mammalian cells induced by triple helix formation and transcription-coupled repair. Science. 1996 Feb 9;271(5250):802–805. doi: 10.1126/science.271.5250.802. [DOI] [PubMed] [Google Scholar]
- Wang Y. Y., Maher V. M., Liskay R. M., McCormick J. J. Carcinogens can induce homologous recombination between duplicated chromosomal sequences in mouse L cells. Mol Cell Biol. 1988 Jan;8(1):196–202. doi: 10.1128/mcb.8.1.196. [DOI] [PMC free article] [PubMed] [Google Scholar]