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. 1997 Sep 1;25(17):3459–3464. doi: 10.1093/nar/25.17.3459

Recruitment of transcription factors to the target site by triplex-forming oligonucleotides.

F Svinarchuk 1, I Nagibneva 1, D Cherny 1, S Ait-Si-Ali 1, L L Pritchard 1, P Robin 1, C Malvy 1, A Harel-Bellan 1, D Chern 1
PMCID: PMC146923  PMID: 9254704

Abstract

Triplex-forming oligonucleotides (TFOs) are generally designed to inhibit transcription or DNA replication but can be used for more diverse purposes. Here we have designed a hairpin-TFO able to recruit transcription factors to a target DNA. The designed oligonucleotide contains a triplex-forming sequence, linked through a nucleotide loop to a double-stranded hairpin including the SRE enhancer of the c-fos gene promoter. We show here that this oligonucleotide can specifically recognise its DNA target at physiological salt and pH conditions. The stability of the triplex formed under these conditions is very high: >90% of the triplex remains intact after 24 h of incubation. Bound to the double-stranded target DNA, the oligonucleotide retains its ability to interact specifically with transcription factors, recruiting them to the proximity of the target DNA. Our results suggest that this type of oligonucleotide may prove useful in the design of new tools for artificial modulation of gene expression.

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Selected References

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  1. Dubochet J., Ducommun M., Zollinger M., Kellenberger E. A new preparation method for dark-field electron microscopy of biomacromolecules. J Ultrastruct Res. 1971 Apr;35(1):147–167. doi: 10.1016/s0022-5320(71)80148-x. [DOI] [PubMed] [Google Scholar]
  2. Frank-Kamenetskii M. D., Mirkin S. M. Triplex DNA structures. Annu Rev Biochem. 1995;64:65–95. doi: 10.1146/annurev.bi.64.070195.000433. [DOI] [PubMed] [Google Scholar]
  3. Giovannangeli C., Diviacco S., Labrousse V., Gryaznov S., Charneau P., Helene C. Accessibility of nuclear DNA to triplex-forming oligonucleotides: the integrated HIV-1 provirus as a target. Proc Natl Acad Sci U S A. 1997 Jan 7;94(1):79–84. doi: 10.1073/pnas.94.1.79. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. 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]
  5. Liberles D. A., Dervan P. B. Design of artificial sequence-specific DNA bending ligands. Proc Natl Acad Sci U S A. 1996 Sep 3;93(18):9510–9514. doi: 10.1073/pnas.93.18.9510. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Magnaghi-Jaulin L., Masutani H., Robin P., Lipinski M., Harel-Bellan A. SRE elements are binding sites for the fusion protein EWS-FLI-1. Nucleic Acids Res. 1996 Mar 15;24(6):1052–1058. doi: 10.1093/nar/24.6.1052. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Maher L. J., 3rd Prospects for the therapeutic use of antigene oligonucleotides. Cancer Invest. 1996;14(1):66–82. doi: 10.3109/07357909609018437. [DOI] [PubMed] [Google Scholar]
  8. Nikolov D. B., Burley S. K. RNA polymerase II transcription initiation: a structural view. Proc Natl Acad Sci U S A. 1997 Jan 7;94(1):15–22. doi: 10.1073/pnas.94.1.15. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Norman C., Runswick M., Pollock R., Treisman R. Isolation and properties of cDNA clones encoding SRF, a transcription factor that binds to the c-fos serum response element. Cell. 1988 Dec 23;55(6):989–1003. doi: 10.1016/0092-8674(88)90244-9. [DOI] [PubMed] [Google Scholar]
  10. Phan-Dinh-Tuy F., Tuil D., Schweighoffer F., Pinset C., Kahn A., Minty A. The 'CC.Ar.GG' box. A protein-binding site common to transcription-regulatory regions of the cardiac actin, c-fos and interleukin-2 receptor genes. Eur J Biochem. 1988 May 2;173(3):507–515. doi: 10.1111/j.1432-1033.1988.tb14027.x. [DOI] [PubMed] [Google Scholar]
  11. Ptashne M., Gann A. A. Activators and targets. Nature. 1990 Jul 26;346(6282):329–331. doi: 10.1038/346329a0. [DOI] [PubMed] [Google Scholar]
  12. Schröter H., Mueller C. G., Meese K., Nordheim A. Synergism in ternary complex formation between the dimeric glycoprotein p67SRF, polypeptide p62TCF and the c-fos serum response element. EMBO J. 1990 Apr;9(4):1123–1130. doi: 10.1002/j.1460-2075.1990.tb08218.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Shaw P. E., Schröter H., Nordheim A. The ability of a ternary complex to form over the serum response element correlates with serum inducibility of the human c-fos promoter. Cell. 1989 Feb 24;56(4):563–572. doi: 10.1016/0092-8674(89)90579-5. [DOI] [PubMed] [Google Scholar]
  14. Shaw P. E. Ternary complex formation over the c-fos serum response element: p62TCF exhibits dual component specificity with contacts to DNA and an extended structure in the DNA-binding domain of p67SRF. EMBO J. 1992 Aug;11(8):3011–3019. doi: 10.1002/j.1460-2075.1992.tb05371.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Strobel S. A., Dervan P. B. Single-site enzymatic cleavage of yeast genomic DNA mediated by triple helix formation. Nature. 1991 Mar 14;350(6314):172–174. doi: 10.1038/350172a0. [DOI] [PubMed] [Google Scholar]
  16. 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]
  17. Sun J. S., Garestier T., Hélène C. Oligonucleotide directed triple helix formation. Curr Opin Struct Biol. 1996 Jun;6(3):327–333. doi: 10.1016/s0959-440x(96)80051-0. [DOI] [PubMed] [Google Scholar]
  18. Svinarchuk F., Bertrand J. R., Malvy C. A short purine oligonucleotide forms a highly stable triple helix with the promoter of the murine c-pim-1 proto-oncogene. Nucleic Acids Res. 1994 Sep 11;22(18):3742–3747. doi: 10.1093/nar/22.18.3742. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Svinarchuk F., Cherny D., Debin A., Delain E., Malvy C. A new approach to overcome potassium-mediated inhibition of triplex formation. Nucleic Acids Res. 1996 Oct 1;24(19):3858–3865. doi: 10.1093/nar/24.19.3858. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Svinarchuk F., Debin A., Bertrand J. R., Malvy C. Investigation of the intracellular stability and formation of a triple helix formed with a short purine oligonucleotide targeted to the murine c-pim-1 proto-oncogene promotor. Nucleic Acids Res. 1996 Jan 15;24(2):295–302. doi: 10.1093/nar/24.2.295. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Svinarchuk F., Monnot M., Merle A., Malvy C., Fermandjian S. The high stability of the triple helices formed between short purine oligonucleotides and SIV/HIV-2 vpx genes is determined by the targeted DNA structure. Nucleic Acids Res. 1995 Oct 11;23(19):3831–3836. doi: 10.1093/nar/23.19.3831. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Svinarchuk F., Paoletti J., Malvy C. An unusually stable purine(purine-pyrimidine) short triplex. The third strand stabilizes double-stranded DNA. J Biol Chem. 1995 Jun 9;270(23):14068–14071. doi: 10.1074/jbc.270.23.14068. [DOI] [PubMed] [Google Scholar]
  23. Treisman R. Identification of a protein-binding site that mediates transcriptional response of the c-fos gene to serum factors. Cell. 1986 Aug 15;46(4):567–574. doi: 10.1016/0092-8674(86)90882-2. [DOI] [PubMed] [Google Scholar]
  24. Treisman R. The SRE: a growth factor responsive transcriptional regulator. Semin Cancer Biol. 1990 Feb;1(1):47–58. [PubMed] [Google Scholar]
  25. Treisman R. Transient accumulation of c-fos RNA following serum stimulation requires a conserved 5' element and c-fos 3' sequences. Cell. 1985 Oct;42(3):889–902. doi: 10.1016/0092-8674(85)90285-5. [DOI] [PubMed] [Google Scholar]
  26. Trouche D., Grigoriev M., Lenormand J. L., Robin P., Leibovitch S. A., Sassone-Corsi P., Harel-Bellan A. Repression of c-fos promoter by MyoD on muscle cell differentiation. Nature. 1993 May 6;363(6424):79–82. doi: 10.1038/363079a0. [DOI] [PubMed] [Google Scholar]
  27. Voloshin O. N., Mirkin S. M., Lyamichev V. I., Belotserkovskii B. P., Frank-Kamenetskii M. D. Chemical probing of homopurine-homopyrimidine mirror repeats in supercoiled DNA. Nature. 1988 Jun 2;333(6172):475–476. doi: 10.1038/333475a0. [DOI] [PubMed] [Google Scholar]

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