Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1995 Nov 11;23(21):4283–4289. doi: 10.1093/nar/23.21.4283

Characteristics of triplex-directed photoadduct formation by psoralen-linked oligodeoxynucleotides.

P J Bates 1, V M Macaulay 1, M J McLean 1, T C Jenkins 1, A P Reszka 1, C A Laughton 1, S Neidle 1
PMCID: PMC307381  PMID: 7501447

Abstract

A triplex-forming oligopyrimidine has been attached at its 5'-end to a photoreactive psoralen derivative and used to target a sequence which forms part of the coding region of the human aromatase gene. The 20 base pair sequence is not a perfect triplex target since it contains three pyrimidine interruptions within the purine-rich strand. Despite this, we have detected triplex-directed photoadduct formation at pH 7.0 between the psoralen-linked oligonucleotide and a 30mer duplex representing the aromatase target. Photoadduct formation was found to be sensitive to pH, temperature, cation concentration and the base composition of the third strand. By varying the base sequence of the target duplex around the psoralen intercalation site, we have characterised the site and mode of psoralen intercalation. The attached psoralen has been found to intercalate at the triplex-duplex junction with a strong preference for one orientation. We have shown that the psoralen will bind at the junction even when there is a preferred TpA step at an adjacent site. We have also compared the binding affinity and photoreactivity of oligodeoxyribonucleotides linked to two different psoralen derivatives and found differences in the rate of crosslinking and the extent of crosslink formation. Finally, we have examined oligodeoxyribonucleotides which are attached to psoralen by polymethylene linkers of different lengths.

Full text

PDF
4283

Images in this article

4285Image
on p.4285
4285Image
on p.4285
4286Image
on p.4286
4287Image
on p.4287
4288Image
on p.4288

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. 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]
  2. 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]
  3. 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]
  4. Corbin C. J., Graham-Lorence S., McPhaul M., Mason J. I., Mendelson C. R., Simpson E. R. Isolation of a full-length cDNA insert encoding human aromatase system cytochrome P-450 and its expression in nonsteroidogenic cells. Proc Natl Acad Sci U S A. 1988 Dec;85(23):8948–8952. doi: 10.1073/pnas.85.23.8948. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Degols G., Clarenc J. P., Lebleu B., Léonetti J. P. Reversible inhibition of gene expression by a psoralen functionalized triple helix forming oligonucleotide in intact cells. J Biol Chem. 1994 Jun 17;269(24):16933–16937. [PubMed] [Google Scholar]
  6. Durland R. H., Kessler D. J., Gunnell S., Duvic M., Pettitt B. M., Hogan M. E. Binding of triple helix forming oligonucleotides to sites in gene promoters. Biochemistry. 1991 Sep 24;30(38):9246–9255. doi: 10.1021/bi00102a017. [DOI] [PubMed] [Google Scholar]
  7. 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]
  8. Ebbinghaus S. W., Gee J. E., Rodu B., Mayfield C. A., Sanders G., Miller D. M. Triplex formation inhibits HER-2/neu transcription in vitro. J Clin Invest. 1993 Nov;92(5):2433–2439. doi: 10.1172/JCI116850. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. 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]
  10. Giovannangeli C., Thuong N. T., Hélène C. Oligonucleotide clamps arrest DNA synthesis on a single-stranded DNA target. Proc Natl Acad Sci U S A. 1993 Nov 1;90(21):10013–10017. doi: 10.1073/pnas.90.21.10013. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. 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]
  12. Grigoriev M., Praseuth D., Robin P., Hemar A., Saison-Behmoaras T., Dautry-Varsat A., Thuong N. T., Hélène C., Harel-Bellan A. A triple helix-forming oligonucleotide-intercalator conjugate acts as a transcriptional repressor via inhibition of NF kappa B binding to interleukin-2 receptor alpha-regulatory sequence. J Biol Chem. 1992 Feb 15;267(5):3389–3395. [PubMed] [Google Scholar]
  13. Hampel K. J., Crosson P., Lee J. S. Polyamines favor DNA triplex formation at neutral pH. Biochemistry. 1991 May 7;30(18):4455–4459. doi: 10.1021/bi00232a012. [DOI] [PubMed] [Google Scholar]
  14. 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]
  15. 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]
  16. Hyde J. E., Hearst J. E. Binding of psoralen derivatives to DNA and chromatin: influence of the ionic environment on dark binding and photoreactivity. Biochemistry. 1978 Apr 4;17(7):1251–1257. doi: 10.1021/bi00600a019. [DOI] [PubMed] [Google Scholar]
  17. 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]
  18. Kanne D., Rapoport H., Hearst J. E. 8-Methoxypsoralen-nucleic acid photoreaction. Effect of methyl substitution on pyrone vs. furan photoaddition. J Med Chem. 1984 Apr;27(4):531–534. doi: 10.1021/jm00370a017. [DOI] [PubMed] [Google Scholar]
  19. Le Doan T., Perrouault L., Praseuth D., Habhoub N., Decout J. L., Thuong N. T., Lhomme J., Hélène C. 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. 1987 Oct 12;15(19):7749–7760. doi: 10.1093/nar/15.19.7749. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Macaulay V. M., Bates P. J., McLean M. J., Rowlands M. G., Jenkins T. C., Ashworth A., Neidle S. Inhibition of aromatase expression by a psoralen-linked triplex-forming oligonucleotide targeted to a coding sequence. FEBS Lett. 1995 Sep 25;372(2-3):222–228. doi: 10.1016/0014-5793(95)00987-k. [DOI] [PubMed] [Google Scholar]
  21. 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]
  22. Mergny J. L., Sun J. S., Rougée M., Montenay-Garestier T., Barcelo F., Chomilier J., Hélène C. Sequence specificity in triple-helix formation: experimental and theoretical studies of the effect of mismatches on triplex stability. Biochemistry. 1991 Oct 8;30(40):9791–9798. doi: 10.1021/bi00104a031. [DOI] [PubMed] [Google Scholar]
  23. 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]
  24. Noonberg S. B., Scott G. K., Hunt C. A., Hogan M. E., Benz C. C. Inhibition of transcription factor binding to the HER2 promoter by triplex-forming oligodeoxyribonucleotides. Gene. 1994 Nov 4;149(1):123–126. doi: 10.1016/0378-1119(94)90420-0. [DOI] [PubMed] [Google Scholar]
  25. Orson F. M., Thomas D. W., McShan W. M., Kessler D. J., Hogan M. E. Oligonucleotide inhibition of IL2R alpha mRNA transcription by promoter region collinear triplex formation in lymphocytes. Nucleic Acids Res. 1991 Jun 25;19(12):3435–3441. doi: 10.1093/nar/19.12.3435. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Pilch D. S., Brousseau R., Shafer R. H. Thermodynamics of triple helix formation: spectrophotometric studies on the d(A)10.2d(T)10 and d(C+3T4C+3).d(G3A4G3).d(C3T4C3) triple helices. Nucleic Acids Res. 1990 Oct 11;18(19):5743–5750. doi: 10.1093/nar/18.19.5743. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Pilch D. S., Levenson C., Shafer R. H. Structure, stability, and thermodynamics of a short intermolecular purine-purine-pyrimidine triple helix. Biochemistry. 1991 Jun 25;30(25):6081–6088. doi: 10.1021/bi00239a001. [DOI] [PubMed] [Google Scholar]
  28. Plum G. E., Park Y. W., Singleton S. F., Dervan P. B., Breslauer K. J. Thermodynamic characterization of the stability and the melting behavior of a DNA triplex: a spectroscopic and calorimetric study. Proc Natl Acad Sci U S A. 1990 Dec;87(23):9436–9440. doi: 10.1073/pnas.87.23.9436. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. 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]
  30. Sandor Z., Bredberg A. Repair of triple helix directed psoralen adducts in human cells. Nucleic Acids Res. 1994 Jun 11;22(11):2051–2056. doi: 10.1093/nar/22.11.2051. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Scaggiante B., Morassutti C., Tolazzi G., Michelutti A., Baccarani M., Quadrifoglio F. Effect of unmodified triple helix-forming oligodeoxyribonucleotide targeted to human multidrug-resistance gene mdr1 in MDR cancer cells. FEBS Lett. 1994 Oct 3;352(3):380–384. doi: 10.1016/0014-5793(94)00995-3. [DOI] [PubMed] [Google Scholar]
  32. Shi Y. B., Spielmann H. P., Hearst J. E. Base-catalyzed reversal of a psoralen-DNA cross-link. Biochemistry. 1988 Jul 12;27(14):5174–5178. doi: 10.1021/bi00414a034. [DOI] [PubMed] [Google Scholar]
  33. Singleton S. F., Dervan P. B. Equilibrium association constants for oligonucleotide-directed triple helix formation at single DNA sites: linkage to cation valence and concentration. Biochemistry. 1993 Dec 7;32(48):13171–13179. doi: 10.1021/bi00211a028. [DOI] [PubMed] [Google Scholar]
  34. Sun J. S., De Bizemont T., Duval-Valentin G., Montenay-Garestier T., Hélène C. Extension of the range of recognition sequences for triple helix formation by oligonucleotides containing guanines and thymines. C R Acad Sci III. 1991;313(13):585–590. [PubMed] [Google Scholar]
  35. Sun J. S., François J. C., Montenay-Garestier T., Saison-Behmoaras T., Roig V., Thuong N. T., Hélène C. Sequence-specific intercalating agents: intercalation at specific sequences on duplex DNA via major groove recognition by oligonucleotide-intercalator conjugates. Proc Natl Acad Sci U S A. 1989 Dec;86(23):9198–9202. doi: 10.1073/pnas.86.23.9198. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Takasugi M., Guendouz A., Chassignol M., Decout J. L., Lhomme J., Thuong N. T., Hélène C. Sequence-specific photo-induced cross-linking of the two strands of double-helical DNA by a psoralen covalently linked to a triple helix-forming oligonucleotide. Proc Natl Acad Sci U S A. 1991 Jul 1;88(13):5602–5606. doi: 10.1073/pnas.88.13.5602. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Yoon K., Hobbs C. A., Koch J., Sardaro M., Kutny R., Weis A. L. Elucidation of the sequence-specific third-strand recognition of four Watson-Crick base pairs in a pyrimidine triple-helix motif: T.AT, C.GC, T.CG, and G.TA. Proc Natl Acad Sci U S A. 1992 May 1;89(9):3840–3844. doi: 10.1073/pnas.89.9.3840. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES