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. 1995 Jun 11;23(11):1956–1963. doi: 10.1093/nar/23.11.1956

Effect of competing self-structure on triplex formation with purine-rich oligodeoxynucleotides containing GA repeats.

S B Noonberg 1, J C François 1, T Garestier 1, C Hélène 1
PMCID: PMC306969  PMID: 7596824

Abstract

Competition between triplex formation with double-stranded DNA and oligonucleotide self-association was investigated in 23mer GA and GT oligonucleotides containing d(GA)5 or d(GT)5 repeats. Whereas triplex formation with GT oligonucleotides was diminished when temperature increased from 4 to 37 degrees C, triplex formation with GA oligonucleotides was enhanced when temperature increased within the same range due to the presence of competing intermolecular GA oligonucleotide self-structure. This self-structure was determined to be a homoduplex stabilized by the internal GA repeats. UV spectroscopy of these homoduplexes demonstrated a single sharp transition with rapid kinetics (Tm = 38.5-43.5 degrees C over strand concentrations of 0.5-4 microM, respectively, with transition enthalpy, delta H = -89 +/- 7 kcal/mol) in 10 mM MgCl2, 100 mM NaCl, pH 7.0. Homoduplex formation was strongly stabilized by multivalent cations (spermine > Mg2+ = Ca2+) and destabilized by low concentrations of monovalent cations (K+ = Li+ = Na+) in the presence of divalent cations. However, unlike GA or GT oligonucleotide-containing triplexes, the homoduplex formed even in the absence of multivalent cations, stabilized by only moderate concentrations of monovalent cations (Li+ > Na+ > K+). Through the development of multiple equilibrium states and the resulting depletion of free oligonucleotide, it was found that the presence of competing self-structure could decrease triplex formation under a variety of experimental conditions.

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Selected References

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  1. Arnott S., Chandrasekaran R., Marttila C. M. Structures for polyinosinic acid and polyguanylic acid. Biochem J. 1974 Aug;141(2):537–543. doi: 10.1042/bj1410537. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. 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]
  3. Cantor C. R., Warshaw M. M., Shapiro H. Oligonucleotide interactions. 3. Circular dichroism studies of the conformation of deoxyoligonucleotides. Biopolymers. 1970;9(9):1059–1077. doi: 10.1002/bip.1970.360090909. [DOI] [PubMed] [Google Scholar]
  4. Cheng A. J., Van Dyke M. W. Monovalent cation effects on intermolecular purine-purine-pyrimidine triple-helix formation. Nucleic Acids Res. 1993 Dec 11;21(24):5630–5635. doi: 10.1093/nar/21.24.5630. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. 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]
  6. 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]
  7. 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]
  8. Escudé C., François J. C., Sun J. S., Ott G., Sprinzl M., Garestier T., Hélène C. Stability of triple helices containing RNA and DNA strands: experimental and molecular modeling studies. Nucleic Acids Res. 1993 Dec 11;21(24):5547–5553. doi: 10.1093/nar/21.24.5547. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Evertsz E. M., Rippe K., Jovin T. M. Parallel-stranded duplex DNA containing blocks of trans purine-purine and purine-pyrimidine base pairs. Nucleic Acids Res. 1994 Aug 25;22(16):3293–3303. doi: 10.1093/nar/22.16.3293. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Gee J. E., Blume S., Snyder R. C., Ray R., Miller D. M. Triplex formation prevents Sp1 binding to the dihydrofolate reductase promoter. J Biol Chem. 1992 Jun 5;267(16):11163–11167. [PubMed] [Google Scholar]
  11. Giovannangéli C., Rougée M., Garestier T., Thuong N. T., Hélène C. Triple-helix formation by oligonucleotides containing the three bases thymine, cytosine, and guanine. Proc Natl Acad Sci U S A. 1992 Sep 15;89(18):8631–8635. doi: 10.1073/pnas.89.18.8631. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. 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]
  13. Grigoriev M., Praseuth D., Guieysse A. L., Robin P., Thuong N. T., Hélène C., Harel-Bellan A. Inhibition of interleukin-2 receptor alpha-subunit gene expression by oligonucleotide-directed triple helix formation. C R Acad Sci III. 1993;316(5):492–495. [PubMed] [Google Scholar]
  14. 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]
  15. Hobbs C. A., Yoon K. Differential regulation of gene expression in vivo by triple helix-forming oligonucleotides as detected by a reporter enzyme. Antisense Res Dev. 1994 Spring;4(1):1–8. doi: 10.1089/ard.1994.4.1. [DOI] [PubMed] [Google Scholar]
  16. Huertas D., Bellsolell L., Casasnovas J. M., Coll M., Azorín F. Alternating d(GA)n DNA sequences form antiparallel stranded homoduplexes stabilized by the formation of G.A base pairs. EMBO J. 1993 Oct;12(10):4029–4038. doi: 10.1002/j.1460-2075.1993.tb06081.x. [DOI] [PMC free article] [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. Jaishree T. N., Wang A. H. NMR studies of pH-dependent conformational polymorphism of alternating (C-T)n sequences. Nucleic Acids Res. 1993 Aug 11;21(16):3839–3844. doi: 10.1093/nar/21.16.3839. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Kim S. W., Lajara R., Rotwein P. Structure and function of a human insulin-like growth factor-I gene promoter. Mol Endocrinol. 1991 Dec;5(12):1964–1972. doi: 10.1210/mend-5-12-1964. [DOI] [PubMed] [Google Scholar]
  20. LANGRIDGE R., RICH A. Molecular structure of helical polycytidylic acid. Nature. 1963 May 25;198:725–728. doi: 10.1038/198725a0. [DOI] [PubMed] [Google Scholar]
  21. Lee J. S. The stability of polypurine tetraplexes in the presence of mono- and divalent cations. Nucleic Acids Res. 1990 Oct 25;18(20):6057–6060. doi: 10.1093/nar/18.20.6057. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. 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]
  23. Malkov V. A., Voloshin O. N., Soyfer V. N., Frank-Kamenetskii M. D. Cation and sequence effects on stability of intermolecular pyrimidine-purine-purine triplex. Nucleic Acids Res. 1993 Feb 11;21(3):585–591. doi: 10.1093/nar/21.3.585. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Manor H., Rao B. S., Martin R. G. Abundance and degree of dispersion of genomic d(GA)n.d(TC)n sequences. J Mol Evol. 1988;27(2):96–101. doi: 10.1007/BF02138367. [DOI] [PubMed] [Google Scholar]
  25. Mayfield C., Ebbinghaus S., Gee J., Jones D., Rodu B., Squibb M., Miller D. Triplex formation by the human Ha-ras promoter inhibits Sp1 binding and in vitro transcription. J Biol Chem. 1994 Jul 8;269(27):18232–18238. [PubMed] [Google Scholar]
  26. Mayfield C., Miller D. Effect of abasic linker substitution on triplex formation, Sp1 binding, and specificity in an oligonucleotide targeted to the human Ha-ras promoter. Nucleic Acids Res. 1994 May 25;22(10):1909–1916. doi: 10.1093/nar/22.10.1909. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Mayfield C., Squibb M., Miller D. Inhibition of nuclear protein binding to the human Ki-ras promoter by triplex-forming oligonucleotides. Biochemistry. 1994 Mar 22;33(11):3358–3363. doi: 10.1021/bi00177a029. [DOI] [PubMed] [Google Scholar]
  28. McShan W. M., Rossen R. D., Laughter A. H., Trial J., Kessler D. J., Zendegui J. G., Hogan M. E., Orson F. M. Inhibition of transcription of HIV-1 in infected human cells by oligodeoxynucleotides designed to form DNA triple helices. J Biol Chem. 1992 Mar 15;267(8):5712–5721. [PubMed] [Google Scholar]
  29. 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]
  30. Olivas W. M., Maher L. J., 3rd Competitive triplex/quadruplex equilibria involving guanine-rich oligonucleotides. Biochemistry. 1995 Jan 10;34(1):278–284. doi: 10.1021/bi00001a034. [DOI] [PubMed] [Google Scholar]
  31. 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]
  32. 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]
  33. Ramsing N. B., Jovin T. M. Parallel stranded duplex DNA. Nucleic Acids Res. 1988 Jul 25;16(14A):6659–6676. doi: 10.1093/nar/16.14.6659. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Rando R. F., DePaolis L., Durland R. H., Jayaraman K., Kessler D. J., Hogan M. E. Inhibition of T7 and T3 RNA polymerase directed transcription elongation in vitro. Nucleic Acids Res. 1994 Feb 25;22(4):678–685. doi: 10.1093/nar/22.4.678. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Rippe K., Fritsch V., Westhof E., Jovin T. M. Alternating d(G-A) sequences form a parallel-stranded DNA homoduplex. EMBO J. 1992 Oct;11(10):3777–3786. doi: 10.1002/j.1460-2075.1992.tb05463.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Rippe K., Jovin T. M. Parallel-stranded duplex DNA. Methods Enzymol. 1992;211:199–220. doi: 10.1016/0076-6879(92)11013-9. [DOI] [PubMed] [Google Scholar]
  37. Roberts R. W., Crothers D. M. Specificity and stringency in DNA triplex formation. Proc Natl Acad Sci U S A. 1991 Nov 1;88(21):9397–9401. doi: 10.1073/pnas.88.21.9397. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Robinson H., Wang A. H. 5'-CGA sequence is a strong motif for homo base-paired parallel-stranded DNA duplex as revealed by NMR analysis. Proc Natl Acad Sci U S A. 1993 Jun 1;90(11):5224–5228. doi: 10.1073/pnas.90.11.5224. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Robinson H., van der Marel G. A., van Boom J. H., Wang A. H. Unusual DNA conformation at low pH revealed by NMR: parallel-stranded DNA duplex with homo base pairs. Biochemistry. 1992 Nov 3;31(43):10510–10517. doi: 10.1021/bi00158a014. [DOI] [PubMed] [Google Scholar]
  40. Roy C. Inhibition of gene transcription by purine rich triplex forming oligodeoxyribonucleotides. Nucleic Acids Res. 1993 Jun 25;21(12):2845–2852. doi: 10.1093/nar/21.12.2845. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Scaria P. V., Shire S. J., Shafer R. H. Quadruplex structure of d(G3T4G3) stabilized by K+ or Na+ is an asymmetric hairpin dimer. Proc Natl Acad Sci U S A. 1992 Nov 1;89(21):10336–10340. doi: 10.1073/pnas.89.21.10336. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. 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]
  43. 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]
  44. Trung Le Doan, Perrouault L., Chassignol M., Nguyen T. T., Hélène C. Sequence-targeted chemical modifications of nucleic acids by complementary oligonucleotides covalently linked to porphyrins. Nucleic Acids Res. 1987 Nov 11;15(21):8643–8659. doi: 10.1093/nar/15.21.8643. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Wang Y., Patel D. J. Solution structure of the d(T-C-G-A) duplex at acidic pH. A parallel-stranded helix containing C+ .C, G.G and A.A pairs. J Mol Biol. 1994 Sep 30;242(4):508–526. [PubMed] [Google Scholar]
  46. Young S. L., Krawczyk S. H., Matteucci M. D., Toole J. J. Triple helix formation inhibits transcription elongation in vitro. Proc Natl Acad Sci U S A. 1991 Nov 15;88(22):10023–10026. doi: 10.1073/pnas.88.22.10023. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Zimmerman S. B., Cohen G. H., Davies D. R. X-ray fiber diffraction and model-building study of polyguanylic acid and polyinosinic acid. J Mol Biol. 1975 Feb 25;92(2):181–192. doi: 10.1016/0022-2836(75)90222-3. [DOI] [PubMed] [Google Scholar]

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