Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1996 Nov 1;24(21):4176–4184. doi: 10.1093/nar/24.21.4176

Efficient triple helix formation by oligodeoxyribonucleotides containing alpha- or beta-2-amino-5-(2-deoxy-D-ribofuranosyl) pyridine residues.

P J Bates 1, C A Laughton 1, T C Jenkins 1, D C Capaldi 1, P D Roselt 1, C B Reese 1, S Neidle 1
PMCID: PMC146246  PMID: 8932369

Abstract

Triple helices containing C+xGxC triplets are destabilised at physiological pH due to the requirement for base protonation of 2'-deoxycytidine (dC), which has a pKa of 4.3. The C nucleoside 2-amino-5-(2'-deoxy-beta-D-ribofuranosyl)pyridine (beta-AP) is structurally analogous to dC but is considerably more basic, with a pKa of 5.93. We have synthesised 5'-psoralen linked oligodeoxyribonucleotides (ODNs) containing thymidine (dT) and either beta-AP or its alpha-anomer (alpha-AP) and have assessed their ability to form triplexes with a double-stranded target derived from standard deoxynucleotides (i.e. beta-anomers). Third strand ODNs derived from dT and beta-AP were found to have considerably higher binding affinities for the target than the corresponding ODNs derived from dT and either dC or 5-methyl-2'-deoxycytidine (5-Me-dC). ODNs containing dT and alpha-AP also showed enhanced triplex formation with the duplex target and, in addition are more stable in serum-containing medium than standard oligopyrimidine-derived ODNs or ODNs derived from dT and beta-AP. Molecular modelling studies showed that an alpha-anomeric AP nucleotide can be accommodated within an otherwise beta-anomeric triplex with only minor perturbation of the triplex structure. Molecular dynamics (MD) simulations on triplexes containing either the alpha- or beta-anomer of (N1-protonated) AP showed that in both cases the base retained two standard hydrogen bonds to its associated guanine when the 'A-type' model of the triplex was used as the start-point for the simulation, but that bifurcated hydrogen bonds resulted when the alternative 'B-type' triplex model was used. The lack of a differential stability between alpha-AP- and beta-AP-containing triplexes at pH >7, predicted from the behaviour of the B-type models, suggests that the A-type models are more appropriate.

Full Text

The Full Text of this article is available as a PDF (225.0 KB).

Selected References

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

  1. Arnott S., Bond P. J., Selsing E., Smith P. J. Models of triple-stranded polynucleotides with optimised stereochemistry. Nucleic Acids Res. 1976 Oct;3(10):2459–2470. doi: 10.1093/nar/3.10.2459. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Arnott S., Selsing E. Structures for the polynucleotide complexes poly(dA) with poly (dT) and poly(dT) with poly(dA) with poly (dT). J Mol Biol. 1974 Sep 15;88(2):509–521. doi: 10.1016/0022-2836(74)90498-7. [DOI] [PubMed] [Google Scholar]
  3. Bates P. J., Dosanjh H. S., Kumar S., Jenkins T. C., Laughton C. A., Neidle S. Detection and kinetic studies of triplex formation by oligodeoxynucleotides using real-time biomolecular interaction analysis (BIA). Nucleic Acids Res. 1995 Sep 25;23(18):3627–3632. doi: 10.1093/nar/23.18.3627. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bates P. J., Macaulay V. M., McLean M. J., Jenkins T. C., Reszka A. P., Laughton C. A., Neidle S. Characteristics of triplex-directed photoadduct formation by psoralen-linked oligodeoxynucleotides. Nucleic Acids Res. 1995 Nov 11;23(21):4283–4289. doi: 10.1093/nar/23.21.4283. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. 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]
  6. Boiziau C., Debart F., Rayner B., Imbach J. L., Toulme J. J. Chimeric alpha-beta oligonucleotides as antisense inhibitors of reverse transcription. FEBS Lett. 1995 Mar 13;361(1):41–45. doi: 10.1016/0014-5793(95)00138-y. [DOI] [PubMed] [Google Scholar]
  7. 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]
  8. Jetter M. C., Hobbs F. W. 7,8-Dihydro-8-oxoadenine as a replacement for cytosine in the third strand of triple helices. Triplex formation without hypochromicity. Biochemistry. 1993 Apr 6;32(13):3249–3254. doi: 10.1021/bi00064a006. [DOI] [PubMed] [Google Scholar]
  9. Krawczyk S. H., Milligan J. F., Wadwani S., Moulds C., Froehler B. C., Matteucci M. D. Oligonucleotide-mediated triple helix formation using an N3-protonated deoxycytidine analog exhibiting pH-independent binding within the physiological range. Proc Natl Acad Sci U S A. 1992 May 1;89(9):3761–3764. doi: 10.1073/pnas.89.9.3761. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Laughton C. A., Neidle S. Molecular dynamics simulation of the DNA triplex d(TC)5.d(GA)5.d(C+T)5. J Mol Biol. 1992 Jan 20;223(2):519–529. doi: 10.1016/0022-2836(92)90667-9. [DOI] [PubMed] [Google Scholar]
  11. Laughton C. A., Neidle S. Prediction of the structure of the Y+.R-.R(+)-type DNA triple helix by molecular modelling. Nucleic Acids Res. 1992 Dec 25;20(24):6535–6541. doi: 10.1093/nar/20.24.6535. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Liquier J., Letellier R., Dagneaux C., Ouali M., Morvan F., Raynier B., Imbach J. L., Taillandier E. Triple helix formation by alpha-oligodeoxynucleotides: a vibrational spectroscopy and molecular modeling study. Biochemistry. 1993 Oct 12;32(40):10591–10598. doi: 10.1021/bi00091a008. [DOI] [PubMed] [Google Scholar]
  13. 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]
  14. Macaya R., Wang E., Schultze P., Sklenár V., Feigon J. Proton nuclear magnetic resonance assignments and structural characterization of an intramolecular DNA triplex. J Mol Biol. 1992 Jun 5;225(3):755–773. doi: 10.1016/0022-2836(92)90399-5. [DOI] [PubMed] [Google Scholar]
  15. Noonberg S. B., François J. C., Praseuth D., Guieysse-Peugeot A. L., Lacoste J., Garestier T., Hélène C. Triplex formation with alpha anomers of purine-rich and pyrimidine-rich oligodeoxynucleotides. Nucleic Acids Res. 1995 Oct 25;23(20):4042–4049. doi: 10.1093/nar/23.20.4042. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Ojwang J., Okleberry K. M., Marshall H. B., Vu H. M., Huffman J. H., Rando R. F. Inhibition of Friend murine leukemia virus activity by guanosine/thymidine oligonucleotides. Antiviral Res. 1994 Sep;25(1):27–41. doi: 10.1016/0166-3542(94)90091-4. [DOI] [PubMed] [Google Scholar]
  17. 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]
  18. Orozco M., Laughton C. A., Herzyk P., Neidle S. Molecular-mechanics modelling of drug-DNA structures; the effects of differing dielectric treatment on helix parameters and comparison with a fully solvated structural model. J Biomol Struct Dyn. 1990 Oct;8(2):359–373. doi: 10.1080/07391102.1990.10507810. [DOI] [PubMed] [Google Scholar]
  19. Radhakrishnan I., Patel D. J. DNA triplexes: solution structures, hydration sites, energetics, interactions, and function. Biochemistry. 1994 Sep 27;33(38):11405–11416. doi: 10.1021/bi00204a001. [DOI] [PubMed] [Google Scholar]
  20. Radhakrishnan I., Patel D. J., Gao X. Three-dimensional homonuclear NOESY-TOCSY of an intramolecular pyrimidine.purine.pyrimidine DNA triplex containing a central G.TA triple: nonexchangeable proton assignments and structural implications. Biochemistry. 1992 Mar 10;31(9):2514–2523. doi: 10.1021/bi00124a011. [DOI] [PubMed] [Google Scholar]
  21. Raghunathan G., Miles H. T., Sasisekharan V. Symmetry and molecular structure of a DNA triple helix: d(T)n.d(A)n.d(T)n. Biochemistry. 1993 Jan 19;32(2):455–462. doi: 10.1021/bi00053a009. [DOI] [PubMed] [Google Scholar]
  22. Rando R. F., Ojwang J., Elbaggari A., Reyes G. R., Tinder R., McGrath M. S., Hogan M. E. Suppression of human immunodeficiency virus type 1 activity in vitro by oligonucleotides which form intramolecular tetrads. J Biol Chem. 1995 Jan 27;270(4):1754–1760. doi: 10.1074/jbc.270.4.1754. [DOI] [PubMed] [Google Scholar]
  23. 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]
  24. 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]
  25. Sun J. S., Giovannangeli C., François J. C., Kurfurst R., Montenay-Garestier T., Asseline U., Saison-Behmoaras T., Thuong N. T., Hélène C. Triple-helix formation by alpha oligodeoxynucleotides and alpha oligodeoxynucleotide-intercalator conjugates. Proc Natl Acad Sci U S A. 1991 Jul 15;88(14):6023–6027. doi: 10.1073/pnas.88.14.6023. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Thenet S., Morvan F., Bertrand J. R., Gautie C., Malvy C. Alpha are more stable than beta anomer oligonucleotides in 3T3 cellular extracts. Biochimie. 1988 Dec;70(12):1729–1732. doi: 10.1016/0300-9084(88)90031-4. [DOI] [PubMed] [Google Scholar]
  27. Vichier-Guerre S., Pompon A., Lefebvre I., Imbach J. L. New insights into the resistance of alpha-oligonucleotides to nucleases. Antisense Res Dev. 1994 Spring;4(1):9–18. doi: 10.1089/ard.1994.4.9. [DOI] [PubMed] [Google Scholar]
  28. 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]
  29. Wang Q., Tsukahara S., Yamakawa H., Takai K., Takaku H. pH-independent inhibition of restriction endonuclease cleavage via triple helix formation by oligonucleotides containing 8-oxo-2'-deoxyadenosine. FEBS Lett. 1994 Nov 21;355(1):11–14. doi: 10.1016/0014-5793(94)01139-7. [DOI] [PubMed] [Google Scholar]
  30. Xodo L. E., Manzini G., Quadrifoglio F., van der Marel G. A., van Boom J. H. Effect of 5-methylcytosine on the stability of triple-stranded DNA--a thermodynamic study. Nucleic Acids Res. 1991 Oct 25;19(20):5625–5631. doi: 10.1093/nar/19.20.5625. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES