Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1994 Jul 11;22(13):2637–2642. doi: 10.1093/nar/22.13.2637

Sequence specificity of the non-natural pyrido[2,3-d]pyrimidine nucleoside in triple helix formation.

A B Staubli 1, P B Dervan 1
PMCID: PMC308221  PMID: 8041626

Abstract

The non-natural pyrido[2,3-d]pyrimidine nucleoside F, which pairs preferentially with guanine (G) and adenine (A) within double-helical DNA, recognizes with high selectivity AT base pairs within triple-helical complexes. These observations suggest that F may exist in different tautomeric forms within double-helical and triple-helical complexes. Analysis of the base stacking properties of this extended ring system using two oligodeoxyribonucleotides containing terminal thymines and/or pyrido[2,3-d]pyrimidines bound to adjacent sites showed a decrease in free energy of binding in a triple-helical complex in the order (5'-3') TT > FT > TF > FF.

Full text

PDF
2637

Images in this article

2639Image
on p.2639
2640Image
on p.2640

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. 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]
  3. Dreyer G. B., Dervan P. B. Sequence-specific cleavage of single-stranded DNA: oligodeoxynucleotide-EDTA X Fe(II). Proc Natl Acad Sci U S A. 1985 Feb;82(4):968–972. doi: 10.1073/pnas.82.4.968. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Griffin L. C., Dervan P. B. Recognition of thymine adenine.base pairs by guanine in a pyrimidine triple helix motif. Science. 1989 Sep 1;245(4921):967–971. doi: 10.1126/science.2549639. [DOI] [PubMed] [Google Scholar]
  5. Inoue H., Imura A., Ohtsuka E. Synthesis and hybridization of dodecadeoxyribonucleotides containing a fluorescent pyridopyrimidine deoxynucleoside. Nucleic Acids Res. 1985 Oct 11;13(19):7119–7128. doi: 10.1093/nar/13.19.7119. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Jayasena S. D., Johnston B. H. Intramolecular triple-helix formation at (PunPyn).(PunPyn) tracts: recognition of alternate strands via Pu.PuPy and Py.PuPy base triplets. Biochemistry. 1992 Jan 21;31(2):320–327. doi: 10.1021/bi00117a002. [DOI] [PubMed] [Google Scholar]
  7. Kiessling L. L., Griffin L. C., Dervan P. B. Flanking sequence effects within the pyrimidine triple-helix motif characterized by affinity cleaving. Biochemistry. 1992 Mar 17;31(10):2829–2834. doi: 10.1021/bi00125a026. [DOI] [PubMed] [Google Scholar]
  8. 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]
  9. Lee J. S., Woodsworth M. L., Latimer L. J., Morgan A. R. Poly(pyrimidine) . poly(purine) synthetic DNAs containing 5-methylcytosine form stable triplexes at neutral pH. Nucleic Acids Res. 1984 Aug 24;12(16):6603–6614. doi: 10.1093/nar/12.16.6603. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Miller P. S., Bhan P., Cushman C. D., Trapane T. L. Recognition of a guanine-cytosine base pair by 8-oxoadenine. Biochemistry. 1992 Jul 28;31(29):6788–6793. doi: 10.1021/bi00144a020. [DOI] [PubMed] [Google Scholar]
  11. 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]
  12. Ono A., Chen C. N., Kan L. S. DNA triplex formation of oligonucleotide analogues consisting of linker groups and octamer segments that have opposite sugar-phosphate backbone polarities. Biochemistry. 1991 Oct 15;30(41):9914–9912. doi: 10.1021/bi00105a015. [DOI] [PubMed] [Google Scholar]
  13. 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]
  14. Radhakrishnan I., Gao X., de los Santos C., Live D., Patel D. J. NMR structural studies of intramolecular (Y+)n.(R+)n(Y-)nDNA triplexes in solution: imino and amino proton and nitrogen markers of G.TA base triple formation. Biochemistry. 1991 Sep 17;30(37):9022–9030. doi: 10.1021/bi00101a016. [DOI] [PubMed] [Google Scholar]
  15. Radhakrishnan I., de los Santos C., Patel D. J. Nuclear magnetic resonance structural studies of intramolecular purine.purine.pyrimidine DNA triplexes in solution. Base triple pairing alignments and strand direction. J Mol Biol. 1991 Oct 20;221(4):1403–1418. [PubMed] [Google Scholar]
  16. Rajagopal P., Feigon J. NMR studies of triple-strand formation from the homopurine-homopyrimidine deoxyribonucleotides d(GA)4 and d(TC)4. Biochemistry. 1989 Sep 19;28(19):7859–7870. doi: 10.1021/bi00445a048. [DOI] [PubMed] [Google Scholar]
  17. Singleton S. F., Dervan P. B. Influence of pH on the equilibrium association constants for oligodeoxyribonucleotide-directed triple helix formation at single DNA sites. Biochemistry. 1992 Nov 17;31(45):10995–11003. doi: 10.1021/bi00160a008. [DOI] [PubMed] [Google Scholar]
  18. Sinha N. D., Biernat J., McManus J., Köster H. Polymer support oligonucleotide synthesis XVIII: use of beta-cyanoethyl-N,N-dialkylamino-/N-morpholino phosphoramidite of deoxynucleosides for the synthesis of DNA fragments simplifying deprotection and isolation of the final product. Nucleic Acids Res. 1984 Jun 11;12(11):4539–4557. doi: 10.1093/nar/12.11.4539. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Sowers L. C., Shaw B. R., Sedwick W. D. Base stacking and molecular polarizability: effect of a methyl group in the 5-position of pyrimidines. Biochem Biophys Res Commun. 1987 Oct 29;148(2):790–794. doi: 10.1016/0006-291x(87)90945-4. [DOI] [PubMed] [Google Scholar]
  20. Stilz H. U., Dervan P. B. Specific recognition of CG base pairs by 2-deoxynebularine within the purine.purine.pyrimidine triple-helix motif. Biochemistry. 1993 Mar 9;32(9):2177–2185. doi: 10.1021/bi00060a008. [DOI] [PubMed] [Google Scholar]

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

RESOURCES