Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1994 Aug 11;22(15):3233–3240. doi: 10.1093/nar/22.15.3233

Binding of T and T analogs to CG base pairs in antiparallel triplexes.

R H Durland 1, T S Rao 1, G R Revankar 1, J H Tinsley 1, M A Myrick 1, D M Seth 1, J Rayford 1, P Singh 1, K Jayaraman 1
PMCID: PMC310301  PMID: 8065940

Abstract

The goal of this study was to address antiparallel triplex formation at duplex targets that do not conform to a strict oligopurine.oligopyrimidine motif. We focused on the ability of natural bases and base analogs incorporated into oligonucleotide third strands to bind to so-called CG inversions. These are sites where a cytosine base is present in an otherwise purine-rich strand of a duplex target. Using a 26-base-triplet test system, we found that of the standard bases, only thymine (T) shows substantial binding to CG inversions. This is quantitatively similar to the report of Beal and Dervan [Science (1991), 251, 1360-1363]. Binding to CG inversions was only slightly weaker than binding to AT base pairs. Binding of T to CG inversions was also evaluated in two other sequences, with qualitatively similar results. Six different analogs of thymine were also tested for binding to CG inversions and AT base pairs. Significant changes in affinity were observed. In particular, 5-fluoro-2'-deoxyuridine was found to increase affinity for CG inversions as well as for AT base pairs. Studies with oligonucleotides containing pyridin-2-one or pyridin-4-one suggest that thymine O4 plays a critical role in the T.CG interaction. Possible models to account for these observations are discussed.

Full text

PDF
3233

Images in this article

3235Image
on p.3235
3236Image
on p.3236
3236Image
on p.3236
3237Image
on p.3237
3238Image
on p.3238
3239Image
on p.3239

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. Beal P. A., Dervan P. B. The influence of single base triplet changes on the stability of a pur.pur.pyr triple helix determined by affinity cleaving. Nucleic Acids Res. 1992 Jun 11;20(11):2773–2776. doi: 10.1093/nar/20.11.2773. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Blume S. W., Gee J. E., Shrestha K., Miller D. M. Triple helix formation by purine-rich oligonucleotides targeted to the human dihydrofolate reductase promoter. Nucleic Acids Res. 1992 Apr 11;20(7):1777–1784. doi: 10.1093/nar/20.7.1777. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Cantor C. R., Tinoco I., Jr Calculated optical properties of 64 trinucleoside diphosphates. Biopolymers. 1967;5(9):821–835. doi: 10.1002/bip.1967.360050905. [DOI] [PubMed] [Google Scholar]
  5. 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]
  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. 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]
  8. Horne D. A., Dervan P. B. Effects of an abasic site on triple helix formation characterized by affinity cleaving. Nucleic Acids Res. 1991 Sep 25;19(18):4963–4965. doi: 10.1093/nar/19.18.4963. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. 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]
  10. 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]
  11. LIPSETT M. N. COMPLEX FORMATION BETWEEN POLYCYTIDYLIC ACID AND GUANINE OLIGONUCLEOTIDES. J Biol Chem. 1964 Apr;239:1256–1260. [PubMed] [Google Scholar]
  12. 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]
  13. 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]
  14. Murphy M., Rieger M., Jayaraman K. Large-scale synthesis of triple helix forming oligonucleotides using a controlled-pore glass support. Biotechniques. 1993 Dec;15(6):1004-6, 1008, 1010. [PubMed] [Google Scholar]
  15. 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]
  16. 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]
  17. 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]
  18. Woodford W. J., Swartz B. A., Pillar C. J., Kampf A., Mertes M. P. Synthesis of the alpha and beta anomers of 1-(2-deoxy-D-ribofuranosyl)-4-pyridone. J Med Chem. 1974 Sep;17(9):1027–1029. doi: 10.1021/jm00255a030. [DOI] [PubMed] [Google Scholar]
  19. 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