Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1997 Apr 1;25(7):1339–1346. doi: 10.1093/nar/25.7.1339

Mechanisms of triplex-caused polymerization arrest.

A S Krasilnikov 1, I G Panyutin 1, G M Samadashwily 1, R Cox 1, Y S Lazurkin 1, S M Mirkin 1
PMCID: PMC146602  PMID: 9060427

Abstract

Pyrimidine/purine/purine triplexes are known to inhibit DNA polymerization. Here we have studied the mechanisms of this inhibition by comparing the efficiency of Vent DNA polymerase on triplex- and duplex-containing templates at different temperatures, Mg2+concentrations and time intervals with the thermal stability of the corresponding structures. Our results show that triplexes can only be by-passed at temperatures where thermal denaturation initiates, while duplexes, in contrast, are overcome at temperatures where they are quite stable. These results show that DNA polymerase cannot untangle triplex regions within DNA templates and seems to entirely depend on their thermal fluctuations. The high stability of triplexes at physiological temperatures and ambient conditions make them a barrier to polymerization.

Full Text

The Full Text of this article is available as a PDF (221.9 KB).

Selected References

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

  1. Alunni-Fabbroni M., Manfioletti G., Manzini G., Xodo L. E. Inhibition of T7 RNA polymerase transcription by phosphate and phosphorothioate triplex-forming oligonucleotides targeted to a R.Y site downstream from the promoter. Eur J Biochem. 1994 Dec 15;226(3):831–839. doi: 10.1111/j.1432-1033.1994.00831.x. [DOI] [PubMed] [Google Scholar]
  2. Baran N., Lapidot A., Manor H. Formation of DNA triplexes accounts for arrests of DNA synthesis at d(TC)n and d(GA)n tracts. Proc Natl Acad Sci U S A. 1991 Jan 15;88(2):507–511. doi: 10.1073/pnas.88.2.507. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Baran N., Lapidot A., Manor H. Unusual sequence element found at the end of an amplicon. Mol Cell Biol. 1987 Jul;7(7):2636–2640. doi: 10.1128/mcb.7.7.2636. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Brinton B. T., Caddle M. S., Heintz N. H. Position and orientation-dependent effects of a eukaryotic Z-triplex DNA motif on episomal DNA replication in COS-7 cells. J Biol Chem. 1991 Mar 15;266(8):5153–5161. [PubMed] [Google Scholar]
  5. Dayn A., Samadashwily G. M., Mirkin S. M. Intramolecular DNA triplexes: unusual sequence requirements and influence on DNA polymerization. Proc Natl Acad Sci U S A. 1992 Dec 1;89(23):11406–11410. doi: 10.1073/pnas.89.23.11406. [DOI] [PMC free article] [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. Frank-Kamenetskii M. D., Mirkin S. M. Triplex DNA structures. Annu Rev Biochem. 1995;64:65–95. doi: 10.1146/annurev.bi.64.070195.000433. [DOI] [PubMed] [Google Scholar]
  8. 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]
  9. Hacia J. G., Dervan P. B., Wold B. J. Inhibition of Klenow fragment DNA polymerase on double-helical templates by oligonucleotide-directed triple-helix formation. Biochemistry. 1994 May 24;33(20):6192–6200. doi: 10.1021/bi00186a019. [DOI] [PubMed] [Google Scholar]
  10. Htun H., Dahlberg J. E. Topology and formation of triple-stranded H-DNA. Science. 1989 Mar 24;243(4898):1571–1576. doi: 10.1126/science.2648571. [DOI] [PubMed] [Google Scholar]
  11. Hélène C. The anti-gene strategy: control of gene expression by triplex-forming-oligonucleotides. Anticancer Drug Des. 1991 Dec;6(6):569–584. [PubMed] [Google Scholar]
  12. Kohwi Y., Panchenko Y. Transcription-dependent recombination induced by triple-helix formation. Genes Dev. 1993 Sep;7(9):1766–1778. doi: 10.1101/gad.7.9.1766. [DOI] [PubMed] [Google Scholar]
  13. Kong H., Kucera R. B., Jack W. E. Characterization of a DNA polymerase from the hyperthermophile archaea Thermococcus litoralis. Vent DNA polymerase, steady state kinetics, thermal stability, processivity, strand displacement, and exonuclease activities. J Biol Chem. 1993 Jan 25;268(3):1965–1975. [PubMed] [Google Scholar]
  14. Liu L. F., Wang J. C. Supercoiling of the DNA template during transcription. Proc Natl Acad Sci U S A. 1987 Oct;84(20):7024–7027. doi: 10.1073/pnas.84.20.7024. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Mirkin S. M., Frank-Kamenetskii M. D. H-DNA and related structures. Annu Rev Biophys Biomol Struct. 1994;23:541–576. doi: 10.1146/annurev.bb.23.060194.002545. [DOI] [PubMed] [Google Scholar]
  16. Mirkin S. M., Lyamichev V. I., Drushlyak K. N., Dobrynin V. N., Filippov S. A., Frank-Kamenetskii M. D. DNA H form requires a homopurine-homopyrimidine mirror repeat. Nature. 1987 Dec 3;330(6147):495–497. doi: 10.1038/330495a0. [DOI] [PubMed] [Google Scholar]
  17. 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]
  18. Rao B. S., Manor H., Martin R. G. Pausing in simian virus 40 DNA replication by a sequence containing (dG-dA)27.(dT-dC)27. Nucleic Acids Res. 1988 Aug 25;16(16):8077–8094. doi: 10.1093/nar/16.16.8077. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Rao B. S. Pausing of simian virus 40 DNA replication fork movement in vivo by (dG-dA)n.(dT-dC)n tracts. Gene. 1994 Mar 25;140(2):233–237. doi: 10.1016/0378-1119(94)90549-5. [DOI] [PubMed] [Google Scholar]
  20. Reaban M. E., Griffin J. A. Induction of RNA-stabilized DNA conformers by transcription of an immunoglobulin switch region. Nature. 1990 Nov 22;348(6299):342–344. doi: 10.1038/348342a0. [DOI] [PubMed] [Google Scholar]
  21. Samadashwily G. M., Dayn A., Mirkin S. M. Suicidal nucleotide sequences for DNA polymerization. EMBO J. 1993 Dec 15;12(13):4975–4983. doi: 10.1002/j.1460-2075.1993.tb06191.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Samadashwily G. M., Mirkin S. M. Trapping DNA polymerases using triplex-forming oligodeoxyribonucleotides. Gene. 1994 Nov 4;149(1):127–136. doi: 10.1016/0378-1119(94)90421-9. [DOI] [PubMed] [Google Scholar]
  23. Scaria P. V., Will S., Levenson C., Shafer R. H. Physicochemical studies of the d(G3T4G3)*d(G3A4G3).d(C3T4C3) triple helix. J Biol Chem. 1995 Mar 31;270(13):7295–7303. doi: 10.1074/jbc.270.13.7295. [DOI] [PubMed] [Google Scholar]
  24. Schroth G. P., Ho P. S. Occurrence of potential cruciform and H-DNA forming sequences in genomic DNA. Nucleic Acids Res. 1995 Jun 11;23(11):1977–1983. doi: 10.1093/nar/23.11.1977. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Sklenár V., Feigon J. Formation of a stable triplex from a single DNA strand. Nature. 1990 Jun 28;345(6278):836–838. doi: 10.1038/345836a0. [DOI] [PubMed] [Google Scholar]
  26. Vo T., Wang S., Kool E. T. Targeting pyrimidine single strands by triplex formation: structural optimization of binding. Nucleic Acids Res. 1995 Aug 11;23(15):2937–2944. doi: 10.1093/nar/23.15.2937. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. 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]

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

RESOURCES