Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1990 Sep 25;18(18):5387–5391. doi: 10.1093/nar/18.18.5387

Long (dA)n.(dT)n tracts can form intramolecular triplexes under superhelical stress.

K R Fox 1
PMCID: PMC332214  PMID: 2216711

Abstract

Plasmids containing long tracts of (dA)n.(dT)n have been prepared and their conformations examined in linear and supercoiled DNA using a series of chemical and enzymic probes which are known to be sensitive to unusual DNA structures. Under superhelical stress and in the presence of magnesium the sequence T69.A69 adopts a conformation at pH 8.0 consistent with the formation of an intramolecular DNA triplex. Site specific cleavage of the supercoiled plasmid by single-strand specific nucleases occurs within the A.T insert; the 5'-end of the purine strand is sensitive to reaction with diethylpyrocarbonate while the central 5-6 bases of the pyrimidine strand are reactive to osmium tetroxide. By contrast shorter inserts of A33.T33 and A23.T23 do not appear to form unusual structures.

Full text

PDF
5388

Images in this article

5388Image
on p.5388
5389Image
on p.5389
5389Image
on p.5389

Selected References

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

  1. Arnott S., Chandrasekaran R., Hall I. H., Puigjaner L. C. Heteronomous DNA. Nucleic Acids Res. 1983 Jun 25;11(12):4141–4155. doi: 10.1093/nar/11.12.4141. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bernués J., Beltrán R., Casasnovas J. M., Azorín F. Structural polymorphism of homopurine--homopyrimidine sequences: the secondary DNA structure adopted by a d(GA.CT)22 sequence in the presence of zinc ions. EMBO J. 1989 Jul;8(7):2087–2094. doi: 10.1002/j.1460-2075.1989.tb03617.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Cockwell K. Y., Giles I. G. Software tools for motif and pattern scanning: program descriptions including a universal sequence reading algorithm. Comput Appl Biosci. 1989 Jul;5(3):227–232. doi: 10.1093/bioinformatics/5.3.227. [DOI] [PubMed] [Google Scholar]
  4. Ebina Y., Ellis L., Jarnagin K., Edery M., Graf L., Clauser E., Ou J. H., Masiarz F., Kan Y. W., Goldfine I. D. The human insulin receptor cDNA: the structural basis for hormone-activated transmembrane signalling. Cell. 1985 Apr;40(4):747–758. doi: 10.1016/0092-8674(85)90334-4. [DOI] [PubMed] [Google Scholar]
  5. Hanvey J. C., Klysik J., Wells R. D. Influence of DNA sequence on the formation of non-B right-handed helices in oligopurine.oligopyrimidine inserts in plasmids. J Biol Chem. 1988 May 25;263(15):7386–7396. [PubMed] [Google Scholar]
  6. Hanvey J. C., Shimizu M., Wells R. D. Intramolecular DNA triplexes in supercoiled plasmids. Proc Natl Acad Sci U S A. 1988 Sep;85(17):6292–6296. doi: 10.1073/pnas.85.17.6292. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Hoppe J., Schumacher L., Eichner W., Weich H. A. The long 3'-untranslated regions of the PDGF-A and -B mRNAs are only distantly related. FEBS Lett. 1987 Nov 2;223(2):243–246. doi: 10.1016/0014-5793(87)80297-1. [DOI] [PubMed] [Google Scholar]
  8. Jinno Y., Matuo S., Nomiyama H., Shimada K., Matsuda I. Novel structure of the 5' end region of the human argininosuccinate synthetase gene. J Biochem. 1985 Nov;98(5):1395–1403. doi: 10.1093/oxfordjournals.jbchem.a135407. [DOI] [PubMed] [Google Scholar]
  9. Johnston B. H. The S1-sensitive form of d(C-T)n.d(A-G)n: chemical evidence for a three-stranded structure in plasmids. Science. 1988 Sep 30;241(4874):1800–1804. doi: 10.1126/science.2845572. [DOI] [PubMed] [Google Scholar]
  10. Kariya Y., Kato K., Hayashizaki Y., Himeno S., Tarui S., Matsubara K. Expression of human gastrin gene in normal and gastrinoma tissues. Gene. 1986;50(1-3):345–352. doi: 10.1016/0378-1119(86)90338-0. [DOI] [PubMed] [Google Scholar]
  11. Katahira M., Sugeta H., Kyogoku Y. A new model for the bending of DNAs containing the oligo(dA) tracts based on NMR observations. Nucleic Acids Res. 1990 Feb 11;18(3):613–618. doi: 10.1093/nar/18.3.613. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Knott T. J., Wallis S. C., Robertson M. E., Priestley L. M., Urdea M., Rall L. B., Scott J. The human apolipoprotein AII gene: structural organization and sites of expression. Nucleic Acids Res. 1985 Sep 11;13(17):6387–6398. doi: 10.1093/nar/13.17.6387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Kohwi Y. Cationic metal-specific structures adopted by the poly(dG) region and the direct repeats in the chicken adult beta A globin gene promoter. Nucleic Acids Res. 1989 Jun 26;17(12):4493–4502. doi: 10.1093/nar/17.12.4493. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Kohwi Y., Kohwi-Shigematsu T. Magnesium ion-dependent triple-helix structure formed by homopurine-homopyrimidine sequences in supercoiled plasmid DNA. Proc Natl Acad Sci U S A. 1988 Jun;85(11):3781–3785. doi: 10.1073/pnas.85.11.3781. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Koo H. S., Wu H. M., Crothers D. M. DNA bending at adenine . thymine tracts. Nature. 1986 Apr 10;320(6062):501–506. doi: 10.1038/320501a0. [DOI] [PubMed] [Google Scholar]
  16. Kunkel G. R., Martinson H. G. Nucleosomes will not form on double-stranded RNa or over poly(dA).poly(dT) tracts in recombinant DNA. Nucleic Acids Res. 1981 Dec 21;9(24):6869–6888. doi: 10.1093/nar/9.24.6869. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. La Volpe A., Simeone A., D'Esposito M., Scotto L., Fidanza V., de Falco A., Boncinelli E. Molecular analysis of the heterogeneity region of the human ribosomal spacer. J Mol Biol. 1985 May 25;183(2):213–223. doi: 10.1016/0022-2836(85)90214-1. [DOI] [PubMed] [Google Scholar]
  18. Lee M. G., Loomis C., Cowan N. J. Sequence of an expressed human beta-tubulin gene containing ten Alu family members. Nucleic Acids Res. 1984 Jul 25;12(14):5823–5836. doi: 10.1093/nar/12.14.5823. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Lyamichev V. I., Mirkin S. M., Kumarev V. P., Baranova L. V., Vologodskii A. V., Frank-Kamenetskii M. D. Energetics of the B-H transition in supercoiled DNA carrying d(CT)x.d(AG)x and d(C)n.d(G)n inserts. Nucleic Acids Res. 1989 Nov 25;17(22):9417–9423. doi: 10.1093/nar/17.22.9417. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. 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]
  21. 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]
  22. Myers J. C., Dickson L. A., de Wet W. J., Bernard M. P., Chu M. L., Di Liberto M., Pepe G., Sangiorgi F. O., Ramirez F. Analysis of the 3' end of the human pro-alpha 2(I) collagen gene. Utilization of multiple polyadenylation sites in cultured fibroblasts. J Biol Chem. 1983 Aug 25;258(16):10128–10135. [PubMed] [Google Scholar]
  23. Nelson H. C., Finch J. T., Luisi B. F., Klug A. The structure of an oligo(dA).oligo(dT) tract and its biological implications. Nature. 1987 Nov 19;330(6145):221–226. doi: 10.1038/330221a0. [DOI] [PubMed] [Google Scholar]
  24. Panyutin I. G., Kovalsky O. I., Budowsky E. I. Magnesium-dependent supercoiling-induced transition in (dG)n.(dC)n stretches and formation of a new G-structure by (dG)n strand. Nucleic Acids Res. 1989 Oct 25;17(20):8257–8271. doi: 10.1093/nar/17.20.8257. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Pilch D. S., Levenson C., Shafer R. H. Structural analysis of the (dA)10.2(dT)10 triple helix. Proc Natl Acad Sci U S A. 1990 Mar;87(5):1942–1946. doi: 10.1073/pnas.87.5.1942. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Riley M., Maling B. Physical and chemical characterization of two- and three-stranded adenine-thymine and adenine-uracil homopolymer complexes. J Mol Biol. 1966 Sep;20(2):359–389. doi: 10.1016/0022-2836(66)90069-6. [DOI] [PubMed] [Google Scholar]
  27. Shimasaki S., Koga M., Esch F., Cooksey K., Mercado M., Koba A., Ueno N., Ying S. Y., Ling N., Guillemin R. Primary structure of the human follistatin precursor and its genomic organization. Proc Natl Acad Sci U S A. 1988 Jun;85(12):4218–4222. doi: 10.1073/pnas.85.12.4218. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Voloshin O. N., Mirkin S. M., Lyamichev V. I., Belotserkovskii B. P., Frank-Kamenetskii M. D. Chemical probing of homopurine-homopyrimidine mirror repeats in supercoiled DNA. Nature. 1988 Jun 2;333(6172):475–476. doi: 10.1038/333475a0. [DOI] [PubMed] [Google Scholar]
  29. Wells R. D., Collier D. A., Hanvey J. C., Shimizu M., Wohlrab F. The chemistry and biology of unusual DNA structures adopted by oligopurine.oligopyrimidine sequences. FASEB J. 1988 Nov;2(14):2939–2949. [PubMed] [Google Scholar]
  30. Yoshikai Y., Clark S. P., Taylor S., Sohn U., Wilson B. I., Minden M. D., Mak T. W. Organization and sequences of the variable, joining and constant region genes of the human T-cell receptor alpha-chain. 1985 Aug 29-Sep 4Nature. 316(6031):837–840. doi: 10.1038/316837a0. [DOI] [PubMed] [Google Scholar]

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

RESOURCES