Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1989 Feb 25;17(4):1549–1561. doi: 10.1093/nar/17.4.1549

Synthetic repeating sequence DNAs containing phosphorothioates: nuclease sensitivity and triplex formation.

L J Latimer 1, K Hampel 1, J S Lee 1
PMCID: PMC331821  PMID: 2922286

Abstract

More than twenty repeating sequence DNAs containing phosphorothioates were prepared from the appropriate dXTPs with DNA polymerase I. The Tms of the modified DNAs were all lower than the parent polymers. A phosphorothioate group 5' to a pyrimidine gave rise to a large decrease than 5' to a purine, e.g., poly(dA).poly(dT) = 50 degrees; poly(dsA).poly(dT) = 44 degrees; poly(dA).poly(dsT) = 33 degrees; and poly(dsA).poly(dsT) = 26 degrees. The presence of phosphorothioate groups had a dramatic effect on triplex formation; poly[d(TC)].poly[d(sGsA)] spontaneously dismutases to a triplex at pH 8 whereas triplex formation in poly[d(sTsC)].poly[d(GA)] was inhibited. Surprisingly poly(dsG).poly(dC) had a Tm which initially decreased with increasing ionic strength. Resistance to digestion with pancreatic DNAse I did not correlate with phosphorothioate content. Poly[d(AsT)], poly[d(TsC)].poly[d(sGA)] and poly[d(sTG)].poly[d(sCA)] were resistant whereas poly[d(sAT)] and poly[d(sTsTG)].poly[d(CsAsA)] were rapidly degraded. Thus phosphorothioate groups cause small conformational changes and may reveal new families of conformational polymorphisms.

Full text

PDF
1549

Selected References

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

  1. Braun R. P., Lee J. S. Equilibrium binding parameters of an autoimmune monoclonal antibody specific for double-stranded DNA. J Immunol. 1987 Jul 1;139(1):175–179. [PubMed] [Google Scholar]
  2. Braun R. P., Lee J. S. Immunogenic duplex nucleic acids are nuclease resistant. J Immunol. 1988 Sep 15;141(6):2084–2089. [PubMed] [Google Scholar]
  3. Braun R. P., Lee J. S. Variations in duplex DNA conformation detected by the binding of monoclonal autoimmune antibodies. Nucleic Acids Res. 1986 Jun 25;14(12):5049–5065. doi: 10.1093/nar/14.12.5049. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Cruse W. B., Salisbury S. A., Brown T., Cosstick R., Eckstein F., Kennard O. Chiral phosphorothioate analogues of B-DNA. The crystal structure of Rp-d[Gp(S)CpGp(S)CpGp(S)C]. J Mol Biol. 1986 Dec 20;192(4):891–905. doi: 10.1016/0022-2836(86)90035-5. [DOI] [PubMed] [Google Scholar]
  5. Eckstein F., Jovin T. M. Assignment of resonances in the phosphorus-31 nuclear magnetic resonance spectrum of poly[d(A-T)] from phosphorothioate substitution. Biochemistry. 1983 Sep 13;22(19):4546–4550. doi: 10.1021/bi00288a030. [DOI] [PubMed] [Google Scholar]
  6. Evans D. H., Lee J. S., Morgan A. R., Olsen R. K. A method for the specific inhibition of poly[d(A-T)] synthesis using the A-T specific quinoxaline antibiotic TANDEM. Can J Biochem. 1982 Feb;60(2):131–136. doi: 10.1139/o82-018. [DOI] [PubMed] [Google Scholar]
  7. Frey P. A., Sammons R. D. Bond order and charge localization in nucleoside phosphorothioates. Science. 1985 May 3;228(4699):541–545. doi: 10.1126/science.2984773. [DOI] [PubMed] [Google Scholar]
  8. HARTMAN K. A., Jr, RICH A. THE TAUTOMERIC FORM OF HELICAL POLYRIBOCYTIDYLIC ACID. J Am Chem Soc. 1965 May 5;87:2033–2039. doi: 10.1021/ja01087a031. [DOI] [PubMed] [Google Scholar]
  9. Jovin T. M., van de Sande J. H., Zarling D. A., Arndt-Jovin D. J., Eckstein F., Füldner H. H., Greider C., Grieger I., Hamori E., Kalisch B. Generation of left-handed Z-DNA in solution and visualization in polytene chromosomes by immunofluorescence. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 1):143–154. doi: 10.1101/sqb.1983.047.01.019. [DOI] [PubMed] [Google Scholar]
  10. 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]
  11. LaPlanche L. A., James T. L., Powell C., Wilson W. D., Uznanski B., Stec W. J., Summers M. F., Zon G. Phosphorothioate-modified oligodeoxyribonucleotides. III. NMR and UV spectroscopic studies of the Rp-Rp, Sp-Sp, and Rp-Sp duplexes, [d(GGSAATTCC)]2, derived from diastereomeric O-ethyl phosphorothioates. Nucleic Acids Res. 1986 Nov 25;14(22):9081–9093. doi: 10.1093/nar/14.22.9081. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Lee J. S., Johnson D. A., Morgan A. R. Complexes formed by (pyrimidine)n . (purine)n DNAs on lowering the pH are three-stranded. Nucleic Acids Res. 1979 Jul 11;6(9):3073–3091. doi: 10.1093/nar/6.9.3073. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. 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]
  14. Lyamichev V. I., Mirkin S. M., Frank-Kamenetskii M. D., Cantor C. R. A stable complex between homopyrimidine oligomers and the homologous regions of duplex DNAs. Nucleic Acids Res. 1988 Mar 25;16(5):2165–2178. doi: 10.1093/nar/16.5.2165. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Matsukura M., Shinozuka K., Zon G., Mitsuya H., Reitz M., Cohen J. S., Broder S. Phosphorothioate analogs of oligodeoxynucleotides: inhibitors of replication and cytopathic effects of human immunodeficiency virus. Proc Natl Acad Sci U S A. 1987 Nov;84(21):7706–7710. doi: 10.1073/pnas.84.21.7706. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Morgan A. R., Lee J. S., Pulleyblank D. E., Murray N. L., Evans D. H. Review: ethidium fluorescence assays. Part 1. Physicochemical studies. Nucleic Acids Res. 1979 Oct 10;7(3):547–569. doi: 10.1093/nar/7.3.547. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Oefner C., Suck D. Crystallographic refinement and structure of DNase I at 2 A resolution. J Mol Biol. 1986 Dec 5;192(3):605–632. doi: 10.1016/0022-2836(86)90280-9. [DOI] [PubMed] [Google Scholar]
  18. 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]
  19. Stein C. A., Subasinghe C., Shinozuka K., Cohen J. S. Physicochemical properties of phosphorothioate oligodeoxynucleotides. Nucleic Acids Res. 1988 Apr 25;16(8):3209–3221. doi: 10.1093/nar/16.8.3209. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Suggs J. W., Taylor D. A. Evidence for sequence-specific conformational changes in DNA from the melting temperatures of DNA phosphorothioate derivatives. Nucleic Acids Res. 1985 Aug 12;13(15):5707–5716. doi: 10.1093/nar/13.15.5707. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES