Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1989 Oct 11;17(19):7749–7759. doi: 10.1093/nar/17.19.7749

alpha-DNA X: alpha and beta tetrathymidilates covalently linked to oxazolopyridocarbazolium (OPC): comparative stabilization of oligo beta-[dT]:oligo beta-[dA] and oligo alpha-[dT]:oligo beta-[dA] duplexes by the intercalating agent.

D Bazile 1, C Gautier 1, B Rayner 1, J L Imbach 1, C Paoletti 1, J Paoletti 1
PMCID: PMC334882  PMID: 2798125

Abstract

The influence of the intercalating oxazolopyridocarbazolium (HOPC) on the stabilization of modified oligonucleotides: alpha-T4c5OPC or beta-T4c5OPC associated to beta-oligo (dA) was studied. It appears that the situation is different from what has been observed for the interaction of these modified oligonucleotides with poly (rA). The higher free energy of formation of the alpha-T4c5OPC :beta-oligo(dA), when compared to beta-T4c5OPC, is essentially due to the overall stability added to this system by the intercalator. This enhanced stability comes from a higher number of binding sites of HOPC for the alpha:beta duplex together with a lower van't Hoff energy of formation of the alpha:beta duplex.

Full text

PDF
7749

Selected References

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

  1. Agrawal S., Goodchild J., Civeira M. P., Thornton A. H., Sarin P. S., Zamecnik P. C. Oligodeoxynucleoside phosphoramidates and phosphorothioates as inhibitors of human immunodeficiency virus. Proc Natl Acad Sci U S A. 1988 Oct;85(19):7079–7083. doi: 10.1073/pnas.85.19.7079. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Asseline U., Toulme F., Thuong N. T., Delarue M., Montenay-Garestier T., Hélène C. Oligodeoxynucleotides covalently linked to intercalating dyes as base sequence-specific ligands. Influence of dye attachment site. EMBO J. 1984 Apr;3(4):795–800. doi: 10.1002/j.1460-2075.1984.tb01887.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Auclair C., Voisin E., Banoun H., Paoletti C., Bernadou J., Meunier B. Potential antitumor agents: synthesis and biological properties of aliphatic amino acid 9-hydroxyellipticinium derivatives. J Med Chem. 1984 Sep;27(9):1161–1166. doi: 10.1021/jm00375a013. [DOI] [PubMed] [Google Scholar]
  4. Banoun H., Le Bret M., Auclair C. Accessibility to bacterial nucleic acids of the intercalating drug aliphatic amino acid ellipticinium derivatives in Escherichia coli and Salmonella typhimurium. Biochemistry. 1985 Jan 29;24(3):701–707. doi: 10.1021/bi00324a024. [DOI] [PubMed] [Google Scholar]
  5. Cassani G. R., Bollum F. J. Oligodeoxythymidylate: polydeoxyadenylate and oligodeoxyadenylate: polydeoxythymidylate interactions. Biochemistry. 1969 Oct;8(10):3928–3936. doi: 10.1021/bi00838a008. [DOI] [PubMed] [Google Scholar]
  6. Cazenave C., Loreau N., Thuong N. T., Toulmé J. J., Hélène C. Enzymatic amplification of translation inhibition of rabbit beta-globin mRNA mediated by anti-messenger oligodeoxynucleotides covalently linked to intercalating agents. Nucleic Acids Res. 1987 Jun 25;15(12):4717–4736. doi: 10.1093/nar/15.12.4717. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Cornelissen A. W., Verspieren M. P., Toulmé J. J., Swinkels B. W., Borst P. The common 5' terminal sequence on trypanosome mRNAs: a target for anti-messenger oligodeoxynucleotides. Nucleic Acids Res. 1986 Jul 25;14(14):5605–5614. doi: 10.1093/nar/14.14.5605. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Crothers D. M. Statistical thermodynamics of nucleic acid melting transitions with coupled binding equilibria. Biopolymers. 1971 Nov;10(11):2147–2160. doi: 10.1002/bip.360101110. [DOI] [PubMed] [Google Scholar]
  9. Delbarre A., Roques B. P., Le Pecq J. B., Lallemand J. Y., Nguyen-Dat-Xuong PMR studies of the self-association of DNA intercalating ellipticine derivatives in aqueous solution. Biophys Chem. 1976 May;4(3):275–279. doi: 10.1016/0301-4622(76)80075-0. [DOI] [PubMed] [Google Scholar]
  10. Durand M., Maurizot J. C., Thuong N. T., Helene C. Circular dichroism studies of an oligo-alpha-thymidylate and of its interactions with complementary sequences. Nucleic Acids Res. 1988 Jun 10;16(11):5039–5053. doi: 10.1093/nar/16.11.5039. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Eckstein F. Nucleoside phosphorothioates. Annu Rev Biochem. 1985;54:367–402. doi: 10.1146/annurev.bi.54.070185.002055. [DOI] [PubMed] [Google Scholar]
  12. Gautier C., Bazile D., Paoletti J. Poly(rA) binding of alpha-anomeric and beta-anomeric tetrathymidylates covalently linked to an intercalating oxazolopyridocarbazolium. Determination of the binding parameters. Biochem Biophys Res Commun. 1988 Jul 15;154(1):252–257. doi: 10.1016/0006-291x(88)90677-8. [DOI] [PubMed] [Google Scholar]
  13. Gautier C., Morvan F., Rayner B., Huynh-Dinh T., Igolen J., Imbach J. L., Paoletti C., Paoletti J. Alpha-DNA. IV: Alpha-anomeric and beta-anomeric tetrathymidylates covalently linked to intercalating oxazolopyridocarbazole. Synthesis, physicochemical properties and poly (rA) binding. Nucleic Acids Res. 1987 Aug 25;15(16):6625–6641. doi: 10.1093/nar/15.16.6625. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Green P. J., Pines O., Inouye M. The role of antisense RNA in gene regulation. Annu Rev Biochem. 1986;55:569–597. doi: 10.1146/annurev.bi.55.070186.003033. [DOI] [PubMed] [Google Scholar]
  15. Holt J. T., Gopal T. V., Moulton A. D., Nienhuis A. W. Inducible production of c-fos antisense RNA inhibits 3T3 cell proliferation. Proc Natl Acad Sci U S A. 1986 Jul;83(13):4794–4798. doi: 10.1073/pnas.83.13.4794. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Holt J. T., Redner R. L., Nienhuis A. W. An oligomer complementary to c-myc mRNA inhibits proliferation of HL-60 promyelocytic cells and induces differentiation. Mol Cell Biol. 1988 Feb;8(2):963–973. doi: 10.1128/mcb.8.2.963. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Hélène C., Montenay-Garestier T., Saison T., Takasugi M., Toulmé J. J., Asseline U., Lancelot G., Maurizot J. C., Toulmé F., Thuong N. T. Oligodeoxynucleotides covalently linked to intercalating agents: a new class of gene regulatory substances. Biochimie. 1985 Jul-Aug;67(7-8):777–783. doi: 10.1016/s0300-9084(85)80167-x. [DOI] [PubMed] [Google Scholar]
  18. Izant J. G., Weintraub H. Constitutive and conditional suppression of exogenous and endogenous genes by anti-sense RNA. Science. 1985 Jul 26;229(4711):345–352. doi: 10.1126/science.2990048. [DOI] [PubMed] [Google Scholar]
  19. Jayaraman K., McParland K., Miller P., Ts'o P. O. Selective inhibition of Escherichia coli protein synthesis and growth by nonionic oligonucleotides complementary to the 3' end of 16S rRNA. Proc Natl Acad Sci U S A. 1981 Mar;78(3):1537–1541. doi: 10.1073/pnas.78.3.1537. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Lemaitre M., Bayard B., Lebleu B. Specific antiviral activity of a poly(L-lysine)-conjugated oligodeoxyribonucleotide sequence complementary to vesicular stomatitis virus N protein mRNA initiation site. Proc Natl Acad Sci U S A. 1987 Feb;84(3):648–652. doi: 10.1073/pnas.84.3.648. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Maher L. J., 3rd, Dolnick B. J. Comparative hybrid arrest by tandem antisense oligodeoxyribonucleotides or oligodeoxyribonucleoside methylphosphonates in a cell-free system. Nucleic Acids Res. 1988 Apr 25;16(8):3341–3358. doi: 10.1093/nar/16.8.3341. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Marcus-Sekura C. J. Techniques for using antisense oligodeoxyribonucleotides to study gene expression. Anal Biochem. 1988 Aug 1;172(2):289–295. doi: 10.1016/0003-2697(88)90447-2. [DOI] [PubMed] [Google Scholar]
  23. Marky L. A., Breslauer K. J. Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves. Biopolymers. 1987 Sep;26(9):1601–1620. doi: 10.1002/bip.360260911. [DOI] [PubMed] [Google Scholar]
  24. Mizuno T., Chou M. Y., Inouye M. A unique mechanism regulating gene expression: translational inhibition by a complementary RNA transcript (micRNA). Proc Natl Acad Sci U S A. 1984 Apr;81(7):1966–1970. doi: 10.1073/pnas.81.7.1966. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Morvan F., Rayner B., Imbach J. L., Thenet S., Bertrand J. R., Paoletti J., Malvy C., Paoletti C. alpha-DNA II. Synthesis of unnatural alpha-anomeric oligodeoxyribonucleotides containing the four usual bases and study of their substrate activities for nucleases. Nucleic Acids Res. 1987 Apr 24;15(8):3421–3437. doi: 10.1093/nar/15.8.3421. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Morvan F., Rayner B., Leonetti J. P., Imbach J. L. alpha-DNA. VII. Solid phase synthesis of alpha-anomeric oligodeoxyribonucleotides. Nucleic Acids Res. 1988 Feb 11;16(3):833–847. doi: 10.1093/nar/16.3.833. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Pestka S., Daugherty B. L., Jung V., Hotta K., Pestka R. K. Anti-mRNA: specific inhibition of translation of single mRNA molecules. Proc Natl Acad Sci U S A. 1984 Dec;81(23):7525–7528. doi: 10.1073/pnas.81.23.7525. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Schleif R. DNA binding by proteins. Science. 1988 Sep 2;241(4870):1182–1187. doi: 10.1126/science.2842864. [DOI] [PubMed] [Google Scholar]
  29. Sizun P., Auclair C., Lescot E., Paoletti C., Perly B., Fermandjian S. Stacking and edge-to-edge associations of antitumoral ellipticine derivatives are controlled in solution by interactions involving their nitrogen sites. Biopolymers. 1988 Jul;27(7):1085–1096. doi: 10.1002/bip.360270704. [DOI] [PubMed] [Google Scholar]
  30. Thenet S., Morvan F., Bertrand J. R., Gautie C., Malvy C. Alpha are more stable than beta anomer oligonucleotides in 3T3 cellular extracts. Biochimie. 1988 Dec;70(12):1729–1732. doi: 10.1016/0300-9084(88)90031-4. [DOI] [PubMed] [Google Scholar]
  31. Thuong N. T., Asseline U., Roig V., Takasugi M., Hélène C. Oligo(alpha-deoxynucleotide)s covalently linked to intercalating agents: differential binding to ribo- and deoxyribopolynucleotides and stability towards nuclease digestion. Proc Natl Acad Sci U S A. 1987 Aug;84(15):5129–5133. doi: 10.1073/pnas.84.15.5129. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Toulmé J. J., Krisch H. M., Loreau N., Thuong N. T., Hélène C. Specific inhibition of mRNA translation by complementary oligonucleotides covalently linked to intercalating agents. Proc Natl Acad Sci U S A. 1986 Mar;83(5):1227–1231. doi: 10.1073/pnas.83.5.1227. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Zerial A., Thuong N. T., Hélène C. Selective inhibition of the cytopathic effect of type A influenza viruses by oligodeoxynucleotides covalently linked to an intercalating agent. Nucleic Acids Res. 1987 Dec 10;15(23):9909–9919. doi: 10.1093/nar/15.23.9909. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES