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. 1988 Jun 10;16(11):5039–5053. doi: 10.1093/nar/16.11.5039

Circular dichroism studies of an oligo-alpha-thymidylate and of its interactions with complementary sequences.

M Durand 1, J C Maurizot 1, N T Thuong 1, C Helene 1
PMCID: PMC336715  PMID: 3387216

Abstract

An octathymidylate synthesized with the alpha anomer of thymidine has been studied using circular dichroism. Its conformation has been compared to that of its analogue containing the naturally occurring beta anomer. In both compounds some degree of intramolecular stacking is present as indicated by the shapes of the circular dichroism spectra and their variations with temperature. As its beta-analogue the alpha-octathymidylate binds to its complementary sequences containing beta-nucleosides. Only complexes with 1A:1T stoechiometry were observed. Binding to ribose- containing oligomers and polymers is much stronger than binding to deoxyribose-containing analogues. Circular dichroism spectra provided evidence for a difference between the geometry of the various complexes formed with an alpha-oligothymidylate and those formed with its beta-anomer-containing analogue.

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Selected References

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  1. 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]
  2. Blake K. R., Murakami A., Miller P. S. Inhibition of rabbit globin mRNA translation by sequence-specific oligodeoxyribonucleotides. Biochemistry. 1985 Oct 22;24(22):6132–6138. doi: 10.1021/bi00343a015. [DOI] [PubMed] [Google Scholar]
  3. Blake K. R., Murakami A., Spitz S. A., Glave S. A., Reddy M. P., Ts'o P. O., Miller P. S. Hybridization arrest of globin synthesis in rabbit reticulocyte lysates and cells by oligodeoxyribonucleoside methylphosphonates. Biochemistry. 1985 Oct 22;24(22):6139–6145. doi: 10.1021/bi00343a016. [DOI] [PubMed] [Google Scholar]
  4. Brahms J., Michelson A. M., Van Holde K. E. Adenylate oligomers in single- and double-strand conformation. J Mol Biol. 1966 Feb;15(2):467–488. doi: 10.1016/s0022-2836(66)80122-5. [DOI] [PubMed] [Google Scholar]
  5. Bush C. A. Theoretical interpretation of the circular dichroism of adenine nucleosides. J Am Chem Soc. 1973 Jan 10;95(1):214–219. doi: 10.1021/ja00782a038. [DOI] [PubMed] [Google Scholar]
  6. Camerman N., Fawcett J. K., Cameran A. Molecular structure of a deoxyribose-dinucleotide, sodium thymidylyl-(5' yields to 3')-thymidylate-(5') hydrate (pTpT), and a possible structural model for polythymidylate. J Mol Biol. 1976 Nov 15;107(4):601–621. doi: 10.1016/s0022-2836(76)80086-1. [DOI] [PubMed] [Google Scholar]
  7. Cazenave C., Loreau N., Toulmé J. J., Hélène C. Anti-messenger oligodeoxynucleotides: specific inhibition of rabbit beta-globin synthesis in wheat germ extracts and Xenopus oocytes. Biochimie. 1986 Sep;68(9):1063–1069. doi: 10.1016/s0300-9084(86)80180-8. [DOI] [PubMed] [Google Scholar]
  8. Cheng D. M., Dhingra M. M., Sarma R. H. Spatial configuration of deoxyribotrinucleoside diphosphates in aqueous solution. Nucleic Acids Res. 1978 Nov;5(11):4399–4416. doi: 10.1093/nar/5.11.4399. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Cheng D. M., Sarma R. H. Intimate details of the conformational characteristics of deoxyribodinucleoside monophosphates in aqueous solution. J Am Chem Soc. 1977 Oct 26;99(22):7333–7348. doi: 10.1021/ja00464a038. [DOI] [PubMed] [Google Scholar]
  10. 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]
  11. Emerson T. R., Swan R. J., Ulbricht T. L. Optical rotatory dispersion of nucleic acid derivatives. 8. The conformation of pyrimidine nucleosides in solution. Biochemistry. 1967 Mar;6(3):843–850. doi: 10.1021/bi00855a026. [DOI] [PubMed] [Google Scholar]
  12. 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]
  13. Gupta K. C. Antisense oligodeoxynucleotides provide insight into mechanism of translation initiation of two Sendai virus mRNAs. J Biol Chem. 1987 Jun 5;262(16):7492–7496. [PubMed] [Google Scholar]
  14. 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]
  15. Ingwall J. S. Circular dichroism of nucleosides. I. Anomeric pairs of the D-pentofuranosides of adenine. J Am Chem Soc. 1972 Jul 26;94(15):5487–5495. doi: 10.1021/ja00770a054. [DOI] [PubMed] [Google Scholar]
  16. Izant J. G., Weintraub H. Inhibition of thymidine kinase gene expression by anti-sense RNA: a molecular approach to genetic analysis. Cell. 1984 Apr;36(4):1007–1015. doi: 10.1016/0092-8674(84)90050-3. [DOI] [PubMed] [Google Scholar]
  17. Kawasaki E. S. Quantitative hybridization-arrest of mRNA in Xenopus oocytes using single-stranded complementary DNA or oligonucleotide probes. Nucleic Acids Res. 1985 Jul 11;13(13):4991–5004. doi: 10.1093/nar/13.13.4991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Kim S. K., Wold B. J. Stable reduction of thymidine kinase activity in cells expressing high levels of anti-sense RNA. Cell. 1985 Aug;42(1):129–138. doi: 10.1016/s0092-8674(85)80108-2. [DOI] [PubMed] [Google Scholar]
  19. Lancelot G., Guesnet J. L., Roig V., Thuong N. T. 2D-NMR studies of the unnatural duplex alpha-d(TCTAAAC)-beta-d(AGATTTG). Nucleic Acids Res. 1987 Sep 25;15(18):7531–7547. doi: 10.1093/nar/15.18.7531. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Le Doan T., Perrouault L., Praseuth D., Habhoub N., Decout J. L., Thuong N. T., Lhomme J., Hélène C. Sequence-specific recognition, photocrosslinking and cleavage of the DNA double helix by an oligo-[alpha]-thymidylate covalently linked to an azidoproflavine derivative. Nucleic Acids Res. 1987 Oct 12;15(19):7749–7760. doi: 10.1093/nar/15.19.7749. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Melton D. A. Injected anti-sense RNAs specifically block messenger RNA translation in vivo. Proc Natl Acad Sci U S A. 1985 Jan;82(1):144–148. doi: 10.1073/pnas.82.1.144. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Miles D. W., Inskeep W. H., Robins M. J., Winkley M. W., Robins R. K., Eyring H. Circular dichroism of nucleoside derivatives. IX. Vicinal effects on the circular dichroism of pyrimidine nucleosides. J Am Chem Soc. 1970 Jul 1;92(13):3872–3881. doi: 10.1021/ja00716a007. [DOI] [PubMed] [Google Scholar]
  23. Miller P. S., Agris C. H., Aurelian L., Blake K. R., Murakami A., Reddy M. P., Spitz S. A., Ts'o P. O. Control of ribonucleic acid function by oligonucleoside methylphosphonates. Biochimie. 1985 Jul-Aug;67(7-8):769–776. doi: 10.1016/s0300-9084(85)80166-8. [DOI] [PubMed] [Google Scholar]
  24. Morvan F., Rayner B., Imbach J. L., Chang D. K., Lown J. W. alpha-DNA. I. Synthesis, characterization by high field 1H-NMR, and base-pairing properties of the unnatural hexadeoxyribonucleotide alpha-[d(CpCpTpTpCpC)] with its complement beta-[d(GpGpApApGpG)]. Nucleic Acids Res. 1986 Jun 25;14(12):5019–5035. doi: 10.1093/nar/14.12.5019. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Morvan F., Rayner B., Imbach J. L., Lee M., Hartley J. A., Chang D. K., Lown J. W. alpha-DNA-V. Parallel annealing, handedness and conformation of the duplex of the unnatural alpha-hexadeoxyribonucleotide alpha-[d(CpApTpGpCpG)] with its beta-complement beta-[d(GpTpApCpGpC)] deduced from high field 1H-NMR. Nucleic Acids Res. 1987 Sep 11;15(17):7027–7044. doi: 10.1093/nar/15.17.7027. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Praseuth D., Chassignol M., Takasugi M., Le Doan T., Thuong N. T., Hélène C. Double helices with parallel strands are formed by nuclease-resistant oligo-[alpha]-deoxynucleotides and oligo-[alpha]-deoxynucleotides covalently linked to an intercalating agent with complementary oligo-[beta]-deoxynucleotides. J Mol Biol. 1987 Aug 20;196(4):939–942. doi: 10.1016/0022-2836(87)90416-5. [DOI] [PubMed] [Google Scholar]
  27. Sun J. S., Asseline U., Rouzaud D., Montenay-Garestier T., Nguyen T. T., Hélène C. Oligo-[alpha]-deoxynucleotides covalently linked to an intercalating agent. Double helices with parallel strands are formed with complementary oligo-[beta]-deoxynucleotides. Nucleic Acids Res. 1987 Aug 11;15(15):6149–6158. doi: 10.1093/nar/15.15.6149. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Séquin U. Nucleosides and nucleotides. Part 7. Four dithymidine monophosphates with different anomeric configurations, their synthesis and behaviour towards phosphodiesterases. Helv Chim Acta. 1974;57(1):68–81. doi: 10.1002/hlca.19740570108. [DOI] [PubMed] [Google Scholar]
  29. 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]
  30. Thuong N. T., Chassignol M., Lancelot G., Mayer R., Hartmann B., Leng M., Hélène C. Synthesis and structural studies of a self-complementary decadeoxynucleotide d(AATTGCAATT). I.-Synthesis and chemical characterization of the decanucleotide. Biochimie. 1981 Oct;63(10):775–784. doi: 10.1016/s0300-9084(81)80037-5. [DOI] [PubMed] [Google Scholar]
  31. Van Holde K. E., Brahms J., Michelson A. M. Base interactions of nucleotide polymers in aqueous solution. J Mol Biol. 1965 Jul;12(3):726–739. doi: 10.1016/s0022-2836(65)80323-0. [DOI] [PubMed] [Google Scholar]
  32. Walder J. A., Eder P. S., Engman D. M., Brentano S. T., Walder R. Y., Knutzon D. S., Dorfman D. M., Donelson J. E. The 35-nucleotide spliced leader sequence is common to all trypanosome messenger RNA's. Science. 1986 Aug 1;233(4763):569–571. doi: 10.1126/science.3523758. [DOI] [PubMed] [Google Scholar]

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