Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1993 Dec 25;21(25):5957–5963. doi: 10.1093/nar/21.25.5957

Preparation of trimers and tetramers of mixed sequence oligodeoxynucleoside methylphosphonates and assignment of configurations at the chiral phosphorus.

E V Vyazovkina 1, J P Rife 1, A V Lebedev 1, E Wickstrom 1
PMCID: PMC310481  PMID: 8290358

Abstract

Synthesis of stereoregular DNA methylphosphonates has been accomplished for homo-oligomers, but remains a formidable problem for oligomers of a defined antisense target sequence. In this work, four trimer and tetramer deoxynucleoside methylphosphonates of mixed sequence (dACA, dCCAA, dAGGG, and dGCAT) were prepared by block coupling of diastereomerically pure dimers with either monomers or other diastereomerically pure dimers. These oligomers were separated chromatographically into individual diastereomers, and the configurations of the chiral methylphosphonate linkages were assigned. Three types of methods were used to assign configuration of a new methylphosphonate linkage: preparation of the same diastereomer through multiple synthetic pathways, base hydrolysis, and acid hydrolysis. Hydrolysis of the diastereomerically pure oligomers into component dimers and monomers was followed by chromatographic comparison with control dimers of known configuration. In all cases studied, oligomers with R configurations displayed faster elution from silica gel than did oligomers with the respective S configuration. NMR spectra of individual diastereomers of dACA were studied, revealing characteristic differences in chemical shifts which may prove useful in configurational assignments of longer oligomers. Thus, these data provide a methodological basis for synthesis and configurational assignment of longer methylphosphonate oligomers to use as antisense probes.

Full text

PDF
5957

Selected References

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

  1. Agris C. H., Blake K. R., Miller P. S., Reddy M. P., Ts'o P. O. Inhibition of vesicular stomatitis virus protein synthesis and infection by sequence-specific oligodeoxyribonucleoside methylphosphonates. Biochemistry. 1986 Oct 7;25(20):6268–6275. doi: 10.1021/bi00368a065. [DOI] [PubMed] [Google Scholar]
  2. Bower M., Summers M. F., Powell C., Shinozuka K., Regan J. B., Zon G., Wilson W. D. Oligodeoxyribonucleoside methylphosphonates. NMR and UV spectroscopic studies of Rp-Rp and Sp-Sp methylphosphonate (Me) modified duplexes of (d[GGAATTCC])2. Nucleic Acids Res. 1987 Jun 25;15(12):4915–4930. doi: 10.1093/nar/15.12.4915. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Durand M., Maurizot J. C., Asseline U., Barbier C., Thuong N. T., Hélène C. Oligothymidylates covalently linked to an acridine derivative and with modified phosphodiester backbone: circular dichroism studies of their interactions with complementary sequences. Nucleic Acids Res. 1989 Mar 11;17(5):1823–1837. doi: 10.1093/nar/17.5.1823. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. 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]
  5. Kibler-Herzog L., Zon G., Uznanski B., Whittier G., Wilson W. D. Duplex stabilities of phosphorothioate, methylphosphonate, and RNA analogs of two DNA 14-mers. Nucleic Acids Res. 1991 Jun 11;19(11):2979–2986. doi: 10.1093/nar/19.11.2979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Lesnikowski Z. J., Jaworska M., Stec W. J. Octa(thymidine methanephosphonates) of partially defined stereochemistry: synthesis and effect of chirality at phosphorus on binding to pentadecadeoxyriboadenylic acid. Nucleic Acids Res. 1990 Apr 25;18(8):2109–2115. doi: 10.1093/nar/18.8.2109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Lesnikowski Z. J., Jaworska M., Stec W. J. Stereoselective synthesis of P-homochiral oligo(thymidine methanephosphonates). Nucleic Acids Res. 1988 Dec 23;16(24):11675–11689. doi: 10.1093/nar/16.24.11675. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Löschner T., Engels J. W. Diastereomeric dinucleoside-methylphosphonates: determination of configuration with the 2-D NMR ROESY technique. Nucleic Acids Res. 1990 Sep 11;18(17):5083–5088. doi: 10.1093/nar/18.17.5083. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. 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]
  10. Miller P. S., Dreon N., Pulford S. M., McParland K. B. Oligothymidylate analogues having stereoregular, alternating methylphosphonate/phosphodiester backbones. Synthesis and physical studies. J Biol Chem. 1980 Oct 25;255(20):9659–9665. [PubMed] [Google Scholar]
  11. Miller P. S., McParland K. B., Jayaraman K., Ts'o P. O. Biochemical and biological effects of nonionic nucleic acid methylphosphonates. Biochemistry. 1981 Mar 31;20(7):1874–1880. doi: 10.1021/bi00510a024. [DOI] [PubMed] [Google Scholar]
  12. Miller P. S., Reddy M. P., Murakami A., Blake K. R., Lin S. B., Agris C. H. Solid-phase syntheses of oligodeoxyribonucleoside methylphosphonates. Biochemistry. 1986 Sep 9;25(18):5092–5097. doi: 10.1021/bi00366a017. [DOI] [PubMed] [Google Scholar]
  13. Miller P. S., Yano J., Yano E., Carroll C., Jayaraman K., Ts'o P. O. Nonionic nucleic acid analogues. Synthesis and characterization of dideoxyribonucleoside methylphosphonates. Biochemistry. 1979 Nov 13;18(23):5134–5143. doi: 10.1021/bi00590a017. [DOI] [PubMed] [Google Scholar]
  14. Smith C. C., Aurelian L., Reddy M. P., Miller P. S., Ts'o P. O. Antiviral effect of an oligo(nucleoside methylphosphonate) complementary to the splice junction of herpes simplex virus type 1 immediate early pre-mRNAs 4 and 5. Proc Natl Acad Sci U S A. 1986 May;83(9):2787–2791. doi: 10.1073/pnas.83.9.2787. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Stec W. J., Lesnikowski Z. J. Stereospecific synthesis of P-chiral analogs of oligonucleotides. Methods Mol Biol. 1993;20:285–313. doi: 10.1385/0-89603-281-7:285. [DOI] [PubMed] [Google Scholar]

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

RESOURCES