Skip to main content
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1993 Aug 25;21(17):3921–3926. doi: 10.1093/nar/21.17.3921

Molecular and crystal structure of Sp-thymidin-3'-yl 4-thiothymidin-5'-yl methylphosphonate.

T Szabó 1, D Noréus 1, R Norrestam 1, J Stawinski 1
PMCID: PMC309967  PMID: 8371969

Abstract

The molecular structure of one diastereomer of the dinucleoside methylphosphonate Tp(Me)sT (1) has been determined by X-ray diffraction methods. The crystal asymmetric unit contains one molecule of 1 and one methanol in an orthorhombic unit cell of dimensions a = 13.241(4), b = 13.844(3), c = 14.944(7) A, space group P2(1)2(1)2(1). Both pyrimidine bases in 1 are oriented anti relative to the 2'-deoxyribose rings, and the sugar conformations are 2E and 2(3)T in the 4-thiothymidine and thymidine moieties, respectively. The deoxyribose-phosphonate backbone has an extended conformation with the bases completely unstacked and almost parallel. The absolute configuration at the phosphorus center in 1 is Sp.

Full text

PDF
3921

Selected References

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

  1. Altona C., Sundaralingam M. Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation. J Am Chem Soc. 1972 Nov 15;94(23):8205–8212. doi: 10.1021/ja00778a043. [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. Callahan L., Han F. S., Watt W., Duchamp D., Kézdy F. J., Agarwal K. B- to Z-DNA transition probed by oligonucleotides containing methylphosphonates. Proc Natl Acad Sci U S A. 1986 Mar;83(6):1617–1621. doi: 10.1073/pnas.83.6.1617. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. 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]
  5. Chacko K. K., Lindner K., Saenger W., Miller P. S. Molecular structure of deoxyadenylyl-3'-methylphosphonate-5'-thymidine dihydrate, (d-ApT x 2H2O), a dinucleoside monophosphate with neutral phosphodiester backbone. An X-ray crystal study. Nucleic Acids Res. 1983 May 11;11(9):2801–2814. doi: 10.1093/nar/11.9.2801. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. 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]
  7. Gorenstein D. G., Luxon B. A., Goldfield E. M., Lai K., Vegeais D. Phosphorus-31 nuclear magnetic resonance of double- and triple-helical nucleic acids. Phosphorus-31 chemical shifts as a probe of phosphorus-oxygen ester bond torsional angles. Biochemistry. 1982 Feb 2;21(3):580–589. doi: 10.1021/bi00532a026. [DOI] [PubMed] [Google Scholar]
  8. Han F., Watt W., Duchamp D. J., Callahan L., Kézdy F. J., Agarwal K. Molecular structure of deoxycytidyl-3'-methylphosphonate (RP) 5'-deoxyguanidine, d[Cp(CH3)G]. A neutral dinucleotide with Watson-Crick base pairing and a right handed helical twist. Nucleic Acids Res. 1990 May 11;18(9):2759–2767. doi: 10.1093/nar/18.9.2759. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Roongta V. A., Jones C. R., Gorenstein D. G. Effect of distortions in the deoxyribose phosphate backbone conformation of duplex oligodeoxyribonucleotide dodecamers containing GT, GG, GA, AC, and GU base-pair mismatches on 31P NMR spectra. Biochemistry. 1990 Jun 5;29(22):5245–5258. doi: 10.1021/bi00474a005. [DOI] [PubMed] [Google Scholar]
  10. Saenger W., Scheit K. H. A pyrimidine nucleoside in the syn conformation: molecular and crystal structure of 4-thiouridine-hydrate. J Mol Biol. 1970 May 28;50(1):153–169. doi: 10.1016/0022-2836(70)90112-9. [DOI] [PubMed] [Google Scholar]
  11. Saenger W., Suck D., Scheit K. H. Crystal and molecular structure of 3'-O-acetyl-2'-deoxy-4-thiothymidine. FEBS Lett. 1969 Nov 29;5(4):262–264. doi: 10.1016/0014-5793(69)80364-9. [DOI] [PubMed] [Google Scholar]
  12. Voet D., Rich A. The crystal structures of purines, pyrimidines and their intermolecular complexes. Prog Nucleic Acid Res Mol Biol. 1970;10:183–265. doi: 10.1016/s0079-6603(08)60565-6. [DOI] [PubMed] [Google Scholar]

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

RESOURCES