Skip to main content
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1996 Apr 1;24(7):1187–1194. doi: 10.1093/nar/24.7.1187

The use of non-uniform deuterium labelling ['NMR-window'] to study the NMR structure of a 21mer RNA hairpin.

A Földesi 1, S I Yamakage 1, F P Nilsson 1, T V Maltseva 1, J Chattopadhyaya 1
PMCID: PMC145781  PMID: 8614618

Abstract

The first synthesis of a non-uniformly deuterium labelled 21mer RNA is reported using our 'NMR-window' concept, showing its unique application in the unambiguous NMR assignment of the non-exchangeable aromatic and sugar protons.

Full Text

The Full Text of this article is available as a PDF (131.3 KB).

Selected References

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

  1. Aboul-ela F., Varani G. Novel techniques in nuclear magnetic resonance for nucleic acids. Curr Opin Biotechnol. 1995 Feb;6(1):89–95. doi: 10.1016/0958-1669(95)80014-x. [DOI] [PubMed] [Google Scholar]
  2. Agback P., Maltseva T. V., Yamakage S. I., Nilson F. P., Földesi A., Chattopadhyaya J. The differences in the T2 relaxation rates of the protons in the partially-deuteriated and fully protonated sugar residues in a large oligo-DNA ('NMR-window') gives complementary structural information. Nucleic Acids Res. 1994 Apr 25;22(8):1404–1412. doi: 10.1093/nar/22.8.1404. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Allain F. H., Varani G. Structure of the P1 helix from group I self-splicing introns. J Mol Biol. 1995 Jul 14;250(3):333–353. doi: 10.1006/jmbi.1995.0381. [DOI] [PubMed] [Google Scholar]
  4. Földesi A., Nilson F. P., Glemarec C., Gioeli C., Chattopadhyaya J. NMR spectroscopic properties (1H at 500 MHz) of deuterated* ribonucleotide-dimers ApU*, GpC*, partially deuterated 2'-deoxyribonucleotide-dimers d(TpA*), d(ApT*), d(GpC*) and their comparison with natural counterparts (1H-NMR window). J Biochem Biophys Methods. 1993 Feb;26(1):1–26. doi: 10.1016/0165-022x(93)90018-j. [DOI] [PubMed] [Google Scholar]
  5. Gasparutto D., Livache T., Bazin H., Duplaa A. M., Guy A., Khorlin A., Molko D., Roget A., Téoule R. Chemical synthesis of a biologically active natural tRNA with its minor bases. Nucleic Acids Res. 1992 Oct 11;20(19):5159–5166. doi: 10.1093/nar/20.19.5159. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Heller S. R. 1-H NMR studies on deuterium-hydrogen exchange at C-5 in uridines. Biochem Biophys Res Commun. 1968 Sep 30;32(6):998–1001. doi: 10.1016/0006-291x(68)90127-7. [DOI] [PubMed] [Google Scholar]
  7. Kim I., Watanabe S., Muto Y., Hosono K., Takai K., Takaku H., Kawai G., Watanabe K., Yokoyama S. Selective deuteration of RNA for NMR signal assignment. Nucleic Acids Symp Ser. 1995;(34):123–124. [PubMed] [Google Scholar]
  8. Maltseva T. V., Agback P., Chattopadhyaya J. How much hydration is necessary for the stabilisation of DNA-duplex? Nucleic Acids Res. 1993 Sep 11;21(18):4246–4252. doi: 10.1093/nar/21.18.4246. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Neuhaus D., Wagner G., Vasák M., Kägi J. H., Wüthrich K. Systematic application of high-resolution, phase-sensitive two-dimensional 1H-NMR techniques for the identification of the amino-acid-proton spin systems in proteins. Rabbit metallothionein-2. Eur J Biochem. 1985 Sep 2;151(2):257–273. doi: 10.1111/j.1432-1033.1985.tb09096.x. [DOI] [PubMed] [Google Scholar]
  10. Puglisi J. D., Wyatt J. R., Tinoco I., Jr Conformation of an RNA pseudoknot. J Mol Biol. 1990 Jul 20;214(2):437–453. doi: 10.1016/0022-2836(90)90192-O. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Rabi J. A., Fox J. J. Nucleosides. LXXIX. Facile base-catalyzed hydrogen isotope labeling at position 6 of pyrimidine nucleosides. J Am Chem Soc. 1973 Mar 7;95(5):1628–1632. doi: 10.1021/ja00786a044. [DOI] [PubMed] [Google Scholar]
  12. Ramesh V. NMR evidence for the RNA stem-loop structure involved in the transcription attenuation of E. coli trp operon. Nucleic Acids Res. 1993 Nov 25;21(23):5485–5488. doi: 10.1093/nar/21.23.5485. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Varani G., Tinoco I., Jr RNA structure and NMR spectroscopy. Q Rev Biophys. 1991 Nov;24(4):479–532. doi: 10.1017/s0033583500003875. [DOI] [PubMed] [Google Scholar]
  14. Wataya Y., Hayatsu H., Kawazoe Y. Cysteine-catalyzed hydrogen isotope exchange at the 5 position of uridylic acid. J Am Chem Soc. 1972 Dec 13;94(25):8927–8928. doi: 10.1021/ja00780a059. [DOI] [PubMed] [Google Scholar]
  15. Westman E., Strömberg R. Removal of t-butyldimethylsilyl protection in RNA-synthesis. Triethylamine trihydrofluoride (TEA, 3HF) is a more reliable alternative to tetrabutylammonium fluoride (TBAF). Nucleic Acids Res. 1994 Jun 25;22(12):2430–2431. doi: 10.1093/nar/22.12.2430. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. White S. A., Nilges M., Huang A., Brünger A. T., Moore P. B. NMR analysis of helix I from the 5S RNA of Escherichia coli. Biochemistry. 1992 Feb 18;31(6):1610–1621. doi: 10.1021/bi00121a005. [DOI] [PubMed] [Google Scholar]
  17. Yamakage S. I., Maltseva T. V., Nilson F. P., Földesi A., Chattopadhyaya J. Deuteriation of sugar protons simplify NMR assignments and structure determination of large oligonucleotide by the 1H-NMR window approach. Nucleic Acids Res. 1993 Nov 11;21(22):5005–5011. doi: 10.1093/nar/21.22.5005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Zhou X. X., Welch C. J., Chattopadhyaya J. Pyridyl groups for protection of the imide functions of uridine and guanosine. Exploration of their displacement reactions for site-specific modifications of uracil and guanine bases. Acta Chem Scand B. 1986 Nov;40(10):806–816. doi: 10.3891/acta.chem.scand.40b-0806. [DOI] [PubMed] [Google Scholar]

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

RESOURCES