Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1983 Aug 25;11(16):5691–5699. doi: 10.1093/nar/11.16.5691

A nuclear magnetic resonance study of the ribotrinucleoside diphophate UpUpC.

A M Gronenborn, B J Kimber, G M Clore, L W McLaughlin
PMCID: PMC326307  PMID: 6412213

Abstract

500 MHz 1H, 67.89 MHz 13C and 80.97 MHz 31P-NMR studies are reported on the ribotrinucleoside diphosphate UpUpC, the triplet codon corresponding to the amino acid phenylalanine. Complete spectral assignments are given and conformational parameters for the backbone and the furanose rings are determined. All three nucleotide units show a near-balance for the N/S equilibrium with a slight preference for the N-type ribose (approximately 60%). The backbone conformation around the C3'-03' bonds show a preference for the trans domain, while the orientation around the C5'-05' bonds is predominantly trans.

Full text

PDF
5691

Selected References

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

  1. Alderfer J. L., Ts'o P. O. Conformational properties of the furanose phosphate backbone in nucleic acids. A carbon-13 nuclear magnetic resonance study. Biochemistry. 1977 May 31;16(11):2410–2416. doi: 10.1021/bi00630a016. [DOI] [PubMed] [Google Scholar]
  2. 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]
  3. Altona C., Sundaralingam M. Conformational analysis of the sugar ring in nucleosides and nucleotides. Improved method for the interpretation of proton magnetic resonance coupling constants. J Am Chem Soc. 1973 Apr 4;95(7):2333–2344. doi: 10.1021/ja00788a038. [DOI] [PubMed] [Google Scholar]
  4. Altona C., Van Boom J. H., Haasnoot C. A. Conformational analysis of a DNA triplet in aqueous solution. Thymidylyl-(3'-5')-thymidylyl-(3'-5')-2'-deoxyadenosine, d(T-T-A), studied by 1H nuclear magnetic resonance at 360 MHz. Eur J Biochem. 1976 Dec 11;71(2):557–562. doi: 10.1111/j.1432-1033.1976.tb11145.x. [DOI] [PubMed] [Google Scholar]
  5. Broyde S. B., Wartell R. M., Stellman S. D., Hingerty B., Langridge R. Classical potential energy calculations for ApA, CpC, GpG, and UpU. The influence of the bases on RNA subunit conformations. Biopolymers. 1975 Aug;14(8):1597–1613. doi: 10.1002/bip.1975.360140805. [DOI] [PubMed] [Google Scholar]
  6. Doornbos J., Wreesmann C. T., Van Boom J. H., Altona C. Conformational analysis of the single-stranded ribonucleic acid A-A-C-C. A one-dimensional and two-dimensional proton NMR study at 500 MHz. Eur J Biochem. 1983 Apr 5;131(3):571–579. doi: 10.1111/j.1432-1033.1983.tb07301.x. [DOI] [PubMed] [Google Scholar]
  7. Doornbos J., den Hartog J. A., van Boom J. H., Altona C. Conformational analysis of the nucleotides A2'-5'A, A2'-5'A2'-5'A and A2'-5'U from nuclear magnetic resonance and circular dichroism studies. Eur J Biochem. 1981 May 15;116(2):403–412. doi: 10.1111/j.1432-1033.1981.tb05349.x. [DOI] [PubMed] [Google Scholar]
  8. Dorman D. E., Roberts J. D. Nuclear magnetic resonance spectroscopy: 13C spectra of some common nucleotides. Proc Natl Acad Sci U S A. 1970 Jan;65(1):19–26. doi: 10.1073/pnas.65.1.19. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Govil G., Smith I. C. A carbon-13 magnetic resonance study of the helix-coil transition in polyuridylic acid. Biopolymers. 1973 Nov;12(11):2589–2598. doi: 10.1002/bip.1973.360121111. [DOI] [PubMed] [Google Scholar]
  10. Guschlbauer W. Conformational analysis of ribonucleosides from proton-proton coupling constants. Biochim Biophys Acta. 1980 Nov 14;610(1):47–55. doi: 10.1016/0005-2787(80)90054-4. [DOI] [PubMed] [Google Scholar]
  11. Hartel A. J., Wille-Hazeleger G., van Boom J. H., Altona C. Conformational analysis of a modified ribotetranucleoside triphosphate: m6(2)A-U-m6(2)A-U studied in aqueous solution by nuclear magnetic resonance at 500 MHz. Nucleic Acids Res. 1981 Mar 25;9(6):1405–1423. doi: 10.1093/nar/9.6.1405. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Hingerty B., Subramanian E., Stellman S. D., Broyde S. B., Sato T., Langridge R. Structure of guanylyl-3',5'-cytidine monophosphate. II. Description of the molecular and crystal structure of the calcium derivative in space group P2(1). Biopolymers. 1975 Jan;14(1):227–236. doi: 10.1002/bip.1975.360140116. [DOI] [PubMed] [Google Scholar]
  13. Lapper R. D., Smith I. C. A 13 C and 1 H nuclear magnetic resonance study of the conformations of 2',3'-cyclic nucleotides. J Am Chem Soc. 1973 May 2;95(9):2878–2880. doi: 10.1021/ja00790a024. [DOI] [PubMed] [Google Scholar]
  14. Lee C. H., Tinoco I., Jr Conformation studies of 13 trinucleoside diphosphates by 360 MHz PMR spectroscopy. A bulged base conformation. I. Base protons and H1' protons. Biophys Chem. 1980 Apr;11(2):283–294. doi: 10.1016/0301-4622(80)80031-7. [DOI] [PubMed] [Google Scholar]
  15. Mantsch H. H., Smith I. C. Fourier-transformed 13 C NMR spectra of polyuridylic acid, uridine, and related nucleotides--the use of 31 POC 13 C couplings for conformational analysis. Biochem Biophys Res Commun. 1972 Jan 31;46(2):808–815. doi: 10.1016/s0006-291x(72)80213-4. [DOI] [PubMed] [Google Scholar]
  16. Olsthoorn C. S., Bostelaar L. J., Van Boom J. H., Altona C. Conformational characteristics of the trinucleoside diphosphate dApdApdA and its constituents from nuclear magnetic resonance and circular dichroism studies. Extrapolation to the stacked conformers. Eur J Biochem. 1980 Nov;112(1):95–110. doi: 10.1111/j.1432-1033.1980.tb04991.x. [DOI] [PubMed] [Google Scholar]
  17. Olsthoorn C. S., Doornbos J., de Leeuw H. P., Altona C. Influence of the 2'-hydroxyl group and of 6-N-methylation on the conformation of adenine dinucleoside monophosphates in solution. A nuclear magnetic resonance and circular dichroism study. Eur J Biochem. 1982 Jul;125(2):367–382. doi: 10.1111/j.1432-1033.1982.tb06693.x. [DOI] [PubMed] [Google Scholar]
  18. Pullman B., Perahia D., Saran A. Molecular orbital calculations on the conformation of nucleic acids and their constituents. 3. Backbone structure of di- and polynucleotides. Biochim Biophys Acta. 1972 Apr 26;269(1):1–14. doi: 10.1016/0005-2787(72)90068-8. [DOI] [PubMed] [Google Scholar]
  19. Schleich T., Cross B. P., Smith I. C. A conformational study of adenylyl-(3',5')-adenosine and adenylyl-(2',5')-adenosine in aqueous solution by carbon-13 magnetic resonance spectroscopy. Nucleic Acids Res. 1976 Feb;3(2):355–370. doi: 10.1093/nar/3.2.355. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Sussman J. L., Seeman N. C., Kim S. H., Berman H. M. Crystal structure of a naturally occurring dinucleoside phoaphate: uridylyl 3',5'-adenosine phosphate model for RNA chain folding. J Mol Biol. 1972 May 28;66(3):403–421. doi: 10.1016/0022-2836(72)90423-8. [DOI] [PubMed] [Google Scholar]

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

RESOURCES