Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1977 Nov;4(11):3727–3741. doi: 10.1093/nar/4.11.3727

Demonstration of a tertiary interaction in solution between the extra arm and the D-stem in two different transfer RNA's by NMR.

P J Salemink, T Yamane, C W Hilbers
PMCID: PMC343196  PMID: 339202

Abstract

According to the X-ray structure of yeast tRNAPhe at 2.5 A resolution, a hydrogen bond is formed between m7G46 and G22. By removal of this m7G46-residue we demonstrate that this interaction is present in solution as well. Comparison of the 1H 360 MHz NMR spectra of intact yeast tRNAPhe and its m7G-excised derivative locates the position of this tertiary H-bond at 12.5 ppm downfield from DSS. Additional evidence for the presence of this interaction in solution comes from a comparison of 1H NMR spectra of E. coli tRNAf1Met and E. coli tRNAf3Met, which differ only in a single position in the extra arm. In tRNAf3Met residue 47 is a m7G-residue, whereas in tRNAf3Met it is A, resulting in the absence of the m7G47 - G23 - C13 triple interaction, characteristic of tRNAf1Met. The resonance position of this tertiary interaction in tRNAf1Met is located around -13.6 ppm, a chemical shift difference of 1.1 ppm with respect to the position observed for tRNAPhe. The origin of this chemical shift difference is discussed in relation to the structure of their respective augmented D-helices.

Full text

PDF
3727

Selected References

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

  1. Brennan T., Sundaralingam M. Structlre of transfer RNA molecules containing the long variable loop. Nucleic Acids Res. 1976 Nov;3(11):3235–3250. doi: 10.1093/nar/3.11.3235. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Crothers D. M., Cole P. E., Hilbers C. W., Shulman R. G. The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA. J Mol Biol. 1974 Jul 25;87(1):63–88. doi: 10.1016/0022-2836(74)90560-9. [DOI] [PubMed] [Google Scholar]
  3. Daniel W. E., Jr, Cohn M. Changes in tertiary structure accompanying a single base change in transfer RNA. Proton magnetic resonance and aminoacylation studies of Escherichia coli tRNAMet f1 and tRNAMet f3 and their spin-labeled (s4U8) derivatives. Biochemistry. 1976 Sep 7;15(18):3917–3924. doi: 10.1021/bi00663a003. [DOI] [PubMed] [Google Scholar]
  4. Daniel W. E., Jr, Cohn M. Proton nuclear magnetic resonance of spin-labeled Escherichia coli tRNAf1MET. Proc Natl Acad Sci U S A. 1975 Jul;72(7):2582–2586. doi: 10.1073/pnas.72.7.2582. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Dube S. K., Marcker K. A., Clark B. F., Cory S. The nucleotide sequence of N-formyl-methionyl-transfer RNA. Products of complete digestion with ribonuclease T-1 and pancreatic ribonuclease and derivation of their sequences. Eur J Biochem. 1969 Mar;8(2):244–255. doi: 10.1111/j.1432-1033.1969.tb00521.x. [DOI] [PubMed] [Google Scholar]
  6. Geerdes H. A., Hilbers C. W. The iminoproton NMR spectrum of yeast tRNA-Phe predicted from crystal coordinates. Nucleic Acids Res. 1977 Jan;4(1):207–221. doi: 10.1093/nar/4.1.207. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Hilbers C. W., Shulman R. G. Assignment of the hydrogen bonded proton resonances in (Escherichia coli) tRNAGlu by sequential melting. Proc Natl Acad Sci U S A. 1974 Aug;71(8):3239–3242. doi: 10.1073/pnas.71.8.3239. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Holmes W. M., Hurd R. E., Reid B. R., Rimerman R. A., Hatfield G. W. Separation of transfer ribonucleic acid by sepharose chromatography using reverse salt gradients. Proc Natl Acad Sci U S A. 1975 Mar;72(3):1068–1071. doi: 10.1073/pnas.72.3.1068. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Kallenbach N. R., Daniel W. E., Jr, Kaminker M. A. Nuclear magnetic resonance study of hydrogen-bonded ring protons in oligonucleotide helices involving classical and nonclassical base pairs. Biochemistry. 1976 Mar 23;15(6):1218–1224. doi: 10.1021/bi00651a007. [DOI] [PubMed] [Google Scholar]
  10. Kim S. H. Three-dimensional structure of transfer RNA. Prog Nucleic Acid Res Mol Biol. 1976;17:181–216. doi: 10.1016/s0079-6603(08)60070-7. [DOI] [PubMed] [Google Scholar]
  11. LAWLEY P. D., BROOKES P. FURTHER STUDIES ON THE ALKYLATION OF NUCLEIC ACIDS AND THEIR CONSTITUENT NUCLEOTIDES. Biochem J. 1963 Oct;89:127–138. doi: 10.1042/bj0890127. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Ladner J. E., Jack A., Robertus J. D., Brown R. S., Rhodes D., Clark B. F., Klug A. Structure of yeast phenylalanine transfer RNA at 2.5 A resolution. Proc Natl Acad Sci U S A. 1975 Nov;72(11):4414–4418. doi: 10.1073/pnas.72.11.4414. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Ogasawara N., Watanabe Y., Inoue Y. Determination of microscopic basic ionization constants of guanylyl-(3'-5')-guanosine. Structure and optical properties of half-protonated guanylyl-(3'-5')guanosine and their models. J Am Chem Soc. 1975 Oct 29;97(22):6571–6576. doi: 10.1021/ja00855a047. [DOI] [PubMed] [Google Scholar]
  14. Pearson R. L., Weiss J. F., Kelmers A. D. Improved separation of transfer RNA's on polychlorotrifuoroethylene-supported reversed-phase chromatography columns. Biochim Biophys Acta. 1971 Feb 11;228(3):770–774. doi: 10.1016/0005-2787(71)90748-9. [DOI] [PubMed] [Google Scholar]
  15. Quigley G. J., Rich A. Structural domains of transfer RNA molecules. Science. 1976 Nov 19;194(4267):796–806. doi: 10.1126/science.790568. [DOI] [PubMed] [Google Scholar]
  16. Quigley G. J., Seeman N. C., Wang A. H., Suddath F. L., Rich A. Yeast phenylalanine transfer RNA: atomic coordinates and torsion angles. Nucleic Acids Res. 1975 Dec;2(12):2329–2341. doi: 10.1093/nar/2.12.2329. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. RajBhandary U. L., Chang S. H. Studies on polynucleotides. LXXXII. Yeast phenylalanine transfer ribonucleic acid: partial digestion with ribonuclease T-1 and derivation of the total primary structure. J Biol Chem. 1968 Feb 10;243(3):598–608. [PubMed] [Google Scholar]
  18. Reid B. R., Ribeiro N. S., Gould G., Robillard G., Hilbers C. W., Shulman R. G. Tertiary hydrogen bonds in the solution structure of transfer RNA. Proc Natl Acad Sci U S A. 1975 Jun;72(6):2049–2053. doi: 10.1073/pnas.72.6.2049. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Reid B. R., Robillard G. T. Demonstration and origin of six tertiary base pair resonances in the NMR spectrum of E. coli tRNA1Val. Nature. 1975 Sep 25;257(5524):287–291. doi: 10.1038/257287a0. [DOI] [PubMed] [Google Scholar]
  20. Rich A., RajBhandary U. L. Transfer RNA: molecular structure, sequence, and properties. Annu Rev Biochem. 1976;45:805–860. doi: 10.1146/annurev.bi.45.070176.004105. [DOI] [PubMed] [Google Scholar]
  21. Robillard G. T., Tarr C. E., Vosman F., Berendsen H. J. Similarity of the crystal and solution structure of yeast tRNAPhe. Nature. 1976 Jul 29;262(5567):363–369. doi: 10.1038/262363a0. [DOI] [PubMed] [Google Scholar]
  22. Römer R., Varadi V. Hydrogen-bonded protons in the tertiary structure of yeast tRNAPhe in solution. Proc Natl Acad Sci U S A. 1977 Apr;74(4):1561–1564. doi: 10.1073/pnas.74.4.1561. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Shulman R. G., Hilbers C. W. Ring-current shifts in the 300 MHz nuclear magnetic resonance spectra of six purified transfer RNA molecules. J Mol Biol. 1973 Jun 25;78(1):57–69. doi: 10.1016/0022-2836(73)90428-2. [DOI] [PubMed] [Google Scholar]
  24. Stout C. D., Mizuno H., Rubin J., Brennan T., Rao S. T., Sundaralingam M. Atomic coordinates and molecular conformation of yeast phenylalanyl tRNA. An independent investigation. Nucleic Acids Res. 1976 Apr;3(4):1111–1123. doi: 10.1093/nar/3.4.1111. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Sussman J. L., Kim S. H. Idealized atomic coordinates of yeast phenylalanine transfer RNA. Biochem Biophys Res Commun. 1976 Jan 12;68(1):89–96. doi: 10.1016/0006-291x(76)90014-0. [DOI] [PubMed] [Google Scholar]
  26. Sussman J. L., Kim S. Three-dimensional structure of a transfer rna in two crystal forms. Science. 1976 May 28;192(4242):853–858. doi: 10.1126/science.775636. [DOI] [PubMed] [Google Scholar]
  27. Wintermeyer W., Zachau H. G. A specific chemical chain scission of tRNA at 7-methylguanosine. FEBS Lett. 1970 Dec;11(3):160–164. doi: 10.1016/0014-5793(70)80518-x. [DOI] [PubMed] [Google Scholar]
  28. Wong K. L., Kearns D. R. NMR evidence for tertiary structure base pair in E. coli tRNA involving S4U8. Nature. 1974 Dec 20;252(5485):738–739. doi: 10.1038/252738a0. [DOI] [PubMed] [Google Scholar]

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

RESOURCES