Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1985 May 10;13(9):3317–3333. doi: 10.1093/nar/13.9.3317

Conformational characteristics of the hexanucleoside pentaphosphate AUAUAU: a 2D NMR study at 500 MHz.

P P Lankhorst, G A van der Marel, G Wille, J H van Boom, C Altona
PMCID: PMC341237  PMID: 2987882

Abstract

All 36 ribose proton resonances and most of the base proton resonances of the hexanucleoside pentaphosphate AUAUAU have been assigned unequivocally using 2D J-resolved spectroscopy, spin echo correlated spectroscopy (SECSY) and 2D NOE spectroscopy (NOESY). The NMR parameters of AUAUAU are compared with those of smaller fragments that contain methylated adenine bases: m62AU, m62AUm62A, m62AUm62AU and m62AUm62AUm62A. Previous studies on this series of compounds have shown that in all these cases purine-pyrimidine-purine sequences prefer to adopt a mixture of states which have as common feature that the interior pyrimidine residues are bulged out, whereas the purine residues stack upon each other. Chemical shift data, proton-proton coupling constants, as well as the observation of imino-proton resonances for AUAUAU show unambiguously that upon lowering the temperature the high-temperature "bulged out" situation reverts to a normal A-RNA-like double helix.

Full text

PDF
3317

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. 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]
  3. Borer P. N., Dengler B., Tinoco I., Jr, Uhlenbeck O. C. Stability of ribonucleic acid double-stranded helices. J Mol Biol. 1974 Jul 15;86(4):843–853. doi: 10.1016/0022-2836(74)90357-x. [DOI] [PubMed] [Google Scholar]
  4. Broido M. S., Zon G., James T. L. Complete assignment of the non-exchangeable proton nmr resonances of [d-(GGAATTCC)]2 using two-dimensional nuclear overhauser effect spectra. Biochem Biophys Res Commun. 1984 Mar 15;119(2):663–670. doi: 10.1016/s0006-291x(84)80301-0. [DOI] [PubMed] [Google Scholar]
  5. Feigon J., Denny W. A., Leupin W., Kearns D. R. Proton nuclear magnetic resonance investigation of the conformation and dynamics in the synthetic deoxyribonucleic acid decamers d(ATATCGATAT) and d(ATATGCATAT). Biochemistry. 1983 Dec 6;22(25):5930–5942. doi: 10.1021/bi00294a037. [DOI] [PubMed] [Google Scholar]
  6. Feigon J., Leupin W., Denny W. A., Kearns D. R. Two-dimensional proton nuclear magnetic resonance investigation of the synthetic deoxyribonucleic acid decamer d(ATATCGATAT)2. Biochemistry. 1983 Dec 6;22(25):5943–5951. doi: 10.1021/bi00294a038. [DOI] [PubMed] [Google Scholar]
  7. Feigon J., Wang A. H., van der Marel G. A., Van Boom J. H., Rich A. A one- and two-dimensional NMR study of the B to Z transition of (m5dC-dG)3 in methanolic solution. Nucleic Acids Res. 1984 Jan 25;12(2):1243–1263. doi: 10.1093/nar/12.2.1243. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Haasnoot C. A., Hilbers C. W. Effective water resonance suppression in 1D- and 2D-FT-1H-NMR spectroscopy of biopolymers in aqueous solution. Biopolymers. 1983 May;22(5):1259–1266. doi: 10.1002/bip.360220502. [DOI] [PubMed] [Google Scholar]
  9. Haasnoot C. A., Westerink H. P., van der Marel G. A., van Boom J. H. Conformational analysis of a hybrid DNA-RNA double helical oligonucleotide in aqueous solution: d(CG)r(CG)d(CG) studied by 1D- and 2D-1H NMR spectroscopy. J Biomol Struct Dyn. 1983 Oct;1(1):131–149. doi: 10.1080/07391102.1983.10507430. [DOI] [PubMed] [Google Scholar]
  10. Hare D. R., Wemmer D. E., Chou S. H., Drobny G., Reid B. R. Assignment of the non-exchangeable proton resonances of d(C-G-C-G-A-A-T-T-C-G-C-G) using two-dimensional nuclear magnetic resonance methods. J Mol Biol. 1983 Dec 15;171(3):319–336. doi: 10.1016/0022-2836(83)90096-7. [DOI] [PubMed] [Google Scholar]
  11. Hartel A. J., Lankhorst P. P., Altona C. Thermodynamics of stacking and of self-association of the dinucleoside monophosphate m2(6)A-U from proton NMR chemical shifts: differential concentration temperature profile method. Eur J Biochem. 1982 Dec 15;129(2):343–357. doi: 10.1111/j.1432-1033.1982.tb07057.x. [DOI] [PubMed] [Google Scholar]
  12. 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]
  13. Lankhorst P. P., Wille G., van Boom J. H., Altona C., Haasnoot C. A. Conformational analysis of a ribopentanucleoside tetraphosphate in aqueous solution. A two-dimensional NMR study at 500 MHz. Nucleic Acids Res. 1983 May 11;11(9):2839–2856. doi: 10.1093/nar/11.9.2839. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Lee C. H. Conformational studies of trinucleoside bisphosphates. 2. Potential energy calculations. Eur J Biochem. 1983 Dec 1;137(1-2):357–363. doi: 10.1111/j.1432-1033.1983.tb07836.x. [DOI] [PubMed] [Google Scholar]
  15. 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]
  16. Lomant A. J., Fresco J. R. Polynucleotides. XIV. Photochemical evidence for an extrahelical, solvent-accessible environment of non-complementary residues in polynucleotide helices. J Mol Biol. 1973 Jul 5;77(3):345–354. doi: 10.1016/0022-2836(73)90442-7. [DOI] [PubMed] [Google Scholar]
  17. Lomant A. J., Fresco J. R. Ultraviolet photochemistry as a probe of polyribonucleotide conformation. Prog Nucleic Acid Res Mol Biol. 1972;12:1–27. doi: 10.1016/s0079-6603(08)60657-1. [DOI] [PubMed] [Google Scholar]
  18. Lown J. W., Hanstock C. C., Bleackley R. C., Imbach J. L., Rayner B., Vasseur J. J. Synthesis, complete 1H assignments and conformations of the self-complementary hexadeoxyribonucleotide [d(CpGpApTpCpG)]2 and its fragments by high field NMR. Nucleic Acids Res. 1984 Mar 12;12(5):2519–2533. doi: 10.1093/nar/12.5.2519. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Mellema J. R., Pieters J. M., van der Marel G. A., van Boom J. H., Haasnoot C. A., Altona C. Sequence-dependent structural variation in single-helical DNA. Proton NMR studies of d(T-A-T-A) and d(A-T-A-T) in aqueous solution. Eur J Biochem. 1984 Sep 3;143(2):285–301. doi: 10.1111/j.1432-1033.1984.tb08371.x. [DOI] [PubMed] [Google Scholar]
  20. Nagayama K., Wüthrich K., Bachmann P., Ernst R. R. Two-dimensional J-resolved 1H n.m.r. spectroscopy for studies of biological macromolecules. Biochem Biophys Res Commun. 1977 Sep 9;78(1):99–105. doi: 10.1016/0006-291x(77)91226-8. [DOI] [PubMed] [Google Scholar]
  21. Nagayama K., Wüthrich K., Ernst R. R. Two-dimensional spin echo correlated spectroscopy (SECSY) for 1H NMR studies of biological macromolecules. Biochem Biophys Res Commun. 1979 Sep 12;90(1):305–311. doi: 10.1016/0006-291x(79)91625-5. [DOI] [PubMed] [Google Scholar]
  22. Noller H. F. Structure of ribosomal RNA. Annu Rev Biochem. 1984;53:119–162. doi: 10.1146/annurev.bi.53.070184.001003. [DOI] [PubMed] [Google Scholar]
  23. 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]
  24. Patel D. J., Tonelli A. E. Assignment of the proton Nmr chemical shifts of the T-N3H and G-N1H proton resonances in isolated AT and GC Watson-Crick base pairs in double-stranded deoxy oligonucleotides in aqueous solution. Biopolymers. 1974;13(10):1943–1964. doi: 10.1002/bip.1974.360131003. [DOI] [PubMed] [Google Scholar]
  25. Peattie D. A., Douthwaite S., Garrett R. A., Noller H. F. A "bulged" double helix in a RNA-protein contact site. Proc Natl Acad Sci U S A. 1981 Dec;78(12):7331–7335. doi: 10.1073/pnas.78.12.7331. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Tran-Dinh S., Neumann J. M., Taboury J., Huynh-Dinh T., Renous S., Genissel B., Igolen J. DNA fragment conformations. 1H-NMR comparative studies of helix-coil transition and conformation of d(C-A-C-G-T-G) and d(G-T-G-C-A-C). Influence of helix formation on proton chemical shifts. Eur J Biochem. 1983 Jul 1;133(3):579–589. doi: 10.1111/j.1432-1033.1983.tb07502.x. [DOI] [PubMed] [Google Scholar]
  27. Woese C. R., Gutell R., Gupta R., Noller H. F. Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids. Microbiol Rev. 1983 Dec;47(4):621–669. doi: 10.1128/mr.47.4.621-669.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES