Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1988 Jul 25;16(14B):7133–7143. doi: 10.1093/nar/16.14.7133

1H NMR study of the solution structure of the self-complementary dodecanucleotide d(TGCA)3.

W C Stevens 1, D H Huang 1, R D Wells 1, N R Krishna 1
PMCID: PMC338356  PMID: 3405759

Abstract

The deoxyoligonucleotide d(TGCA)3 is a candidate for exhibiting unusual conformations. Its 1H NMR spectrum under low salt conditions has been obtained at 400 MHz and assigned using two-dimensional NMR techniques. The sugar puckers and glycosidic torsions have been determined by inspecting the relative intensities of the intranucleotide NOEs and COSY crosspeaks. At low electrolyte concentration (100 mM NaCl) the molecule exists as a right-handed duplex with twelve Watson-Crick base-pairs and deoxyribose moieties assuming the O1'-endo to C1'-exo pucker.

Full text

PDF
7133

Selected References

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

  1. Assa-Munt N., Granot J., Behling R. W., Kearns D. R. 1H NMR relaxation studies of the hydrogen-bonded imino protons of poly(dA-dT). Biochemistry. 1984 Feb 28;23(5):944–955. doi: 10.1021/bi00300a023. [DOI] [PubMed] [Google Scholar]
  2. Chary K. V., Hosur R. V., Govil G., Tan Z. K., Miles H. T. Novel solution conformation of DNA observed in d(GAATTCGAATTC) by two-dimensional NMR spectroscopy. Biochemistry. 1987 Mar 10;26(5):1315–1322. doi: 10.1021/bi00379a017. [DOI] [PubMed] [Google Scholar]
  3. Chen F. M. Kinetic and equilibrium binding studies of actinomycin D with some d(TGCA)-containing dodecamers. Biochemistry. 1988 Mar 22;27(6):1843–1848. doi: 10.1021/bi00406a008. [DOI] [PubMed] [Google Scholar]
  4. 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]
  5. Feigon J., Wang A. H., van der Marel G. A., van Boom J. H., Rich A. Z-DNA forms without an alternating purine-pyrimidine sequence in solution. Science. 1985 Oct 4;230(4721):82–84. doi: 10.1126/science.4035359. [DOI] [PubMed] [Google Scholar]
  6. Frechet D., Cheng D. M., Kan L. S., Ts'o P. O. Nuclear Overhauser effect as a tool for the complete assignment of nonexchangeable proton resonances in short deoxyribonucleic acid helices. Biochemistry. 1983 Oct 25;22(22):5194–5200. doi: 10.1021/bi00291a020. [DOI] [PubMed] [Google Scholar]
  7. Hare D. R., Reid B. R. Three-dimensional structure of a DNA hairpin in solution: two-dimensional NMR studies and distance geometry calculations on d(CGCGTTTTCGCG). Biochemistry. 1986 Sep 9;25(18):5341–5350. doi: 10.1021/bi00366a053. [DOI] [PubMed] [Google Scholar]
  8. 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]
  9. Jaworski A., Hsieh W. T., Blaho J. A., Larson J. E., Wells R. D. Left-handed DNA in vivo. Science. 1987 Nov 6;238(4828):773–777. doi: 10.1126/science.3313728. [DOI] [PubMed] [Google Scholar]
  10. Kilpatrick M. W., Klysik J., Singleton C. K., Zarling D. A., Jovin T. M., Hanau L. H., Erlanger B. F., Wells R. D. Intervening sequences in human fetal globin genes adopt left-handed Z helices. J Biol Chem. 1984 Jun 10;259(11):7268–7274. [PubMed] [Google Scholar]
  11. Kime M. J., Moore P. B. Nuclear Overhauser experiments at 500 MHz on the downfield proton spectrum of a ribonuclease-resistant fragment of 5S ribonucleic acid. Biochemistry. 1983 May 24;22(11):2615–2622. doi: 10.1021/bi00280a004. [DOI] [PubMed] [Google Scholar]
  12. McLean M. J., Blaho J. A., Kilpatrick M. W., Wells R. D. Consecutive A X T pairs can adopt a left-handed DNA structure. Proc Natl Acad Sci U S A. 1986 Aug;83(16):5884–5888. doi: 10.1073/pnas.83.16.5884. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Nilges M., Clore G. M., Gronenborn A. M., Brunger A. T., Karplus M., Nilsson L. Refinement of the solution structure of the DNA hexamer 5'd(GCATGC)2: combined use of nuclear magnetic resonance and restrained molecular dynamics. Biochemistry. 1987 Jun 16;26(12):3718–3733. doi: 10.1021/bi00386a068. [DOI] [PubMed] [Google Scholar]
  14. Nordheim A., Lafer E. M., Peck L. J., Wang J. C., Stollar B. D., Rich A. Negatively supercoiled plasmids contain left-handed Z-DNA segments as detected by specific antibody binding. Cell. 1982 Dec;31(2 Pt 1):309–318. doi: 10.1016/0092-8674(82)90124-6. [DOI] [PubMed] [Google Scholar]
  15. Orbons L. P., van der Marel G. A., van Boom J. H., Altona C. An NMR study of the polymorphous behavior of the mismatched DNA octamer d(m5C-G-m5C-G-T-G-m5C-G) in solution. The B, Z, and hairpin forms. J Biomol Struct Dyn. 1987 Jun;4(6):939–963. doi: 10.1080/07391102.1987.10507691. [DOI] [PubMed] [Google Scholar]
  16. Patel D. J., Kozlowski S. A., Nordheim A., Rich A. Right-handed and left-handed DNA: studies of B- and Z-DNA by using proton nuclear Overhauser effect and P NMR. Proc Natl Acad Sci U S A. 1982 Mar;79(5):1413–1417. doi: 10.1073/pnas.79.5.1413. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Patel D. J., Shapiro L., Hare D. Sequence-dependent conformations of DNA duplexes: the TATA segment of the d(G-G-T-A-T-A-C-C) duplex in aqueous solution. Biopolymers. 1986 Apr;25(4):693–706. doi: 10.1002/bip.360250412. [DOI] [PubMed] [Google Scholar]
  18. Reid D. G., Salisbury S. A., Bellard S., Shakked Z., Williams D. H. Proton nuclear Overhauser effect study of the structure of a deoxyoligonucleotide duplex in aqueous solution. Biochemistry. 1983 Apr 12;22(8):2019–2025. doi: 10.1021/bi00277a044. [DOI] [PubMed] [Google Scholar]
  19. Rich A., Nordheim A., Wang A. H. The chemistry and biology of left-handed Z-DNA. Annu Rev Biochem. 1984;53:791–846. doi: 10.1146/annurev.bi.53.070184.004043. [DOI] [PubMed] [Google Scholar]
  20. Scheek R. M., Boelens R., Russo N., van Boom J. H., Kaptein R. Sequential resonance assignments in 1H NMR spectra of oligonucleotides by two-dimensional NMR spectroscopy. Biochemistry. 1984 Mar 27;23(7):1371–1376. doi: 10.1021/bi00302a006. [DOI] [PubMed] [Google Scholar]
  21. Weiss M. A., Patel D. J., Sauer R. T., Karplus M. Two-dimensional 1H NMR study of the lambda operator site OL1: a sequential assignment strategy and its application. Proc Natl Acad Sci U S A. 1984 Jan;81(1):130–134. doi: 10.1073/pnas.81.1.130. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Wells R. D. Unusual DNA structures. J Biol Chem. 1988 Jan 25;263(3):1095–1098. [PubMed] [Google Scholar]

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

RESOURCES