Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1985 May 10;13(9):3343–3355. doi: 10.1093/nar/13.9.3343

Influence of uracil defect on DNA structure: 1H NMR investigation at 500 MHz.

A M Delort, J M Neumann, D Molko, M Hervé, R Téoule, S Tran Dinh
PMCID: PMC341239  PMID: 4000973

Abstract

The local structure of two self complementary oligonucleotides d(GTAC-GTAC) and d(GTACGUAC) which differ only by the presence of uracil, not a normal component of DNA, have been investigated by 1H NMR at 500 MHz. The two octamers exhibit the same thermodynamical constants (t 1/2, delta H), their exchangeable protons broaden and disappear at the same temperature. The T-U substitution did not induce any significant changes on non exchangeable protons resonances from 2-D COSY and 2-D NOESY experiments. So the two octamers exhibit the same global structure. The only variation was detected by 1D NOE measurements: the base orientations around the N glycosidic bonds (chi angles) are different.

Full text

PDF
3343

Images in this article

3346Image
on p.3346
3347Image
on p.3347
3348Image
on p.3348

Selected References

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

  1. Banaszuk A. M., Deugau K. V., Sherwood J., Michalak M., Glick B. R. An efficient method for the sequence analysis of oligodeoxyribonucleotides. Anal Biochem. 1983 Feb 1;128(2):281–286. doi: 10.1016/0003-2697(83)90376-7. [DOI] [PubMed] [Google Scholar]
  2. Chen C., Cohen J. S., Behe M. B to Z transition of double-stranded poly[deoxyguanylyl(3'-5')-5-methyldeoxycytidine] in solution by phosphorus-31 and carbon-13 nuclear magnetic resonance spectroscopy. Biochemistry. 1983 Apr 26;22(9):2136–2142. doi: 10.1021/bi00278a013. [DOI] [PubMed] [Google Scholar]
  3. Clore G. M., Gronenborn A. M. A nuclear-Overhauser-enhancement study of the solution structure of a double-stranded DNA undecamer comprising a portion of the specific target site for the cyclic-AMP-receptor protein in the gal operon. Sequential resonance assignment. Eur J Biochem. 1984 May 15;141(1):119–129. doi: 10.1111/j.1432-1033.1984.tb08166.x. [DOI] [PubMed] [Google Scholar]
  4. Delort A. M., Duplaa A. M., Molko D., Teoule R., Leblanc J. P., Laval J. Excision of uracil residues in DNA: mechanism of action of Escherichia coli and Micrococcus luteus uracil-DNA glycosylases. Nucleic Acids Res. 1985 Jan 25;13(2):319–335. doi: 10.1093/nar/13.2.319. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Efimov V. A., Reverdatto S. V., Chakhmakhcheva O. G. New effective method for the synthesis of oligonucleotides via phosphotriester intermediates. Nucleic Acids Res. 1982 Nov 11;10(21):6675–6694. doi: 10.1093/nar/10.21.6675. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. 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]
  7. Giessner-Prettre C., Pullman B., Tran-Dinh S., Neumann J. M., Huynh-Dinh T., Igolen J. Proton NMR study of the B----Z transition of d(CGm5CG)2 and d(CGm5CGCG)2: theory and experiment. Nucleic Acids Res. 1984 Apr 11;12(7):3271–3281. doi: 10.1093/nar/12.7.3271. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Guéron M., Chachaty C., Son T. D. Properties of purine nucleotides studied by the Overhauser effect: conformations, flexibility, aggregation. Ann N Y Acad Sci. 1973 Dec 31;222:307–323. doi: 10.1111/j.1749-6632.1973.tb15270.x. [DOI] [PubMed] [Google Scholar]
  9. Hanawalt P. C., Cooper P. K., Ganesan A. K., Smith C. A. DNA repair in bacteria and mammalian cells. Annu Rev Biochem. 1979;48:783–836. doi: 10.1146/annurev.bi.48.070179.004031. [DOI] [PubMed] [Google Scholar]
  10. Kan L. S., Cheng D. M., Jayaraman K., Leutzinger E. E., Miller P. S., Ts'o P. O. Proton nuclear magnetic resonance study of a self-complementary decadeoxyribonucleotide, C-C-A-A-G-C-T-T-G-G. Biochemistry. 1982 Dec 21;21(26):6723–6732. doi: 10.1021/bi00269a017. [DOI] [PubMed] [Google Scholar]
  11. Lindahl T. DNA repair enzymes. Annu Rev Biochem. 1982;51:61–87. doi: 10.1146/annurev.bi.51.070182.000425. [DOI] [PubMed] [Google Scholar]
  12. 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]
  13. Maxam A. M., Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977 Feb;74(2):560–564. doi: 10.1073/pnas.74.2.560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Neumann J. M., Bernassau J. M., Guéron M., Tran-Dinh S. Comparative conformations of uridine and pseudouridine and their derivatives. Eur J Biochem. 1980 Jul;108(2):457–463. doi: 10.1111/j.1432-1033.1980.tb04742.x. [DOI] [PubMed] [Google Scholar]
  15. Neumann J. M., Huynh-Dinh T., Kan S. K., Genissel B., Igolen J., Tran-Dinh S. DNA fragment conformations. 1H-NMR and relaxation studies of 2'-deoxyadenylyl(3'-5')thymidylyl-(3'-5')deoxyguanosylyl(3'-5')thymidine, d(A-T-G-T), in neutral aqueous solution. Eur J Biochem. 1982 Jan;121(2):317–323. doi: 10.1111/j.1432-1033.1982.tb05788.x. [DOI] [PubMed] [Google Scholar]
  16. Patel D. J., Canuel L. L. Helix-coil transition of the self-complementary dG-dG-dA-dA-dT-dT-dC-dC duplex. Eur J Biochem. 1979 May 15;96(2):267–276. doi: 10.1111/j.1432-1033.1979.tb13037.x. [DOI] [PubMed] [Google Scholar]
  17. Patel D. J. Peptide antibiotic-oligonucleotide interactions. Nuclear magnetic resonance investigations of complex formation between actinomycin D and d-ApTpGpCpApT in aqueous solution. Biochemistry. 1974 May 21;13(11):2396–2402. doi: 10.1021/bi00708a025. [DOI] [PubMed] [Google Scholar]
  18. Sanderson M. R., Mellema J. R., van der Marel G. A., Wille G., van Boom J. H., Altona C. Assignment of non-exchangeable base proton and H1' resonances of a deoxyoctanucleoside heptaphosphate d(G-G-C*-C*-G-G-C-C) by using the nuclear Overhauser effect. Nucleic Acids Res. 1983 May 25;11(10):3333–3346. doi: 10.1093/nar/11.10.3333. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Sanderson M. R., Mellema J. R., van der Marel G. A., Wille G., van Boom J. H., Altona C. Assignment of non-exchangeable base proton and H1' resonances of a deoxyoctanucleoside heptaphosphate d(G-G-C*-C*-G-G-C-C) by using the nuclear Overhauser effect. Nucleic Acids Res. 1983 May 25;11(10):3333–3346. doi: 10.1093/nar/11.10.3333. [DOI] [PMC free article] [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. Shapiro R., Klein R. S. The deamination of cytidine and cytosine by acidic buffer solutions. Mutagenic implications. Biochemistry. 1966 Jul;5(7):2358–2362. doi: 10.1021/bi00871a026. [DOI] [PubMed] [Google Scholar]
  22. Taboury J. A., Adam S., Taillandier E., Neumann J. M., Tran-Dinh S., Huynh-Dinh T., Langlois d'Estaintot B., Conti M., Igolen J. The B----Z transition in two synthetic oligonucleotides: d(C-2-amino-ACGTG) and d(m5CGCAm5CGTGCG) studied by IR, NMR and CD spectroscopies. Nucleic Acids Res. 1984 Aug 10;12(15):6291–6305. doi: 10.1093/nar/12.15.6291. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Tran-Dinh S., Neumann J. M., Huynh-Dinh T., Allard P., Lallemand J. Y., Igolen J. DNA fragment conformations IV - Helix-coil transition and conformation of d-CCATGG in aqueous solution by 1H-NMR spectroscopy. Nucleic Acids Res. 1982 Sep 11;10(17):5319–5332. doi: 10.1093/nar/10.17.5319. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Tran-Dinh S., Neumann J. M., Huynh-Dinh T., Genissel B., Igolen J., Simonnot G. DNA fragment conformations. 1H-NMR studies of helix-coil transition, conformations and dynamic structures of the self-complementary deoxyhexanucleotide d(A-C-A-T-G-T) in aqueous solution. Eur J Biochem. 1982 Jun;124(3):415–425. [PubMed] [Google Scholar]
  25. 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]
  26. Tye B. K., Lehman I. R. Excision repair of uracil incorporated in DNA as a result of a defect in dUTPase. J Mol Biol. 1977 Dec 5;117(2):293–306. doi: 10.1016/0022-2836(77)90128-0. [DOI] [PubMed] [Google Scholar]
  27. Téoule R., Derbyshire R., Guy A., Molko D., Roget A. A novel class of condensing reagents in phosphodiester oligodeoxyribonucleotides synthesis. Application of the constituents of free terminal carboxy oxytocine gene. Nucleic Acids Symp Ser. 1980;(7):23–37. [PubMed] [Google Scholar]

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

RESOURCES