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. 1988 Jul 11;16(13):5713–5726. doi: 10.1093/nar/16.13.5713

Resonance assignments of non-exchangeable protons in B type DNA oligomers, an overview.

F J van de Ven 1, C W Hilbers 1
PMCID: PMC336824  PMID: 2840632

Abstract

The chemical shifts of 1H resonances of non exchangeable protons (except H5', H5" and adenine H2) of over six hundred nucleotides have been collected. The influence which the base of the nucleotide itself as well as the bases on its 5' and 3' side exert on the chemical shifts of the various resonances has been investigated. Most of the resonances appear to be predominantly influenced by only one base. For H2', H2", H3', H4' and H6/H8 this is the base of the central nucleotide, for H5(C) and CH3(T) it is the one on the 5' side and for H1' it is the one on the 3' side. Chemical shift distribution profiles are presented which allow an estimation of the probability of finding a particular resonance at a particular position in the spectrum.

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Selected References

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

  1. Assa-Munt N., Kearns D. R. Poly(dA-dT) has a right-handed B conformation in solution: a two-dimensional NMR study. Biochemistry. 1984 Feb 28;23(5):791–796. doi: 10.1021/bi00300a001. [DOI] [PubMed] [Google Scholar]
  2. Behling R. W., Kearns D. R. 1H two-dimensional nuclear Overhauser effect and relaxation studies of poly(dA).poly(dT) Biochemistry. 1986 Jun 3;25(11):3335–3346. doi: 10.1021/bi00359a037. [DOI] [PubMed] [Google Scholar]
  3. 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]
  4. Buck F., Hahn K. D., Brill W., Rüterjans H., Chernov B. K., Skryabin K. G., Kirpichnikov M. P., Bayev A. A. NMR studies of DNA recognition sequences and their interaction with proteins. The phage lambda OR1 operator, a symmetric lac operator and their specific complexes with cro protein and lac repressor "headpiece". J Biomol Struct Dyn. 1986 Apr;3(5):899–911. doi: 10.1080/07391102.1986.10508472. [DOI] [PubMed] [Google Scholar]
  5. Calladine C. R., Drew H. R. A base-centred explanation of the B-to-A transition in DNA. J Mol Biol. 1984 Sep 25;178(3):773–782. doi: 10.1016/0022-2836(84)90251-1. [DOI] [PubMed] [Google Scholar]
  6. Calladine C. R., Drew H. R. Principles of sequence-dependent flexure of DNA. J Mol Biol. 1986 Dec 20;192(4):907–918. doi: 10.1016/0022-2836(86)90036-7. [DOI] [PubMed] [Google Scholar]
  7. 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]
  8. Chazin W. J., Wüthrich K., Hyberts S., Rance M., Denny W. A., Leupin W. 1H nuclear magnetic resonance assignments for d-(GCATTAATGC)2 using experimental refinements of established procedures. J Mol Biol. 1986 Aug 5;190(3):439–453. doi: 10.1016/0022-2836(86)90014-8. [DOI] [PubMed] [Google Scholar]
  9. 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]
  10. Clore G. M., Lauble H., Frenkiel T. A., Gronenborn A. M. A two-dimensional NMR study of the solution structure of a DNA dodecamer comprising the concensus sequence for the specific DNA-binding sites of the glucocorticoid receptor protein. Eur J Biochem. 1984 Dec 17;145(3):629–636. doi: 10.1111/j.1432-1033.1984.tb08603.x. [DOI] [PubMed] [Google Scholar]
  11. Debart F., Rayner B., Imbach J. L., Chang D. K., Lown J. W. Structure and conformation of the duplex consensus acceptor exon:intron junction d[(CpTpApCpApGpGpT). (ApCpCpTpGpTpApG)] deduced from high-field 1H-NMR of non-exchangeable and imino protons. J Biomol Struct Dyn. 1986 Dec;4(3):343–363. doi: 10.1080/07391102.1986.10506354. [DOI] [PubMed] [Google Scholar]
  12. Frey M. H., Leupin W., Sørensen O. W., Denny W. A., Ernst R. R. Sequence-specific assignment of the backbone 1H-and 31P-NMR lines in a short DNA duplex with homo- and heteronuclear correlated spectroscopy. Biopolymers. 1985 Dec;24(12):2371–2380. doi: 10.1002/bip.360241214. [DOI] [PubMed] [Google Scholar]
  13. Giessner-Prettre C., Pullman B. Quantum mechanical calculations of NMR chemical shifts in nucleic acids. Q Rev Biophys. 1987 Nov;20(3-4):113–172. doi: 10.1017/s0033583500004169. [DOI] [PubMed] [Google Scholar]
  14. Gronenborn A. M., Clore G. M., Kimber B. J. An investigation into the solution structures of two self-complementary DNA oligomers, 5'-d(C-G-T-A-C-G) and 5'-d(A-C-G-C-G-C-G-T), by means of nuclear-Overhauser-enhancement measurements. Biochem J. 1984 Aug 1;221(3):723–736. doi: 10.1042/bj2210723. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. 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]
  16. Jamin N., James T. L., Zon G. Two-dimensional nuclear Overhauser enhancement investigation of the solution structure and dynamics of the DNA octamer [d(GGTATACC)]2. Eur J Biochem. 1985 Oct 1;152(1):157–166. doi: 10.1111/j.1432-1033.1985.tb09176.x. [DOI] [PubMed] [Google Scholar]
  17. Keniry M. A., Levenson C., Shafer R. H. The conformation of the d(ACCCGGGT) duplex in aqueous solution. J Biomol Struct Dyn. 1987 Apr;4(5):745–756. doi: 10.1080/07391102.1987.10507676. [DOI] [PubMed] [Google Scholar]
  18. Kintanar A., Klevit R. E., Reid B. R. Two-dimensional NMR investigation of a bent DNA fragment: assignment of the proton resonances and preliminary structure analysis. Nucleic Acids Res. 1987 Jul 24;15(14):5845–5862. doi: 10.1093/nar/15.14.5845. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Kumar M. R., Hosur R. V., Roy K. B., Miles H. T., Govil G. Resonance assignment of the 500-MHz proton NMR spectrum of self-complementary dodecanucleotide d-GGATCCGGATCC: altered conformations at BamHI cleavage sites. Biochemistry. 1985 Dec 17;24(26):7703–7711. doi: 10.1021/bi00347a030. [DOI] [PubMed] [Google Scholar]
  20. Lefèvre J. F., Lane A. N., Jardetzky O. Solution structure of the Trp operator of Escherichia coli determined by NMR. Biochemistry. 1987 Aug 11;26(16):5076–5090. doi: 10.1021/bi00390a029. [DOI] [PubMed] [Google Scholar]
  21. 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]
  22. Lown J. W., Hanstock C. C., Lobe C. G., Bleackley C. Complete 1H assignments of the non-exchangeable protons of the non self-complementary heptadeoxyribonucleotide d[(GTCGTCA).(TGACGAC)] and its component strands by high field NMR. J Biomol Struct Dyn. 1985 Jun;2(6):1107–1124. doi: 10.1080/07391102.1985.10507627. [DOI] [PubMed] [Google Scholar]
  23. Marion D., Lancelot G. Sequential assignment of the 1H and 31P resonances of the double stranded deoxynucleotide d (ATGCAT)2 by 2D-NMR correlation spectroscopy. Biochem Biophys Res Commun. 1984 Nov 14;124(3):774–783. doi: 10.1016/0006-291x(84)91025-8. [DOI] [PubMed] [Google Scholar]
  24. Mirau P. A., Kearns D. R. Comparison of the conformation of poly(dI-dC) with poly(dI-dbr5C) and the B and Z forms of poly(dG-dC). One- and two-dimensional NMR studies. Biochemistry. 1984 Nov 6;23(23):5439–5446. doi: 10.1021/bi00318a010. [DOI] [PubMed] [Google Scholar]
  25. 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]
  26. Nilges M., Clore G. M., Gronenborn A. M., Piel N., McLaughlin L. W. Refinement of the solution structure of the DNA decamer 5'd(CTGGATCCAG)2: combined use of nuclear magnetic resonance and restrained molecular dynamics. Biochemistry. 1987 Jun 16;26(12):3734–3744. doi: 10.1021/bi00386a069. [DOI] [PubMed] [Google Scholar]
  27. Patel D. J., Shapiro L., Hare D. Sequence-dependent conformation of DNA duplexes. The AATT segment of the d(G-G-A-A-T-T-C-C) duplex in aqueous solution. J Biol Chem. 1986 Jan 25;261(3):1223–1229. [PubMed] [Google Scholar]
  28. Rinkel L. J., Sanderson M. R., van der Marel G. A., van Boom J. H., Altona C. Conformational analysis of the octamer d(G-G-C-C-G-G-C-C) in aqueous solution. A one-dimensional and two-dimensional proton NMR study at 300 MHz and 500 MHz. Eur J Biochem. 1986 Aug 15;159(1):85–93. doi: 10.1111/j.1432-1033.1986.tb09836.x. [DOI] [PubMed] [Google Scholar]
  29. Rinkel L. J., van der Marel G. A., van Boom J. H., Altona C. Influence of the base sequence on the conformational behaviour of DNA polynucleotides in solution. Eur J Biochem. 1987 Jul 1;166(1):87–101. doi: 10.1111/j.1432-1033.1987.tb13487.x. [DOI] [PubMed] [Google Scholar]
  30. Roy S., Borah B., Zon G., Cohen J. S. Conformation of the oligonucleotide d(AAAAAATTTTTT)2 by two-dimensional nuclear Overhauser effect spectroscopy and its relevance to poly(dA).poly(dT). Biopolymers. 1987 Apr;26(4):525–536. doi: 10.1002/bip.360260406. [DOI] [PubMed] [Google Scholar]
  31. 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]
  32. Schroeder S. A., Fu J. M., Jones C. R., Gorenstein D. G. Assignment of phosphorus-31 and nonexchangeable proton resonances in a symmetrical 14 base pair lac pseudooperator DNA fragment. Biochemistry. 1987 Jun 30;26(13):3812–3821. doi: 10.1021/bi00387a012. [DOI] [PubMed] [Google Scholar]
  33. Sheth A., Ravikumar M., Hosur R. V., Govil G., Tan Z. K., Roy K. B., Miles H. T. Sequential resonance assignment of the 500-MHz nmr spectrum of d-(CG)6 and its structure under low-salt conditions. Biopolymers. 1987 Aug;26(8):1301–1313. doi: 10.1002/bip.360260807. [DOI] [PubMed] [Google Scholar]
  34. Suzuki E., Pattabiraman N., Zon G., James T. L. Solution structure of [d(A-T)5]2 via complete relaxation matrix analysis of two-dimensional nuclear Overhauser effect spectra and molecular mechanics calculations: evidence for a hydration tunnel. Biochemistry. 1986 Nov 4;25(22):6854–6865. doi: 10.1021/bi00370a019. [DOI] [PubMed] [Google Scholar]
  35. 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]
  36. 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]
  37. 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]
  38. Wemmer D. E., Chou S. H., Hare D. R., Reid B. R. Duplex-hairpin transitions in DNA: NMR studies on CGCGTATACGCG. Nucleic Acids Res. 1985 May 24;13(10):3755–3772. doi: 10.1093/nar/13.10.3755. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Wemmer D. E., Chou S. H., Hare D. R., Reid B. R. Sequence-specific recognition of DNA: assignment of nonexchangeable proton resonances in the consensus Pribnow promoter DNA sequence by two-dimensional NMR. Biochemistry. 1984 May 8;23(10):2262–2268. doi: 10.1021/bi00305a027. [DOI] [PubMed] [Google Scholar]
  40. Wemmer D. E., Chou S. H., Reid B. R. Sequence-specific recognition of DNA. Nuclear magnetic resonance assignments and structural comparison of wild-type and mutant lambda OR3 operator DNA. J Mol Biol. 1984 Nov 25;180(1):41–60. doi: 10.1016/0022-2836(84)90429-7. [DOI] [PubMed] [Google Scholar]
  41. den Hartog J. H., Altona C., van Boom J. H., van der Marel G. A., Haasnoot C. A., Reedijk J. cis-diamminedichloroplatinum(II) induced distortion of a single and double stranded deoxydecanucleosidenonaphosphate studied by nuclear magnetic resonance. J Biomol Struct Dyn. 1985 Jun;2(6):1137–1155. doi: 10.1080/07391102.1985.10507629. [DOI] [PubMed] [Google Scholar]

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