Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1995 Oct 11;23(19):3962–3966. doi: 10.1093/nar/23.19.3962

The effects of sequence context on base dynamics at TpA steps in DNA studied by NMR.

K McAteer 1, P D Ellis 1, M A Kennedy 1
PMCID: PMC307317  PMID: 7479043

Abstract

Base dynamics, heretofore observed only at TpA steps in DNA, were investigated as a function of sequence context by NMR spectroscopy. The large amplitude conformational dynamics have been previously observed in TnAn segments where n > or = 2. In order to determine whether the dynamic characteristics occur in more general sequence contexts, we examined four self-complementary DNA sequences, [d(CTTTA-NATNTAAAG)2] (where N = A, C, T, G and N = complement of N). The anomalous broadening of the TpA adenine H2 resonance which is indicative of large amplitude base motion was observed in all nine unique four nucleotide contexts. Furthermore, all the adenine H2 resonances experienced a linewidth maximum as a function of temperature, which is a characteristic of the dynamic process. Interestingly, the temperature of the linewidth maximum varied with sequence indicating that the thermodynamics of TpA base dynamics are also sequence dependent. In one example, neither a T preceding nor an A trailing the TpA step was required for base dynamics. These results show that base dynamics, heretofore observed in only a few isolated sequences, occurs at all TpA steps which are either preceded or followed by a thymine or adenine, respectively, and may be characteristic of all TpA steps in DNA notwithstanding sequence context.

Full text

PDF
3962

Selected References

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

  1. Addess K. J., Gilbert D. E., Olsen R. K., Feigon J. Proton NMR studies of [N-MeCys3,N-MeCys7]TANDEM binding to DNA oligonucleotides: sequence-specific binding at the TpA site. Biochemistry. 1992 Jan 21;31(2):339–350. doi: 10.1021/bi00117a005. [DOI] [PubMed] [Google Scholar]
  2. Brash D. E., Haseltine W. A. UV-induced mutation hotspots occur at DNA damage hotspots. Nature. 1982 Jul 8;298(5870):189–192. doi: 10.1038/298189a0. [DOI] [PubMed] [Google Scholar]
  3. Celda B., Widmer H., Leupin W., Chazin W. J., Denny W. A., Wüthrich K. Conformational studies of d-(AAAAATTTTT)2 using constraints from nuclear overhauser effects and from quantitative analysis of the cross-peak fine structures in two-dimensional 1H nuclear magnetic resonance spectra. Biochemistry. 1989 Feb 21;28(4):1462–1471. doi: 10.1021/bi00430a006. [DOI] [PubMed] [Google Scholar]
  4. Chuprina V. P., Fedoroff OYu, Reid B. R. New insights into the structure of An tracts and B'-B' bends in DNA. Biochemistry. 1991 Jan 15;30(2):561–568. doi: 10.1021/bi00216a034. [DOI] [PubMed] [Google Scholar]
  5. Chuprina V. P., Lipanov A. A., Fedoroff OYu, Kim S. G., Kintanar A., Reid B. R. Sequence effects on local DNA topology. Proc Natl Acad Sci U S A. 1991 Oct 15;88(20):9087–9091. doi: 10.1073/pnas.88.20.9087. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Crothers D. M., Haran T. E., Nadeau J. G. Intrinsically bent DNA. J Biol Chem. 1990 May 5;265(13):7093–7096. [PubMed] [Google Scholar]
  7. Goodsell D. S., Dickerson R. E. Bending and curvature calculations in B-DNA. Nucleic Acids Res. 1994 Dec 11;22(24):5497–5503. doi: 10.1093/nar/22.24.5497. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Gupta G., Sarma M. H., Sarma R. H. On the question of DNA bending: two-dimensional NMR studies on d(GTTTTAAAAC)2 in solution. Biochemistry. 1988 Oct 4;27(20):7909–7919. doi: 10.1021/bi00420a049. [DOI] [PubMed] [Google Scholar]
  9. Hagerman P. J. Sequence-directed curvature of DNA. Nature. 1986 May 22;321(6068):449–450. doi: 10.1038/321449a0. [DOI] [PubMed] [Google Scholar]
  10. Hagerman P. J. Sequence-directed curvature of DNA. Annu Rev Biochem. 1990;59:755–781. doi: 10.1146/annurev.bi.59.070190.003543. [DOI] [PubMed] [Google Scholar]
  11. Kennedy M. A., Nuutero S. T., Davis J. T., Drobny G. P., Reid B. R. Mobility at the TpA cleavage site in the T3A3-containing AhaIII and PmeI restriction sequences. Biochemistry. 1993 Aug 10;32(31):8022–8035. doi: 10.1021/bi00082a025. [DOI] [PubMed] [Google Scholar]
  12. Kim J. L., Nikolov D. B., Burley S. K. Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature. 1993 Oct 7;365(6446):520–527. doi: 10.1038/365520a0. [DOI] [PubMed] [Google Scholar]
  13. Kim S. G., Reid B. R. Solution structure of the TnAn DNA duplex GCCGTTAACGCG containing the HpaI restriction site. Biochemistry. 1992 Dec 8;31(48):12103–12116. doi: 10.1021/bi00163a020. [DOI] [PubMed] [Google Scholar]
  14. Kroon P. A., Kreishman G. P., Nelson J. H., Chan S. I. The effects of chain length on the secondary structure of oligoadenylates. Biopolymers. 1974 Dec;13(12):2571–2592. doi: 10.1002/bip.1974.360131214. [DOI] [PubMed] [Google Scholar]
  15. Lane A. N. N.m.r. assignments and temperature-dependent conformational transitions of a mutant trp operator-promoter in solution. Biochem J. 1989 May 1;259(3):715–724. doi: 10.1042/bj2590715. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Lane A. N. The solution conformations of a mutant trp operator determined by n.m.r. spectroscopy. Biochem J. 1991 Jan 15;273(Pt 2):383–391. doi: 10.1042/bj2730383. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Lefevre J. F., Lane A. N., Jardetzky O. A temperature dependent transition in the Pribnow box of the trp promoter. FEBS Lett. 1985 Oct 7;190(1):37–40. doi: 10.1016/0014-5793(85)80422-1. [DOI] [PubMed] [Google Scholar]
  18. Lefèvre J. F., Lane A. N., Jardetzky O. A description of conformational transitions in the Pribnow box of the trp promoter of Escherichia coli. Biochemistry. 1988 Feb 23;27(4):1086–1094. doi: 10.1021/bi00404a002. [DOI] [PubMed] [Google Scholar]
  19. 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]
  20. Leroy J. L., Charretier E., Kochoyan M., Guéron M. Evidence from base-pair kinetics for two types of adenine tract structures in solution: their relation to DNA curvature. Biochemistry. 1988 Dec 13;27(25):8894–8898. doi: 10.1021/bi00425a004. [DOI] [PubMed] [Google Scholar]
  21. Lipanov A. A., Chuprina V. P. The structure of poly(dA):poly(dT) in a condensed state and in solution. Nucleic Acids Res. 1987 Jul 24;15(14):5833–5844. doi: 10.1093/nar/15.14.5833. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Price M. A., Tullius T. D. How the structure of an adenine tract depends on sequence context: a new model for the structure of TnAn DNA sequences. Biochemistry. 1993 Jan 12;32(1):127–136. doi: 10.1021/bi00052a018. [DOI] [PubMed] [Google Scholar]
  23. Schmitz U., Sethson I., Egan W. M., James T. L. Solution structure of a DNA octamer containing the Pribnow box via restrained molecular dynamics simulation with distance and torsion angle constraints derived from two-dimensional nuclear magnetic resonance spectral fitting. J Mol Biol. 1992 Sep 20;227(2):510–531. doi: 10.1016/0022-2836(92)90904-x. [DOI] [PubMed] [Google Scholar]
  24. Zhurkin V. B., Ulyanov N. B., Gorin A. A., Jernigan R. L. Static and statistical bending of DNA evaluated by Monte Carlo simulations. Proc Natl Acad Sci U S A. 1991 Aug 15;88(16):7046–7050. doi: 10.1073/pnas.88.16.7046. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES