Similar conformations of hairpins with TTT and TTTT sequences NMR and molecular modeling evidence for T · T base pairs in the TTTT hairpin

European Journal of Biochemistry

Volumn 236, Issue 3, 1996, Pages 960-969

  Kuklenyik, Zsuzsanna ^a   Yao, Shijie ^a   Marzilli, Luigi G ^a  

^a EMORY UNIVERSITY   (United States)

Author keywords

DNA; Hairpin conformation; Molecular modeling; NMR

Indexed keywords

ARTICLE; DNA STRUCTURE; NUCLEAR MAGNETIC RESONANCE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL;

BASE COMPOSITION; BASE SEQUENCE; DNA; HYDROGEN BONDING; IMMUNORADIOMETRIC ASSAY; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OLIGODEOXYRIBONUCLEOTIDES; THYMINE;

EID: 0029943715     PISSN: 00142956     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1432-1033.1996.00960.x     Document Type: Article

References (39)

1. Banks, K. M., Hare, D. R. & Reid, B. R. (1989) Three dimensional solution structure of a DNA duplex containing the BclI restriction sequence: two-dimensional NMR studies, distance geometry calculations, and refinement by back-calculation of the NOESY spectrum, Biochemistry 28, 6996-7010.
2. Bax, A., Freeman, R. & Morris, G. (1981) Correlation of proton chemical shifts by two-dimensional Fourier transform NMR, J. Magn. Reson. 42, 164-168.
3. Bax, A. & Subramanian, S. (1986) Sensitivity-enhanced two-dimensional heteronuclear shift correlation NMR spectroscopy, J. Magn. Reson. 7, 565-569.
4. Baxter, S. M., Greizerstein, M. B., Kushlan, D. M. & Ashley, G. W. (1993) Conformational properties of DNA hairpins with TTT and TTTT loops, Biochemistry 32, 8702-8711.
5. Blommers, M. J. J., Haasnoot, C. A. G., Hilbers, C. W., van Boom, J. H. & van der Marel, G. A. (1987) NMR studies of loopfolding in a DNA hairpin molecule, Structure and dynamics of biopolymers, NATO ASI Ser. Ser. E Appl. Sci. 133, 78-91.
6. Blommers, M. J. J., van de Ven, F. J. M., van der Marel, G. A., van Boom, J. H. & Hilbers, C. W. (1991) The three-dimensional structure of a DNA hairpin in solution. Two-dimensional NMR studies and structural analysis of d(ATCCTATTTATAGGAT). Eur. J. Biol. 201, 33-51.
7. Boelens, R., Koning, T. M. G., van der Marel, G. A., van Boom, J. H. & Kaptein, R. (1989) Iterative procedure for structure determination from proton-proton NOEs using a full relaxation approach. Application to a DNA octamer, J. Magn. Reson. 82, 290-308.
8. Boulard, Y., Gabarro-Arpa, J., Cognet, J. A. H., Le Bret, M., Guy, A., Téoule, R., Guschlbauer, W. & Fazakerley, G. V. (1991) The solution structure of a DNA hairpin containing a loop of three thymines determined by nuclear magnetic resonance and molecular mechanics. Nucleic Acids Res. 19, 5159-5167.
9. Boyd, J. & Redfield, C. (1986) Analysis of cross peak fine structure in multiple-quantum filtered COSY spectra, J. Magn. Reson. 68, 67-84.
10. Gacy, A. M. & McMurray, C. T. (1994) Hairpin formation within the human enkephalin enhencer region. 1. Kinetic analysis, Biochemistry 33, 11 951-11 959.
11. 5 monomer and dimer, Biochemistry 24, 5698-5702.
12. Giessner-Prettre, C. & Pullman, B. (1987) Quantum mechanical calculations of NMR chemical shifts in nucleic acids, Q. Rev. Biophys. 20, 113-172.
13. González, A., Talavera, A., Almendral, J. M. & Viñuela, E. (1986) Hairpin loop structure of African swine fever virus DNA, Nucleic Acids Res. 14, 6835-6844.
14. Gonzalez, C., Rullman, J. A. C., Bonvin, A. M. J. J., Boelens, R. & Kaptein, R. (1991) Toward an NMR R Factor, J. Magn. Reson. 91, 659-664.
15. Gorenstein, D. G. (1984) Phosphorous-31 chemical shifts: principles and empirical observations, in Phosphorus-31 NMR: principles and applications, pp. 19-21, 233ff., Academic Press, Inc., New York.
16. Hare, D. R. & Reid, B. R. (1986) Three-dimensional structure of a DNA hairpin in solution: two-dimensional NMR studies and distance geometry calculation on d(CGCGTTTTCGCG), Biochemistry 25, 5341-5350.
17. Hilbers, C. W., Heus, H. A., van Dongen, M. J. P. & Wijmenga, S. S. (1994). The hairpin elements of nucleic acid structure: DNA and RNA folding, Nucleic Acids Mol. Biol. 8, 56-104.
18. Hore, P. J. (1983) Solvent suppression in Fourier transform nuclear magnetic resonance, J. Magn. Reson. 55, 283-300.
19. Iwamoto, M., Mukundan, S. Jr & Marzilli, L. G. (1994) DNA adduct formation by platinum anticancer drugs, J. Am. Chem. Soc. 116, 6238-6244.
20. 13C NMR spectroscopy, Inorg. Chem. 30, 228-239.
21. 1H-NMR, Biochemistry 31, 3564-3574.
22. Kline, T. P., Marzilli, L. G., Live, D. & Zon, G. (1990) NMR studies of an oligonucleotide with an unusual structure induced by platinum anticancer drugs, Biochem. Pharmacol. 40, 97-113.
23. 31P-NMR chemical shifts and infrared spectra of phosphate disasters, Biopolymers 23, 2157-2172.
24. Majumdar, A. & Hosur, R. V. (1992) Simulation of 2D NMR spectra for determination of solution conformation of nucleic acids, Prog. NMR Spectrosc. 24, 109-158.
25. Metzler, W. J., Hare, D. R. & Pardi, A. (1989) Limited sampling of conformational space by the distance geometry algorithm: implications for structures generated by NMR data, Biochemistry 28, 7045-7052.
26. Mooren, M. M. W., Pulleyblank, D. E., Wijmenga, S. S., van de Ven, F. J. M. & Hilbers, C. W. (1994) The solution structure of the hairpin formed by d(TCTCTC-TTT-GAGAGA), Biochemistry 33, 7315-7325.
27. 31P NMR spectra and restrained molecular dynamics structure of a mismatched GA decamer oligodeoxyribonucleotide duplex, Biochemistry 29, 8845-8858.
28. Pieters, J. M. L., de Vroom, E., van der Marel, G. A., van Boom, J. H., Koning, T. M. G., Kaptein, R. & Altona, C. (1990) Hairpin structures in DNA containing arabinofuranosylcytosine. A conbination of nuclear magnetic resonance and molecular dynamics, Biochemistry 29, 788-799.
29. Saenger, W. (1988) Principles of nucleic acid structure, Springer-Verlag, New York.
30. 1H resonances in oligonucleotides by two-dimensional NMR spectroscopy, FEBS Lett. 208, 94-98.
31. Starcuk, Z. & Sklenâr, V. (1985) New hard pulse sequences for the solvent signal suppression in Fourier-transformation NMR. 1, J. Magn. Reson. 61, 567-570.
32. Stolarski, R., Egan, W. & James, T. L. (1992) Solution structure of the EcoRI DNA octamer containing 5-fluorouracil via restrained molecular dynamics using distance and torsion angle constraints extracted from NMR spectral simulations, Biochemistry 31, 7027-7042.
33. Summers, M. F., South, T. L., Kim, B. & Hare, D. R. (1990) High-resolution structure of an HIV zinc fingerlike domain via a new NMR-based distance geometry approach, Biochemistry 29, 329-340.
34. van de Ven, F. J. M. & Hilbers, C. W. (1988) Nucleic acid and nuclear magnetic resonance, Eur. J. Biochem. 178, 1-38.
35. Veal, J. M. & Wilson, W. D. (1991) Modeling of nucleic acid complexes with cationic ligands: a specialized molecular mechanics force field and its application, J. Biomol. Struct. Dyn. 8, 1119-1145.
36. Weaver, D. T. & DePamphilis, M. L. (1984) The role of palindromic and non-palindromic sequences in arresting DNA synthesis in vitro and in vivo, J. Mol. Biol. 180, 961-986.
37. Weiner, S. J., Kollman, P. A., Nguyen, D. T. & Case, D. A. (1986) An all atom force field for simulations of proteins and nucleic acids, Comput. Chem. 7, 230-252.
38. 5, Biochemistry 27, 6960-6967.
39. Wüthrich, K. (1986) NMR of proteins and nucleic acids, pp. 203, John Wiley & Sons, Inc, New York.