Measurement of deoxyribose 3J(HH) scalar couplings reveals protein binding-induced changes in the sugar puckers of the DNA

Journal of the American Chemical Society

Volumn 120, Issue 4, 1998, Pages 821-822

  Szyperski, Thomas ^a   Fernández, César ^a   Ono, Akira ^b   Kainosho, Masatsune ^b   Wüthrich, Kurt ^a  

^a ETH ZURICH   (Switzerland)

^b TOKYO METROPOLITAN UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBOSE; DNA BINDING PROTEIN; DOUBLE STRANDED DNA; SUGAR;

ARTICLE; ASSAY; CONTROLLED STUDY; DNA BINDING; DNA DETERMINATION; DNA STRUCTURE; MEASUREMENT; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PROTON NUCLEAR MAGNETIC RESONANCE;

EID: 2642699939     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja973055i     Document Type: Article

References (33)

1. XY, vicinal scalar coupling between protons X and Y; DNA, deoxyribonucleic acid; Antp, Antennapedia; HD, homeodomain; Antp(C39S), mutant 68-residue Antp homeodomain polypeptide with the homeodomain sequence in positions 1 to 60 and Cys39 replaced by Ser; DSS, 2,2-dimethyl-2-silapentane-5-sulfonic acid.
2. Wüthrich, K. NMR of Proteins and Nucleic Acids; Wiley: New York, 1986.
3. (a) Rinkel, L. J.; Altona, C. J. Biomol. Struct. Dyn. 1987, 4, 621-649.
4. (b) Celda, B.; Widmer, H.; Leupin, W.; Chazin, W. J.; Denny, W. A.; Wüthrich, K. Biochemistry 1989, 28, 1462-1471.
5. (c) Majumdar, A.; Hosur, R. V. Prog. NMR Spectrosc. 1992, 24, 109-158.
6. (d) Wijmenga, S. S., Mooren, M. M. W.; Hilbers, C. W. in NMR of Macromolecules; Roberts, G. C. K., Ed.; Oxford University Press: Oxford, 1993; pp 217-288.
7. (a) Rance, M.; Sørensen, O. W.; Bodenhausen, G.; Wagner, G.; Ernst, R. R.; Wüthrich, K. Biochem. Biophys. Res. Commun. 1983, 117, 479-485.
8. (b) Griesinger, C.; Sørensen, O. W.; Ernst, R. R. J. Am. Chem. Soc. 1985, 107, 6394-6396.
9. (c) Widmer, H.; Wüthrich, K. J. Magn. Reson. 1987, 74, 316-336.
10. (a) Eggenberger, U.; Karimi-Nejad, Y.; Thüring, H.; Rüterjans, H.; Griesinger, C. J. Biomol. NMR 1992, 2, 583-590.
11. (b) Schwalbe, H.; Marino, J. P.; Glaser, S. J.; Griesinger, C. J. Am. Chem. Soc. 1995, 117, 7251-7252.
12. Varani, G.; Aboul-ela, F.; Allain, F. H.-T. Prog. NMR Spectrosc. 1996, 29, 51-127.
13. Ono, A.; Tate, S.; Ishido, Y. A.; Kainosho, M. J. Biomol. NMR 1994, 4, 581-586.
14. Grzesiek, S.; Kuboniwa, H.; Hinck, A. P.; Bax, A. J. Am. Chem. Soc. 1995, 117, 5312-5315.
15. Saenger, W. Principles of Nucleic Acid Structure; Springer: New York, 1984.
16. Haasnoot, C. A. G.; DeLeuw, F. A. A. M.; Altona, C. Tetrahedron 1980, 36, 2783-2792.
17. See ref 8 in the following: Szyperski, T.; Ono, A.; Fernández, C.; Iwai, H.; Tate, S.; Wüthrich, K.; Kainosho, M. J. Am. Chem. Soc. 1997, 119, 9901-9902.
18. Müller, M.; Affolter, M.; Leupin, W.; Otting, G.; Wüthrich, K.; Gehring, W. J. EMBO J. 1988, 7, 4299-4304.
19. Billeter, M.; Qian, Y. Q.; Otting, G.; Müller, M.; Gehring, W.; Wüthrich, K. J. Mol. Biol. 1993, 234, 1084-1097.
20. Bax, A.; Vuister, G. W.; Grzesiek, S.; Delaglio, F.; Wang, A. C.; Tschudin, R.; Zhu, G. Methods Enzymol. 1993, 239, 79-105.
21. Harbison, G. J. Am. Chem. Soc. 1993, 115, 3026-3027.
22. Vuister, G. W.; Bax, A. J. Am. Chem. Soc. 1993, 115, 7772-7777.
23. (a) Santoro, J.; King, G. C. J. Magn. Reson. 1992, 97, 202-207.
24. (b) Vuister, G. W.; Bax, A. J. Magn. Reson. 1992, 98, 428-435.
25. 1H) values are: Free DNA H1′, 240 ±20 ms; H3′, 200 ± 10 ms; H5′/H5″, 180 ± 20 ms. Complex H1′, 120 ± 20 ms; H3′, 100 ± 20 ms; H5′/H5″, 110 ± 20 ms.
26. Vuister, G. W.; Yamazaki, T.; Torchia, D. A.; Bax, A. J. Biomol. NMR. 1993, 3, 297-306.
27. 2 to the experimental values, the difference between experimental and calculated apparent coupling provides a good estimate for the correction.
28. Hartmann, B.; Lavery, R. Quart. Rev. Biophys. 1996, 29, 309-368.
29. 2
30. Privé, G. G.; Yanagi, K.; Dickerson, R. E. J. Mol. Biol. 1991, 217, 177-199.
31. (a) Lahm, A.; Suck, D. J. Mol. Biol. 1991, 221, 645-667.
32. (b) Kim, J. L.; Burley, S. K. Nat. Struct. Biol. 1994, 9, 638-653.
33. Shaka, A. J.; Lee, C. J.; Pines, A. J. J. Magn. Reson. 1983, 52, 335-338.