Structural features of the DNA hairpin d(ATCCTA-GTTA-TAGGAT): Formation of a G-A base pair in the loop

Nucleic Acids Research

Volumn 25, Issue 8, 1997, Pages 1537-1547

  Van Dongen, Maria J P ^a   Mooren, Margret M W ^a   Willems, Esther F A ^a   Van Der Marel, Gijs A ^b   Van Boom, Jacques H ^b   Wijmenga, Sybren S ^a,c   Hilbers, Cornelis W ^a  

^a RADBOUD UNIVERSITY NIJMEGEN   (Netherlands)

^b LEIDEN UNIVERSITY   (Netherlands)

^c UMEÅ UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; DNA; GUANINE;

ARTICLE; BASE PAIRING; DNA CONFORMATION; DNA SEQUENCE; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL;

ADENINE; BASE COMPOSITION; COMPUTER GRAPHICS; DNA; GUANINE; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; OLIGODEOXYRIBONUCLEOTIDES;

EID: 0030824912     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/25.8.1537     Document Type: Article

References (49)

1. Hilbers, C.W., Heus, H.A., van Dongen, M.J.P. and Wijmenga, S.S. (1994) In Eckstein, F. and Lilley, D.M.J. (eds), Nucleic Acids and Molecular Biology. Springer-Verlag, Berlin, Germany, Vol. 8, pp. 56-104.
2. Hirao, I., Nishimura, Y., Naroka, T., Watanabe, K., Arata, Y. and Miura, K.-i. (1989) Nucleic Acids Res., 17, 2223-2231.
3. Hirao, I., Nishimura, Y., Tagawa, Y.-i., Watanabe, K. and Miura, K.-i. (1992) Nucleic Acids Res., 20, 3891-3896.
4. Hirao, I., Nishimura, Y., Tagawa, Y.-i., Watanabe, K. and Miura, K.-i. (1994) Nucleic Acids Res., 22, 576-582.
5. Heus, H.A. and Pardi, A. (1991) Science, 253, 191-193.
6. SantaLucia, J., Jr, Kierzek, R. and Turner, D.H. (1992) Science, 256, 217-219.
7. Orita, M., Nishikawa, F., Shimanaya, T., Taira, K., Endo, Y. and Nishikawa, S. (1993) Nucleic Acids Res., 21, 5670-5678.
8. Sandusky, P., Wooten, E.W., Kurochkin, A.V., Kavanaugh, Th., Mandecki, W. and Zuiderweg, E. (1995) Nucleic Acids Res., 23, 4717-4725.
9. Zhu, L., Chou, S.-H., Xu, J. and Reid, B.R. (1995) Nature Struct. Biol., 2, 1012-1017.
10. Woese, C.R., Winker, S. and Gutell, R.R. (1990) Proc. Natl. Acad. Sci. USA, 87, 8467-8471.
11. Catasti, P., Gupta, G., Garcia, A.E., Ratliff, R., Hong, L., Yau, P., Moyzis, R.K. and Bradbury, E.M. (1994) Biochemistry, 33, 3819-3830.
12. Ferrer, N., Azorín, F., Villasante, A., Gutierrez, C. and Abad, J.P. (1995) J. Mol. Biol., 245, 8-21.
13. Li, Y., Zon, G. and Wilson, W.D. (1991) Proc. Natl. Acad. Sci. USA, 88, 26-30.
14. Li, Y., Zon, G. and Wilson, W.D. (1991) Biochemistry, 30, 7566-7572.
15. Chou, S.-H., Cheng, J.W. and Reid, B.R. (1992) J. Mol. Biol., 228, 138-155.
16. Chou, S.-H., Cheng, J.W., Fedoroff, O. and Reid, B.R. (1994) J. Mol. Biol., 241, 467-479.
17. SantaLucia, J., Jr and Turner, D.H. (1993) Biochemistry, 32, 12612-12623.
18. Gautheret, D., Konings, D. and Gutell, R.R. (1994) J. Mol. Biol., 242, 1-8.
19. Cheng, Y.K., Chou, S.-H. and Reid, B.R. (1992) J. Mol. Biol., 228, 1037-1041.
20. Walter, A.E., Wu, M. and Turner, D.H. (1994) Biochemistry, 33, 11349-11354.
21. Antao, V.P. and Tinoco, I., Jr (1992) Nucleic Acids Res., 20, 819-824.
22. Jucker, F.M., Heus, H.A., Ping, F.Y., Moors, E.H.M. and Pardi, A. (1996) J. Mol. Biol., 264, 968-980.
23. Hilbers, C.W., Blommers, M.J.J., Van de Ven, F.J.M., Van Boom, J.H. and Van der Marel, G.A. (1991) Nucleosides Nucleotides, 10, 61-80.
24. Van Dongen, M.J.P., Wijmenga, S.S., Van der Marel, G.A., Van Boom, J.H. and Hilbers, C.W. (1996) J. Mol. Biol., 263, 715-729.
25. Van Boom, J.H., Van der Marel, G.A., Westerink, H.P., Van Boeckel, C.A.A., Mellema, J.R., Altona, C., Hilbers, C.W., Haasnoot, C.A.G., de Bruin, S.H. and Berendsen, R.G. (1983) Cold Spring Harbor Symp. Quant. Biol., 47, 403-409.
26. Van de Ven, F.J.M., Blommers, M.J.J., Schouten, R.E. and Hilbers, C.W. (1991) J. Magn. Resonance, 94, 140-151.
27. Cantor, C.R. and Schimmel, P.R. (1980) Biophysical Chemistry, Vol. II. W.H.Freeman and Co., San Francisco, CA.
28. Blommers, M.J.J., Van de Ven, F.J.M., Van der Marel, G.A., Van Boom, J.H. and Hilbers, C.W. (1991) Eur. Biochem., 201, 33-51.
29. Wijmenga, S.S., Mooren, M.M.W. and Hilbers, C.W. (1993) In Roberts, G.C.K. (ed.), NMR of Macromolecules, A Practical Approach. Oxford University Press, New York, NY, pp. 217-288.
30. Güntert, P. (1995) DIANA User's Manual and Instructions, Version 2.8. Institut für Molekularbiologie und Biophysik, ETH. Zurich, Switzerland.
31. Güntert, P., Braun, W. and Wüthrich, K. (1991) J. Mol. Biol., 217, 517-530.
32. Saenger, W. (1984) Principles of Nucleic Acid Structure, Springer Verlag, New York, NY
33. Wüthrich, K. (1986) NMR of Proteins and Nucleic Acids. John Wiley & Sons, New York, NY.
34. Keepers, J.W. and James, Th.L. (1984) J. Magn. Resonance, 57, 404-426.
35. Mooren, M.M.W., Pulleyblank, D.E., Wijmenga, S.S., Van de Ven, F.J.M. and Hilbers, C.W. (1994) Biochemistry, 33, 7315-7325.
36. Brünger, A.T. (1992) X-PLOR Manual, Version 3.1. Yale University Press, New Haven, CT.
37. Brown, T., Hunter, W.N., Kneale, G. and Kennard, O. (1986) Proc. Natl. Acad. Sci. USA, 83, 2402-2406.
38. Gao, X.L. and Patel, D.J. (1988) J. Am. Chem. Soc., 110, 5178-5182.
39. Ippel, J.H. (1993) Loop folding in DNA minihairpins. Conformational studies. Thesis University of Leiden, Leiden, The Netherlands, pp 209-239.
40. Varani, G., Cheong, C. and Tinoco, I., Jr (1991) Biochemistry, 30, 3280-3289.
41. Allain, F.H.-T. and Varani, G. (1995) J. Mol. Biol., 250, 333-353.
42. Bloomfield, V.A., Crothers, D.M. and Tinoco, I., Jr (1974) Physical Chemistry of Nucleic Acids. Harper & Row, New York, NY
43. Sklenar, V. and Bax, A. (1987) J. Magn. Resonance, 74, 469-479.
44. Jeener, J., Meier, B.H., Bachmann, P. and Ernst, R.R. (1979) J. Chem. Phys., 71, 4546-4553.
45. Marion, D. and Wüthrich, K. (1983) Biochem. Biophys. Res. Commun., 113, 967-974.
46. Rance, M., Sørensen, O.W., Bodenhausen, G., Wagner, G., Ernst, R.R. and Wüthrich, K. (1983) Biochem. Biophys. Res. Commun., 117, 479-485.
47. Bax, A. and Davis, D.G. (1985) J. Magn. Resonance B, 65, 355-366.
48. Griesinger, C., Otting, G., Wüthrich, K. and Ernst, R.R. (1988) J. Am. Chem. Soc., 110, 7870-7872.
49. Sklenar, V., Miyashiro, H., Zon, G., Miles, H.T. and Bax, A. (1986) FEBS Lett., 208, 94-98.