Global structure of three-way DNA junctions with and without additional unpaired bases: A fluorescence resonance energy transfer analysis

Biochemistry

Volumn 36, Issue 44, 1997, Pages 13530-13538

  Stühmeier, Frank ^a   Welch, Jonathan B ^b   Murchie, Alastair I H ^b   Lilley, David M J ^b   Clegg, Robert M ^a  

^a MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

^b IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DNA DETERMINATION; DNA STRUCTURE; ENERGY TRANSFER; FLUORESCENCE; PRIORITY JOURNAL; STRUCTURE ANALYSIS;

BASE COMPOSITION; BASE SEQUENCE; DNA; ENERGY TRANSFER; FLUORESCEIN; FLUORESCENT DYES; NUCLEIC ACID CONFORMATION; RHODAMINES; SODIUM CHLORIDE; SOLUTIONS; SPECTROMETRY, FLUORESCENCE;

EID: 0030815232     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi9702445     Document Type: Article

References (65)

1. Altona, C., Pikkemaat, J. A., & Overmars, F. J. J. (1996) Curr. Opin. Struct. Biol. 6, 305-316.
2. Anshelevich, V. V., Vologodskii, A. V., Lukashin, A. V., & Frank-Kamenetskii, M. D. (1984) Biopolymers 23, 39-58.
3. Beaucage, S. L., & Caruthers, M. H. (1981) Tetrahedron Lett. 22, 1859-1862.
4. Bennett, R. J., & West, S. C. (1995) J. Mol. Biol. 252, 213-226.
5. Bhattacharyya, A., & Lilley, D. M. J. (1989) Nucleic Acids Res. 17, 6821-6840.
6. Bhattacharyya, A., Murchie, A. I. H., & Lilley, D. M. J. (1990) Nature 343, 484-487.
7. Bhattacharyya, A., Murchie, A. I. H., von Kitzing, E., Diekmann, S., Kemper, B., & Lilley, D. M. J. (1991) J. Mol. Biol. 221, 1191-1207.
8. Bianchi, M. E., Beltrame, M., & Paonessa, G. (1989) Science 243, 1056-1059.
9. Bianchi, M. E., Falciola, L., Ferrari, S., & Lilley, D. M. J. (1992) EMBO J. 11, 1055-1063.
10. Clegg, R. M. (1992) Methods Enzymol. 211, 353-388.
11. Clegg, R. M. (1996) in Fluorescence Imaging Spectroscopy and Microscopy (Wang, X. F., & Herman, B., Eds.) pp 179-252, John Wiley & Sons, Inc., New York.
12. Clegg, R. M., Murchie, A. I. H., Zechel, A., Carlberg, C., Diekmann, S., & Lilley, D. M. J. (1992) Biochemistry 31, 4846-4856.
13. Clegg, R. M., Murchie, A. I. H., Zechel, A., & Lilley, D. M. J. (1993) Proc. Natl. Acad. Sci. U.SA. 90, 2994-2998.
14. Clegg, R. M., Murchie, A. I. H., & Lilley, D. M. J. (1994) Biophys. J. 66, 99-109.
15. Connolly, B. A. (1987) Nucleic Acids Res. 15, 3131-3139.
16. Cooper, J. P., & Hagerman, P. J. (1990) Biochemistry 29, 9261-9268.
17. Craig, M. E., Crothers, D. M., & Doty, P. (1971) J. Mol. Biol. 62, 383-401.
18. Dale, R. E., & Eisinger, J. (1974) Biopolymers 13, 1573-1605.
19. Demas, J. N., & Crosby, G. A. (1971) J. Phys. Chem. 75, 991-1094.
20. Duckett, D. R., & Lilley, D. M. (1990) EMBO J. 9, 1659-1664.
21. Duckett, D. R., Murchie, A. I. H., Diekmann, S., von Kitzing, E., Kemper, B., & Lilley, D. M. J. (1988) Cell 55, 79-89.
22. Duckett, D. R., Murchie, A. I. H., Clegg, R. M., Zechel, A., von Kitzing, E., Diekmann, S., & Lilley, D. M. J. (1990) in Human Genome Initiative & DNA Recombination (Sarma, R. H., & Sarma, M. H., Eds.) pp 157-181, Adenine Press, Guilderland, NY.
23. Duckett, D. R., Murchie, A. I. H., Bhattacharyya, A., Clegg, R. M., Diekmann, S., von Kitzing, E., & Lilley, D. M. J. (1992) Eur. J. Biochem. 207, 285-295.
24. Duckett, D. R., Giraud Panis, M.-E., & Lilley, D. M. J. (1995a) J. Mol. Biol. 246, 95-107.
25. Duckett, D. R., Murchie, A. I. H., & Lilley, D. M. J. (1995b) Cell 83, 1027-1036.
26. Eggleston, A. K., & West, S. C. (1996) Trends Genet. 12, 20-26.
27. Eis, P. S., & Millar, D. P. (1993) Biochemistry 32, 13852-13860.
28. Förster, T. (1948) Ann. Phys. 2, 55-75.
29. Förster, T. (1949) Z. Naturforsch. 4a, 321-327.
30. Gohlke, C., Murchie, A. I. H., Lilley, D. M. J., & Clegg, R. M. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 11660-11664.
31. Jablonski, A. (1957) Acta Phys. Pol. 16, 471-479.
32. Jares-Erijman, E. A., & Jovin, T. M. (1996) J. Mol. Biol. 257, 596-617.
33. Lakowicz, J. R. (1983) Principles of fluorescence Spectroscopy, Plenum Press, New York.
34. Leontis, N. B., Kwok, W., & Newman, J. S. (1991) Nucleic Acids Res. 19, 759-766.
35. Leontis, N. B., Hills, M. T., Piotto, M., Malhotra, A., Nussbaum, J., & Gorenstein, D. G. (1993) J. Biomol. Struct. Dyn. 11, 215-223.
36. Leontis, N. B., Hills, M. T., Piotto, M., Ouporov, I. V., Malhotra, A., & Gorenstein, D. G. (1994) Biophys. J. 68, 251-265.
37. Leontis, N. B., Hills, M. T., Piotto, M., Ouporov, I. V., Malhotra, A., & Gorenstein, D. G. (1995) Biophys. J. 68, 251-265.
38. Lilley, D. M. J., & Clegg, R. M. (1993a) Q. Rev. Biophys. 26, 131-175.
39. Lilley, D. M. J., & Clegg, R. M. (1993b) Annu. Rev. Biophys. Biomol. Struct. 22, 299-328.
40. Lilley, D. M. J., Clegg, R. M., Diekmann, S., Seeman, N. C., Kitzing, E. v., & Hagerman, P. M. (1995) Eur. J. Biochem. 239, 1-2.
41. Millar, D. P. (1996) Curr. Opin. Struct. Biol. 6, 322-326.
42. Murchie, A. I. H., Clegg, R. M., von Kitzing, E., Duckett, D. R., Dieckmann, S., & Lilley, D. M. J. (1989) Nature 341, 763-766.
43. Nickel, B. (1989) J. Lumin. 44, 1-18.
44. Ouporov, I. V., & Leontis, N. B. (1995) Biophys. J. 68, 266-274.
45. Overmans, F. J. J., Pikkemaat, J. A., Elst, H. v. d., Boom, J. H. v., & Altona, C. (1996) J. Mol. Biol. 255, 702-713.
46. Parsons, C. A., Stasiak, A., Bennett, R. J., & West, S. C. (1995) Nature 374, 375-378.
47. Pöhler, J. R. G., Duckett, D. R., & Lilley, D. M. J. (1994) J. Mol. Biol. 238, 62-74.
48. Pöhler, J. R. G., Giraud-Panis, M.-J. E., & Lilley, D. M. J. (1996) J. Mol. Biol. 260, 678-696.
49. Pörschke, D., & Eigen, M. (1971) J. Mol. Biol. 62, 361-381.
50. Rosen, M. A., & Patel, D. J. (1993a) Biochemistry 32, 6563-6575.
51. Rosen, M. A., & Patel, D. J. (1993b) Biochemistry 32, 6576-6587.
52. Rosen, M. A., Live, D., & Patel, D. J. (1992) Biochemistry 31, 4004-4014.
53. Seeman, N. C., & Kallenbach, N. R. (1994) Annual Review of Biophysics & Biomolecular Structure, pp 53-86, Annual Reviews Inc., Palo Alto.
54. Sinha, N. D., Biernat, J., McManus, J., & Koster, H. (1984) Nucleic Acids Res. 12, 4539-4557.
55. Stühmeier, F., Lilley, D. M. J., & Clegg, R. M. (1997) Biochemistry 36, 13539-13551.
56. Teo, S. H., Grasser, K. D., Hardman, C. H., Broadhurst, R. W., Laue, E. D., & Thomas, J. O. (1995) EMBO J. 14, 3844-3853.
57. Tuschl, T., Gohlke, C., Jovin, T. M., Westhof, E., & Eckstein, F. (1994) Science 266, 785-789.
58. Vámosi, G., Gohlke, C., & Clegg, R. M. (1996) Biophys. J. 71, 972-994.
59. Van Der Meer, B. W., Coker, G., III, & Chen, S.-Y. S. (1994) Reson. Energy Transfer, VCH Publishers, Inc., New York.
60. von Kitzing, E., Lilley, D. M. J., & Diekmann, S. (1990) Nucleic Acids Res. 18, 2671-2683.
61. Welch, J. B., Duckett, D. R., & Lilley, D. M. (1993) Nucleic Acids Res. 21, 4548-4555.
62. Welch, J. B., Walter, F., & Lilley, D. M. (1995) Journal of Molecular Biology 251, 507-519.
63. White, M. F., & Lilley, D. M. J. (1996) J. Mol. Biol. 266, 122-134.
64. Yang, M., & Millar, D. P. (1996) Biochemistry 35, 7959-7967.
65. Zhong, M., Rashes, M. S., Leontis, N. B., & Kallenbach, N. R. (1994) Biochemistry 33, 3660-3667.