Helix-coil transition of a four-way DNA junction observed by multiple fluorescence parameters

Journal of Physical Chemistry B

Volumn 112, Issue 41, 2008, Pages 13136-13148

  Vámosi, György ^a   Clegg, Robert M ^b  

^a INSTITUTE OF EXPERIMENTAL MEDICINE   (Hungary)

^b University of Illinois at Urbana Champaign   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANISOTROPY; BIOCHEMISTRY; CONCENTRATION (PROCESS); CURVE FITTING; DENATURATION; DNA; ENERGY TRANSFER; ENTHALPY; FLUORESCENCE; GENES; LIGHT EMISSION; LUMINESCENCE; MOLECULES; NUCLEIC ACIDS; ORGANIC ACIDS; POLYMER BLENDS; PYROLYSIS;

ARM MODELS; BASE PAIRS; BRANCHED MOLECULES; COIL TRANSITIONS; CONFORMATIONAL CHANGES; COOPERATIVE UNITS; ENTROPY VALUES; EQUILIBRIUM CONCENTRATIONS; EXPERIMENTAL CURVES; EXPERIMENTAL DATUMS; FLUORESCENCE ANISOTROPIES; FLUORESCENCE INTENSITIES; HELIX LENGTHS; INTERMEDIATE STATES; MELTING BEHAVIORS; MELTING CURVES; REACTION MECHANISMS; REACTION MODELS; RESONANCE ENERGIES; SINGLE STEPS; SPECTROSCOPIC MEASUREMENTS; STANDARD ENTHALPIES; STRUCTURE CHANGING; THERMODYNAMIC MODELS; TOTAL LENGTHS; VAN'T HOFF ENTHALPIES; ZIPPER MODELS;

MELTING;

EID: 55149118976     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp8034055     Document Type: Article

References (76)

1. Holliday, R. Genet. Res. 1964, 5, 282.
2. Lilley, D. M.; Clegg, R. M. Annu. Rev. Biophys. Biomol. Struct. 1993, 22, 299.
3. Seeman, N. C.; Kallenbach, N. R. Annu. Rev. Biophys. Biomol. Struct. 1994, 23, 53.
4. Kowalczykowski, S. C.; Dixon, D. A.; Eggleston, A. K.; Lauder, S. D.; Rehrauer, W. M. Microbiol. Rev. 1994, 58, 401.
5. Duckett, D. R.; Murchie, A. I.; Giraud Parus, M. J.; Pohler, J. R.; Lilley, D. M. Philos. Trans. R Soc. London, Ser. B 1995, 347, 27.
6. Shinagawa, H.; Iwasaki, H. Adv. Biophys. 1995, 31, 49.
7. White, M. F.; Giraud Parus, M. J.; Pohler, J. R.; Lilley, D. M. J. Mol. Biol. 1997, 209, 647.
8. Lilley, D. M. J.; Norman, D. G. Nat. Struct. Biol. 1999, 6, 897.
9. McKinney, S. A.; Declais, A. C.; Lilley, D. M.; Ha, T. Nat. Struct. Biol. 2002, 23, 23.
10. West, S. C. Annu. Rev. Genet. 1997, 31, 213.
11. Duckett, D. R.; Murchie, A. I.; Diekmann, S.; von Kitzing, E.; Kemper, B.; Lilley, D. M. Cell 1988, 55, 79.
12. Cooper, J. P.; Hagerman, P. J. J. Mol. Biol. 1987, 198, 711.
13. Clegg, R. M.; Murchie, A. I.; Lilley, D. M. Biophys. J. 1994, 66, 99.
14. Murchie, A. I.; Clegg, R. M.; von Kitzing, E.; Duckett, D. R.; Diekmann, S.; Lilley, D. M. Nature 1989, 341, 763.
15. Cooper, J. P.; Hagerman, P. J. Biochemistry 1990, 29, 9261.
16. Clegg, R. M.; Murchie, A. I.; Zechel, A.; Carlberg, C.; Diekmann, S.; Lilley, D. M. Biochemistry 1992, 31, 4846.
17. Cooper, J. P.; Hagerman, P. J. Proc. Natl. Acad. Sci. U.S.A. 1989, 86, 7336.
18. Carlström, G.; Chazin, W. J. Biochemistry 1996, 35, 3534.
19. Overmars, F. J.; Altona, C. J. Mol. Biol. 1997, 273, 519.
20. Miick, S. M.; Fee, R. S.; Millar, D. P.; Chazin, W. J. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 9080.
21. Millar, D. P.; Fee, R. S Biophys. J. Abstr. 1997, 72, A6.
22. Joo, C.; McKinney, S. A.; Lilley, D. M.; Ha, T. J. Mol. Biol. 2004, 341, 739.
23. McKinney, S. A.; Tan, E.; Wilson, T. J.; Nahas, M. K.; Declais, A. C.; Clegg, R. M.; Lilley, D. M.; Ha, T. Biochem. Soc. Trans. 2004, 32, 41.
24. Grainger, R. J.; Murchie, A. I.; Lilley, D. M. Biochemistry 1998, 37, 23.
25. von Kitzing, E.; Lilley, D. M.; Diekmann, S. Nucleic Acids Res. 1990, 18, 2671.
26. Clegg, R. M.; Murchie, A. I. H.; Zechel, A.; Carlberg, C.; Diekmann, S.; Lilley, D. M. J. Biochemistry 1992, 31, 4846.
27. Clegg, R. M. Methods Enzymol. 1992, 211, 353.
28. Clegg, R. M.; Murchie, A. I. H.; Zechel, A.; Lilley, D. M. J. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 2994.
29. Clegg, R. M.; Murchie, A. I. H.; Lilley, D. M. J. Biophys. J. 1994, 66, 99.
30. Mergny, J. L.; Boutorine, A. S.; Garestier, T.; Belloc, F.; Rougee, M.; Bulychev, N. V.; Koshkin, A. A.; Bourson, J.; Lebedev, A. V.; Valeur, B.; Thuong, N. T.; Hélène, C. Nucleic Acids Res. 1994, 22, 920.
31. Tuschl, T.; Gohlke, C.; Jovin, T. M.; Westhof, E.; Eckstein, F. Science 1994, 266, 785.
32. Gohlke, C.; Murchie, A. I.; Lilley, D. M.; Clegg, R. M. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 11660.
33. Millar, D. P. Curr. Opin. Struct. biol. 1996, 6, 322.
34. Bassi, G. S.; Murchie, A. I.; Walter, F.; Clegg, R. M.; Lilley, D. M. EMBO J. 1997, 16, 7481.
35. Stuhmeier, F.; Welch, J. B.; Murchie, A. I.; Lilley, D. M.; Clegg, R. M. Biochemistry 1997, 36, 13530.
36. Tóth, K.; Sauermann, V.; Langowsi, J. Biochemistry 1998, 37, 8173.
37. Toth, K.; Bran, N.; Langowski, J. Biochemistry 2001, 40, 6921.
38. Klostermeier, D.; Millar, D. P. Biochemistry 2000, 39, 12970.
39. Klostermeier, D.; Millar, D. P. Biochemistry 2001, 40, 11211.
40. Klostermeier, D.; Millar, D. P. Biopolymers 2001, 61, 159.
41. Wilson, T. J.; Zhao, Z. Y.; Maxwell, K.; Kontogiannis. L.; Lilley, D. M. Biochemistry 2001, 40, 2291.
42. Murchie, A. I.; Thomson, J. B.; Walter, F.; Lilley, D. M. Mol. Cell 1998, 1, 873.
43. Walter, F.; Murchie, A. I.; Lilley, D. M. Biochemistry 1998, 37, 17629.
44. Walter, F.; Murchie, A. I.; Thomson, J. B.; Lilley, D. M. Biochemistry 1998, 37, 14195.
45. Walter, F.; Murchie, A. I.; Ducken, D. R.; Lilley, D. M. RNA 1998, 4, 719.
46. Stuhmeier, F.; Hillisch, A.; Clegg, R. M.; Diekman, S. J. Mol. Biol. 2000, 302, 1081.
47. Hillisch, A.; Lorenz, M.; Diekmann, S. Curr. Opin. Struct. Biol. 2001, 11, 201.
48. Vámosi, G.; Gohlke, C.; Clegg, R. M. Biophys. J. 1996, 71, 972.
49. Cardullo, R. A.; Agrawal, S.; Flores, C.; Zamecnik, P. C.; Wolf, D. E. Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 8790.
50. Stuhmeier, F.; Lilley, D. M.; Clegg, R. M. Biochemistry 1997, 36, 13539.
51. Morrison, L. E.; Stols, L. M. Biochemistry 1993, 32, 3095.
52. Parkhurst, K. M.; Parkhurst, L. J. Biochemistry 1995, 34, 285.
53. Vámosi, G.; Clegg, R. M. Biochemistry 1998, 37, 14300.
54. Gelfand, C. A.; Plum, G. E.; Mielewczyk, S.; Remeta, D. P.; Breslauer, K. J. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 6113.
55. Howell, W. M.; Jobs, M.; Brookes, A. J. Genome Res. 2002, 12, 1401.
56. Gohlke, C.; Murchie, A. I. H.; Lilley, D. M. J.; Clegg, R. M. Manuscript in preparation.
57. Gohlke, C. Untersuchungen zur Struktur doppelsträngigcr DNA mit ungepaarten Nukleotiden in einem Strang. M.S. Thesis (Diplom), GeorgAugust Universität, Götingen, Germany, 1994.
58. Poland, D.; Scheraga, H. A. Theory of Helix-Coil Transitions in Biopolymers; Academic Press: New York, 1970.
59. Shida, T.; Iwasaki, H.: Shinagawa, H.; Kyogoku, Y. J. Biochem. (Tokyo) 1996, 119, 653.
60. Chen, J. H.; Churchill, M. E.; Tullius, T. D.; Kallenbach, N. R.; Seeman, N. C. Biochemistry 1988, 27, 6032.
61. Walter, F. Untersuchung äusserer Bedingungen für die Ausbildung einer X-Struktur der vier-strängigen DNA-Kreuzstruktur. M.S. Thesis (Diplom), Georg-August-Universitätzu Göttingen, 1992.
62. Marky, L. A.; Kallenbach, N. R.; McDonough, K. A.; Seeman, N. C.; Breslauer, K. J. Biopolymers 1987, 26, 1621.
63. Makube, N.; Klump, H.; Pikkemaat, J.; Altona, C. Arch. Biochem. Biophys. 1999, 364, 53.
64. Beaucage, S. L.; Caruthers, M. H. Tetrahedron Lett. 1981, 22, 1859.
65. Connolly, B. A. Nucleic Acids Res. 1987, 15, 3131.
66. Förster, T. Ann. Phys. 1948, 2, 55.
67. Förster, T. Z. Naturforsch. 1949, 4a, 321.
68. Clegg, R. M. Fluorescence resonance energy transfer. In Fluorescence Imaging Spectroscopy and Microscopy, Wang, X. F., Herman, B., Eds.; John Wiley & Sons, Inc.: New York, 1996; Vol. 137, p 179.
69. Dale, R. E.; Eisinger, J.; Blumberg, W. E. Biophys. J. 1979, 26, 161.
70. Edman, L.; Mets, U.; Rigler, R. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 6710.
71. Breslauer, K. J.; Frank, R.; Blöcker, H.; Marky, L. A. Proc. Natl. Acad. Sci. U.S.A. 1986, 83, 3746.
72. SantaLucia, J., Jr.; Allawi, H. T.; Seneviratne, P. A. Biochemistry 1996, 35, 3555.
73. SantaLucia, J., Jr Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 1460.
74. Wartell, R. M.; Benight, A. S. Phys. Rep. 1985, 126, 67.
75. Applequist, J.; Damle, V. J. Am. Chem. Soc. 1965, 87.
76. Blake, R. D.; Bizzaro, J. W.; Blake, J. D.; Day, G. R.; Delcourt, S. G.; Knowles, J.: Marx, K. A.; SantaLucia, J. Bioinformatics 1999, 15, 370.