Resonance Raman spectroscopy of 4-thiothymidine and oligodeoxynucleotides containing this base both free in solution and bound to the restriction endonuclease EcoRV

Biochemistry

Volumn 35, Issue 26, 1996, Pages 8723-8733

  Thorogood, Harry ^a   Waters, Timothy R ^b,e   Parker, Anthony W ^c   Wharton, Christopher W ^d   Connolly, Bernard A ^a  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

^b UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

^c RUTHERFORD APPLETON LABORATORY   (United Kingdom)

^d UNIVERSITY OF BIRMINGHAM   (United Kingdom)

^e UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

4' THIOTHYMIDINE; DNA; OLIGODEOXYNUCLEOTIDE; RESTRICTION ENDONUCLEASE; THYMIDINE DERIVATIVE; UNCLASSIFIED DRUG;

ARTICLE; CRYSTAL STRUCTURE; DNA STRUCTURE; HYDROGEN BOND; MOLECULAR MODEL; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN BINDING; RAMAN SPECTROMETRY; STRUCTURE ANALYSIS;

BASE SEQUENCE; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; MOLECULAR SEQUENCE DATA; OLIGODEOXYRIBONUCLEOTIDES; PROTEIN BINDING; SPECTRUM ANALYSIS, RAMAN; THERMODYNAMICS; THIONUCLEOSIDES; THYMIDINE;

EID: 0029984146     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi960230j     Document Type: Article

References (78)

1. Badger, R. M., & Bauer, S. H. (1937) J Chem. Phys. 5, 839-851.
2. Beamer, L. J., & Pabo, C. O. (1992) J. Mol. Biol. 227, 177-196.
3. Benevides, J. M., Wang, A. H.-J., van der Marel, G. A., van Boom, J. H., Rich, A., & Thomas, G. J., Jr. (1984) Nucleic Acids Res. 12, 5913-5925.
4. Benevides, J. M., Wang, A. H.-J., Rich, A., Kyogoku, Y., van der Marel, G. A., van Boom, J. H., & Thomas, G. J., Jr. (1986) Biochemistry 25, 41-50.
5. Benevides, J. M., Wang, A. H.-J., van der Marel, G. A., van Boom, J. H., & Thomas, G. J., Jr. (1988) Biochemistry 27, 931-938.
6. Benevides, J. M., Weiss, M. A., & Thomas, G. J., Jr. (1991a) Biochemistry 30, 4381-4388.
7. Benevides, J. M., Weiss, M. A., & Thomas, G. J., Jr. (1991b) Biochemistry 30, 5955-5963.
8. Benevides, J. M., Stow, P. L., Ilag, L. L., Incardona, N. L., & Thomas, G. J., Jr. (1991c) Biochemistry 30, 4855-4863.
9. Benevides, J. M., Kukolj, G., Autexier, C., Aubrey, K. L., DuBow, M. S., & Thomas, G. J., Jr. (1994a) Biochemistry 33, 10701-10710.
10. Benevides, J. M., Weiss, M. A., & Thomas, G. J., Jr. (1994b) J. Biol. Chem. 269, 10869-10878.
11. Billeter, M., Qian, Y. Q., Otting, G., Müller, M., Gehring, W., & Wüthrich, K. (1993) J. Mol. Biol. 234, 1084-1097.
12. Chuprina, V. P., Rullman, J. A. C., Lamerichs, R. M. J. M., van Boom, J. H., Boelens, R., & Kaptein, R. (1993) J. Mol. Biol. 234, 446-462.
13. Clivio, P., Fourrey, J.-L., Gasche, J., Audic, A., Favre, A., Perrin, C., & Woisard, A. (1992) Tetrahedron Lett. 33, 65-68.
14. Coleman, R. S., & Siedlecki, J. M. (1992) J. Am. Chem. Soc. 114, 9229-9230.
15. Connolly, B. A. (1991) in Oligonucleotides and Analogues: A Practical Approach (Eckstein, F., Ed.) pp 155-183, Oxford University Press, Oxford, U.K.
16. Connolly, B. A., & Newman, P. C. (1989) Nucleic Acids Res. 17, 4957-4974.
17. Crothers, D. M., & Zimm, B. H. (1964) J. Mol. Biol. 9, 1-9.
18. D'Arcy, A., Brown, R. S., Zabeau, M., van Resandt, R. W., & Winkler, F. K. (1985) J. Biol. Chem. 260, 1987-1990.
19. Dickerson, R. E. (1992) Methods Enzymol. 149, 76-110.
20. Dijkstra, S., Benevides, J. M., & Thomas, G. J., Jr. (1991) J. Mol. Struct. 242, 283-301.
21. Drew, H. R., McCall, M., & Calladine, C. R. (1988) Annu. Rev. Cell. Biol. 4, 1-20.
22. Evertsz, E. M., Thomas, G. A., Jr., & Peticolas, W. L. (1991) Biochemistry 30, 1149-1155.
23. Favre, A. (1990) in Bioorganic Photochemistry, Vol. 1: Photochemistry and the Nucleic Acids (Morrison, H., Ed.) pp 379-425, Wiley Interscience, New York.
24. Favre, A., Michelson, A. M., & Yaniv, M. (1969) Biochem. Biophys. Res. Commun. 37, 266-271.
25. Feigon, J., Sklenar, V., Wang, E., Gilbert, D. E., Macaya, R., & Schultz, P. (1992) Methods Enzymol. 211, 235-253.
26. Fliess, A., Rosenthal, A., Schwellnus, K., Blocker, H., Frank, A., & Pingoud, A. (1986) Nucleic Acids Res. 14, 3463-3474.
27. Fliess, A., Wolfes, A., Seela, F., & Pingoud, A. (1988) Nucleic Acids Res. 16, 11781-11793.
28. Fodor, S. P. A., Rava, R. P., Hays, T. R., & Spiro, T. G. (1985) J. Am. Chem. Soc. 107, 1520-1529.
29. Fox, J. J., van Praag, D., Wempen, I., Doerr, I. L., Cheong, L., Knoll, J. E., Eidinoff, M., Bendich, A., & Brown, G. B. (1959) J. Am. Chem. Soc. 81, 178-187.
30. Freier, S. M., Sugimoto, N., Sinclair, A., Alkema, D., Neilson, T., Kierzek, R., Caruthers, M. H., & Turner, D. H. (1986) Biochemistry 25, 3214-3219.
31. Gans, P. (1971) Vibrating Molecules, Chapman and Hall, London.
32. Halford, S. E., Taylor, J. D., Vermote, C. L., & Vipond, I. B. (1993) in Nucleic Acids and Molecular Biology (Eckstein, F., & Lilley, D. M. J., Eds.) Vol. 7, pp 47-69, Springer Verlag, Berlin.
33. Harrison, S. C. (1991) Nature 353, 715-719.
34. Incardona, N. L., Prescott, B., Sargent, O. P., & Thomas, G. J., Jr. (1987) Biochemistry 26, 1532-1538.
35. Klimauskas, S., Kumar, S., Roberts, R. J., & Cheng, X. (1994) Cell 76, 357-369.
36. Kostrewa, D., & Winkler, F. K. (1995) Biochemistry 34, 683-696.
37. Luke, P. A., McCallum, S. A., & Haiford, S. E. (1987) in Gene Amplification and Analysis: Restriction Endonucleases and Methylases (Chirikjian, J. G., Ed.) Vol. 5, pp 185-207, Elsevier, New York.
38. MacMillan, A. M., & Verdine, G. L. (1991) Tetrahedron 14, 2603-2616.
39. Matousek, P., Parker, A. W., Toner, W. T., & Towrie, M. (1993) Annual Report of the Central Laser Facility, RAL-(Chilton, Didcot, Oxon. OX11 0QX, UK)-93-031, p 220.
40. Mazarelli, J., Scholtissek, S., & McLaughlin, L. W. (1989) Biochemistry 28, 4616-4622.
41. Newman, P. C., Nwosu, V. U., Williams, D. M., Cosstick, R., Seela, F., & Connolly, B. A. (1990a) Biochemistry 29, 9891-9901.
42. Newman, P. C., Williams, D. M., Cosstick, R., Seela, F., & Connolly, B. A. (1990b) Biochemistry 29, 9902-9910.
43. Nikiforov, T. T., & Connolly, B. A. (1991) Tetrahedron Lett. 32, 3851-3854.
44. Nikiforov, T. T., & Connolly, B. A. (1992a) Tetrahedron Lett. 33, 2379-2382.
45. Nikiforov, T. T., & Connolly, B. A. (1992b) Nucleic Acids Res. 20, 1209-1214.
46. Nishimura, Y., & Tsuboi, M. (1980) Science 210, 1358-1360.
47. Nishimura, Y., Hirakawa, A. Y., Tsuboi, M., & Nishimura, S. (1976) Nature 260, 173-174.
48. Nishimura, Y., Hirakawa, A. Y., & Tsuboi, M. (1978) in Advances in Infrared and Raman Spectroscopy (Clark, R. J. H., & Hester, R. E., Eds.) Vol. 5, pp 217-275, Heydon, London.
49. Nishimura, Y., Tsuboi, M., Kato, S., & Morokuma, F. (1981) J. Am. Chem. Soc. 103, 1354-1358.
50. Nishimura, Y., Torigoe, C., & Tsuboi, M., (1986) Nucleic Acids Res. 14, 2737-2748.
51. Ominchinski, J. G., Clore, G. M., Schaad, O., Felsenfeld, G., Trainor, C., Appella, E., Stahl, S. J., & Gronenborn, A. M. (1993) Science 261, 438-446.
52. Otto, C., De Mul, F. F. M., & Greve, J. (1987) Biopolymers 26, 1667-1689.
53. Otwinowski, Z., Schevitz, R. W., Zhang, R,-G., Lawson, C. L., Joachimiak, A., Marmorstein, R. Q., Luisi, B. F., & Sigler, P. B. (1988) Atare 335, 321-329.
54. Pabo, C. O., & Sauer, R. T. (1992) Annu. Rev. Biochem. 61, 1053-1095.
55. Peticolas, W. L., & Evertsz, E. (1992) Methods Enzymol. 211, 335-352.
56. Peticolas, W. L., Kubasek, W. L., Thomas, G. A., Jr., & Tsuboi, M. (1987) in Biological Applications of Raman Spectroscopy (Spiro, T. G., Ed.) Vol. 1, pp 81-133, Wiley Interscience, New York.
57. Schrader, B. (1989) Raman/Infrared Atlas of Organic Compounds, 2nd ed., VCH, New York.
58. Somers, W. S., & Phillips, S. E. V. (1992) Nature 359, 387-393.
59. Takeuchi, H., & Sasamori, J. (1994) Biopolymers 35, 359-367.
60. Taylor, J. D., & Halford, S. E. (1989) Biochemistry 28, 6198-6207.
61. Taylor, J. D., Badcoe, T. G., Clarke, A. R., & Halford, S. E. (1991) Biochemistry 30, 8743-8753.
62. Thamann, T. J., Lord, R. C., Wang, A. H.-J., & Rich, A. (1981) Nucleic Acids Res. 9, 5443-5457.
63. Thielking, V., Selent, U., Kohler, E., Wolfes, H., Pieper, U., Gieger, R., Urbanke, C., Winkler, F. K., & Pingoud, A. (1991) Biochemistry 30, 6416-6422.
64. Thomas, G. J., Jr., & Wang, A. H.-J. (1988) in Nucleic Acids and Molecular Biology (Eckstein, F., & Lilley, D. M. J., Eds.) Vol. 2, pp 1-40, Springer-Verlag, Berlin.
65. Thomas, G. J., Jr., Kubasek, W. L., Peticolas, W. L., Greene, P., Grable, J., & Rosenberg, J. M. (1989) Biochemistry 28, 2001-2009.
66. Toyama, A., Takeuchi, H., & Harada, I. (1991) J. Mol. Struct. 242, 87-98.
67. Travers, A. A. (1989) Annu. Rev. Biochem. 58, 427-452.
68. Tsuboi, M., Nishimura, Y., Hirakawa, A. Y., & Peticolas, W. L. (1987) in Biological Applications of Roman Spectroscopy, Vol. 2, pp 109-179 (Spiro, T. G. Ed.) Wiley Interscience, New York.
69. Vermote, C. L. M., & Halford, S. E. (1992) Biochemistry 31, 6082-6089.
70. Vermote, C. L. M., Vipond, I. B., & Halford, S. E. (1992) Biochemistry 31, 6089-6097.
71. Vipond, I. B., & Halford, S. E. (1993) Mol. Microbiol. 9, 225-231.
72. Wang, A. H.-J., Quigley, G. J., Kolpak, F. J., van der Marel, G., & van Boom, J. H. (1981) Science 211, 171-176.
73. Wenz, C., Selent, U., Wende, W., Jeltsch., A., Wolfes, H., & Pingoud, A. (1994) Biochim. Biophys. Acta 1219, 73-80.
74. Weston, S., Lahm, A., & Suck, D. (1992) J. Mol. Biol. 226, 1237-1256.
75. White, A. J., & Wharton, C. W. (1990) Biochem. J. 270, 627-637.
76. Winkler, F. K. (1992) Curr. Opin. Struct. Biol. 2, 93-99.
77. Winkler, F. K., Banner, D. W., Oefner, C., Tsernoglou, D., Brown, R. S., Heathman, S. P., Bryan, R. K., Martin, P. D., Petratos, K., & Wilson, K. (1993) EMBO J. 335, 789-795.
78. Xu, Y.-Z., Zheng, Q., & Swann, P. F. (1992) J. Org. Chem. 57, 3839-2845.