Helix morphology changes in b-dna induced by spontaneous bI⇌BII Substate Interconversion

Journal of Biomolecular Structure and Dynamics

Volumn 17, Issue 2, 1999, Pages 223-235

  Winger, Rudolf H ^a   Liedl, Klaus R ^a   Pichler, Arthur ^a   Hallbrucker, Andreas ^a   Mayer, Erwin ^a  

^a UNIVERSITY OF INNSBRUCK   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; CONFORMATIONAL TRANSITION; DNA HELIX; DNA SEQUENCE; DNA STRUCTURE; MOLECULAR DYNAMICS; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; X RAY ANALYSIS;

COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; DNA; MODELS, MOLECULAR; MONTE CARLO METHOD; NUCLEIC ACID CONFORMATION; SUBSTRATE SPECIFICITY;

EID: 0032755536     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.1999.10508355     Document Type: Article

References (87)

1. Berman, H. M., 1994. Curr. Opin. Struct. Biol., 4:345–350.
2. Neidle, S., 1997. Biopolymers (Nucleic Acid Sci.), 44:105–121.
3. Phillips, S. E. V., and Moras, D., 1993. Curr. Opin. Struct. Biol., 3:1–2.
4. Suzuki, M., and Yagi, N., 1996. J. Mol. Biol., 255:677–687.
5. Kunkel, T. A., and Wilson, S. H., 1998. Nature Struct. Biol., 5:95–99.
6. Thuong, N. T., and Helene, C., 1993. Angew. Chem., 105:697–23.
7. Suck, D., Lahm, A., and Oefner, C., 1988. Nature, 332:464–468.
8. Otwinowski, Z., Schevitz, R. W., Zhang, R. G., Lawson, C. L., Joachimiak, A., Marmorstein, R. Q., Luisi, B. F., and Sigler, P. B., 1988. Nature, 335:321–329.
9. Wolberger, C., Dong, Y. C., Ptashne, M., and Harrison, S. C., 1988. Nature, 335:789–795.
10. Jordan, S. R., and Pabo, C. O., 1988. Science, 242:893–899.
11. Carrondo, M. A., Coll, M., Aymami, J., Wang, A. H., van der Marel, G. A., van Boom, J. H., and Rich, A., 1989. Biochemistry, 28:7849–7859.
12. Luisi, B. F., Xu, W. X., Otwinowski, Z., Freedman, L. P., Yamamoto, K. R., and Sigler, P. B., 1991. Nature, 352:497–505.
13. Somers, W. S., and Phillips, S. E., 1992. Nature, 359:387–393.
14. Beamer, L. J., and Pabo, C. O., 1992. J. Mol. Biol., 227:177–196.
15. Beese, L. S., Derbyshire, V., and Steitz, T. A., 1993. Science, 260:352–355.
16. Shakked, Z., Guzikevich-Guerstein, G., Frolow, F., Rabinovich, D., Joachimiak, A., and Sigler, P. B., 1994. Nature, 368:469–473.
17. Luger, K., Mäder, A. W., Richmond, R. K., Sargent, D. F., and Richmond, T. J., 1997. Nature, 389:251–260.
18. Becker, S., Groner, B., and Müller, C. W., 1998. Nature, 394:145–151.
19. Chen, Y.-Q., Gosh, S., and Gosh, G., 1998. Nature Struct. Biol., 5:67–73.
20. Privé, G. G., Heinemann, U., Chandrasegaran, S., Kan, L.-S., Kopka, M. L., and Dickerson, R. E., 1987. Science, 238:498–504.
21. Grzeskowiak, K., Yanagi, K., Privé, G. G., and Dickerson, R. E., 1991. J. Biol. Chem., 266:8861–8883.
22. Hartmann, B., Piazzola, D., and Lavery, R., 1993. Nucleic Acids Res., 21:561–568.
23. Dickerson, R. E., 1998. Nucleic Acids Res., 26:1906–1926.
24. Gupta, G., Bansal, M., and Sasiskharan, V., 1980. Proc. Natl. Acad. Sci. U.S.A., 77:6486–6490.
25. Shindo, H., Fujiwara, T., Akutsu, H., Masumoto, U., and Shimidzu, M., 1984. J. Mol. Biol., 174:221229
26. Sklenar, V., and Bax, A., 1987. J. Am. Chem. Soc., 109:7525–7526.
27. Gorenstein, D. G., 1992. Methods Enzymol., 211:254–286.
28. Gorenstein, D. G., 1994. Chem. Rev, 94:1315–1338.
29. Chou, S., Cheng, J., Fedoroff, O. Y., Chuprina, V. P., and Reid, B. R., 1992. J. Am. Chem. Soc., 114:3114–3115.
30. Tisné, C., Hantz, E., Hartmann, B., and Delepierre, M., 1998. J. Mol. Biol., 279:127–142.
31. Rüisser, S., Hallbruckerand, A., and Mayer, E., 1997. J Am. Chem. Soc., 119:12251–12256.
32. Lefebvre, A., Mauffret, O., Lescot, E., Hartmann, B., and Fermandjian, S., 1996. Biochemistry, 35:12560–12569.
33. Bertrand, H. O., Ha-Duong, T., Fermandjian, S., and Hartmann, B., 1998. Nucleic Acids Res., 26:1261–1267.
34. Cheatham, T. E., III and Kollman, P. A., 1997. J. Am. Chem. Soc., 119:4805–4825.
35. Young, M. A., Ravishanker, G., and Beveridge, D. L., 1997. Biophysical Journal, 73:2313–2336.
36. Winger, R. H., Liedl, K. R., Rüisser, S., Pichler, A., Hallbrucker, A., and Mayer, E., 1998. J. Phys. Chem. B, 102:8934–8940.
37. Pichler, A., Rüisser, S., Mitterböck, M., Huber, C. G., Winger, R. H., Liedl, K. R., Hallbrucker, A., and Mayer, E., 1999. Biophysical Journal accepted
38. Schneider, B., Neidle, S., and Berman, H. M., 1997. Biopolymers, 42:113–124.
39. Berman, H. M., 1997. Biopolymers, 44:23–44.
40. Hogan, M. E., and Jardetzky, O., 1979. Proc. Natl. Acad. Sci. U.S.A., 76:6341–6345.
41. Roongta, V. A., Jones, C. R., and Gorenstein, D. G., 1990. Biochemistry, 29:5245–5258.
42. Ravishanker, G., Auffnger, P., Langley, D. R., Jayaram, B., Young, M. A., and Beveridge, D. L., Reviews in Computational Chemistry Vol. 11, chapter Treatment of Counterions in Computer Simulations of DNA, pages 317–372 (Wiley-VCH, New York, 1997)
43. Young, M. A., Jayaram, B., and Beveridge, D. L., 1997. J. Am. Chem. Soc., 119:59–69.
44. Duan, Y., Wilkosz, P., Crowley, M., and Rosenberg, J. M., 1997. J. Mol. Biol., 272:553–572.
45. Sprous, D., Young, M. A., and Beveridge, D. L., 1998. J. Phys. Chem. B, 102:4658–4667.
46. Drew, H. R., Samson, S., and Dickerson, R. E., 1982. Proc. Natl. Acad. Sci. U.S.A., 79:4040–4044.
47. Wing, R., Drew, H., Takano, T., Broka, C., Tanaka, S., Itakura, K., and Dickerson, R. E., 1980. Nature, 287:755–758.
48. Drew, H. R., Wing, R. M., Takanao, T., Broka, C., Tanaka, S., Itakura, K., and Dickerson, R. E., 1981. Proc. Natl. Acad. Sci. U.S.A., 78:2179–2183.
49. Dickerson, R. E., and Drew, H. R., 1981. J. Mol. Biol., 149:761–786.
50. Drew, H. R., and Dickerson, R. E., 1981. J. Mol. Biol., 151:535–556.
51. Dickerson, R. E., and Drew, H. R., 1981. Proc. Natl. Acad. Sci. U.S.A., 78:7318–7322.
52. Fratini, A. V., Kopka, M. L., Drew, H. R., and Dickerson, R. E., 1982. J. Biol. Chem., 257:14686–14707.
53. Kopka, M. L., Fratini, A. V., Drew, H. R., and Dickerson, R. E., 1983. J. Mol. Biol., 163:129–146.
54. Westhof, E., 1987. J. Biomol. Struct. Dyn., 5:581–600.
55. Shui, X., McFail-Isom, L., Hu, G. G., and Williams, L. D., 1998. Biochemistry, 37:8341–8355.
56. Tereshko, V., Minasov, G., and Egli, M., 1999. J. Am. Chem. Soc., 121:470–471.
57. Lane, A. N., Jenkins, T. C., Brown, T., and Neidle, S., 1991. Biochemistry, 30:1372–1385.
58. Whitka, J. M., Swaminathan, S., Srinivasan, J., Beveridge, D. L., and Bolton, P. H., 1992. Science, 255:597–599.
59. Denisov, V. P., Carlstöm, G., Venu, K., and Halle, B., 1997. J. Mol. Biol., 268:118–136.
60. Robinson, B. H., Mailer, C., and Drobny, G., 1997. Annu. Rev. Biophys. Biomol. Struct., 26:629–658.
61. Hatcher, M. E., Mattiello, D. L., Meints, G. A., Orban, J., and Drobny, G. P., 1998. J. Am. Chem. Soc., 120:9850–9862.
62. Weidlich, T., Lindsay, S. M., Rui, Q., Rupprecht, A., Peticolas, W. L., and Thomas, G. A., 1990. J. Biomol. Struct. Dyn., 8:139–171.
63. Prévost, C., Louise-May, S., Ravishanker, G., Lavery, R., and Beveridge, D. L., 1993. Biopolymers, 33:335–350.
64. Swaminathan, S., Ravishanker, G., and Beveridge, D. L., 1991. J. Am. Chem. Soc., 113:5027–5040.
65. Miaskiewicz, K., Osman, R., and Weinstein, H., 1993. J. Am. Chem. Soc., 115:1526–1537.
66. Duan, Y., Wilkosz, P., and Rosenberg, J. M., 1996. J. Mol. Biol., 264:546–555.
67. Monaco, R. R., Polkosnik, W., and Dwarakanath, S., 1997. J. Biomol. Struct. Dyn., 15:63–67.
68. Cieplak, P., Cheatham, T. E., III and Kollman, P. A., 1997. J. Am. Chem. Soc., 119:6722–6730.
69. Packer, M., and Hunter, C., 1998. J. Mol. Biol., 280:407–420.
70. Arnott, S., Campbell-Smith, P. J., and Chandrasekaran, R., 1976. CRC Handbook of Biochemistry and Molecular Biology, chapter Atomic coordinates and molecular conformation for DNA-DNA, RNA-RNA, and DNA-RNA helices 411–422. Boca Raton:CRC Press. pages
71. Chandrasekaran, R., and Amott, S., 1996. J. Biomol. Struct. Dyn., 13:1015–1027.
72. Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheatham, T. E., III, Ferguson, D. M., Seibel, G. L., Singh, U. C., Weiner, P. K., and Kollman, P. A., 1995. AMBER 4.1. University of California San Francisco
73. Jorgensen, W. L., 1981. J. Am. Chem. Soc., 103:335–340.
74. Cornell, W. D., Cieplak, P., Bayly, C., Gould, I. R., Merz, K. M., Jr., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., and Kollman, P. A., 1995. J. Am. Chem. Soc., 117:5179–5197.
75. York, D. M., Wlodawer, A., Pedersen, L. G., and Darden, T. A., 1994. Proc. Natl. Acad. Sci. U.S.A., 91:8715–8718.
76. Cheatham, T., Miller, J., Fox, T., Darden, T., and Kollman, P., 1995. J. Am. Chem. Soc., 117:4193–4194.
77. Berendsen, H. J.C., Postma, J. P.M., van Gunsteren, W. F., DiNola, A., and Haak, J. R., 1984. J. Chem. Phys., 81:3684–3690.
78. Ravishanker, G., Swaminathan, S., Beveridge, D. L., Lavery, R., and Sklenar, H., 1989. J. Biomol. Struct. Dyn., 6:669–699.
79. Lavery, R., and Sklenar, H., 1988. J. Biomol. Struct. Dyn., 6:63–91.
80. Dickerson, R. E., Goodsell, D. S., and Kopka, M. L., 1996. J. Mol. Biol., 256:108–125.
81. Petsko, G. A., and Ringe, D., 1984. Annu. Rev. Biophys. Bioeng., 13:331–371.
82. Beckers, M. L.M., and Buydens, L. M.C., 1998. J. Comput. Chem., 19:695–715.
83. Poncin, M., Hartmann, B., and Lavery, R., 1992. J. Mol. Biol., 226:775–794.
84. Diekmann, S., 1989. J. Mol. Biol., 205:787–791.
85. Lefebvre, A., Fermandjian, S., and Hartmann, B., 1997. Nucleic Acids Res., 25:3855–3862.
86. Neidle, S., 1998. Nature Struct. Biol., 5:754–756.
87. Saenger, W., 1984. Principles of Nucleic Acid Structure New York, USA:(Springer.