Dna multimode interaction with berenil and pentamidine; double helix stiffening, unbending and bending

Journal of Biomolecular Structure and Dynamics

Volumn 17, Issue 2, 1999, Pages 311-331

  Reinert, Karl Ernst ^a  

^a FRIEDRICH SCHILLER UNIVERSITY JENA   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ANTITRYPANOSOMAL AGENT; DIMINAZENE ACETURATE; DNA; PENTAMIDINE;

ARTICLE; CONFORMATIONAL TRANSITION; DNA CONFORMATION; DNA HELIX; DNA SEQUENCE; DNA STRUCTURE; DRUG DNA INTERACTION; LIGAND BINDING; PRIORITY JOURNAL; VISCOMETRY;

EUKARYOTA; ZIZIPHUS MAURITIANA;

EID: 0032738499     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.1999.10508364     Document Type: Article

References (98)

1. DeClercq, E., and Damm, O., 1980. J. Med. Chem., 23:787–795.
2. Sands, M., Kron, M. A., and Brown, R. B., 1985. Rev. Infect. Dis., 7:635–634.
3. Walzer, R. D., Kim, C. K., Foy, J., Linke, M. J., and Cushion, M. T., 1988. Antimicrob. Agents Chemother., 32:896–905.
4. Zimmer, C. h., and Wähnert, U., 1986. Progr. Biophys. Molec. Biol., 47:31–112.
5. Zimmer, C. h., and Luck, G., 1992. in. Advances in DNA Sequence Specific Agents, Vol., 1:51–88. JAI Press Ine
6. Neidle, S., and Waring, M. J., eds. 1993. Molecular Aspects of Anticancer Drug-DNA Interaction London:Macmillan Press.
7. Lown, J. W., 1993. Molecular Aspects of Anticancer Drug-DNA Interaction. Edited by:Neidle, S., and Waring, M. J., Vol. 1, 322–355. London:Macmillan.
8. Geierstanger, B. H., and Wemmer, D. E., 1995. Ann. Rev. Biophys. Biomol. Struct., 24:463–493.
9. Neidle, S., 1997. Biopolymers, 44:105–121.
10. Reinert, K. E., Stutter, E., Zimmer, Ch, and Lown, J. W., 1995. J. Biomolec. Str. & Dyn., 12:847–855.
11. Brown, D. G., Sanderson, M. R., Skelly, J. V., Jenkins, T. C., Brown, T., Garman, E., Stuart, D. I., and Neidle, S., 1990. EMBO J., 9:1329–1334.
12. Brown, D. G., Sanderson, M. R., Garman, E., and Neidle, S., 1992. J. Mol.Biol., 226:481–490.
13. Lane, A. N., Jenkins, T. C., Brown, T., and Neidle, S., 1991. Biochemistry, 30:1372–1385.
14. Jenkins, T. C., Lane, A. N., Neidle, S., and Brown, D. G., 1993. Eur. J. Biochem., 273:1175–1184.
15. Portugal, J., and Waring, M. J., 1987. Eur. J. Biochem., 167:281–289.
16. Abu-Daya, A., Brown, P. M., and Fox, K. R., 1995. Nucl. Acids Res., 23:3385–3392.
17. Schmitz, H. U., and Hübner, W., 1993. Biophysical Chemistry, 48:61–74.
18. Pilch, D. S., Kirolos, M. A., Liu, X. L., Plum, G. E., and Breslauer, K. J., 1995. Biochemistry, 34:9962–9976.
19. Newton, B. A., 1967. Biochem. J., 105:50P–51P.
20. Zimmer, C. h., Luck, G., Burckhardt, G., Krowicki, K., and Lown, J. W., 1988. Structure & Expression, Vol. 2:DNA and ist Drug Complexes Edited by:Sarma, R. H., and Sarma, M. H., 291303Adenine Press.
21. Luck, G., Zimmer, C. h., and Schweizer, D., 1988. Studia Biophysica, 125:107–119.
22. Edwards, K. J., Jenkins, T. C., and Neidle, S., 1992. Biochemistry, 31:7104–7109.
23. Tanford, C. h., 1961. Physical Chemistry of Macromolecules New York:J. Wiley & Sons.
24. Triebel, H., Reinert, K. E., and Strassburger, J., 1970. Studia Biophysica, 2:1–296. /22, 287
25. Reinert, K. E., 1972. J. Mol. Biol., 72:593–607.
26. Reinert, K. E., 1993. J. Biomolec. Struct. & Dyn., 10:973–990.
27. Reinert, K. E., Stutter, E., and Schweiß, H., 1979. Nucl. Acids Res., 7:1379–1392.
28. Reinert, K. E., Thrum, H., and Sarfert, E., 1980. Nucl. Acids Res., 8:5519–5531.
29. Reinert, K. E., Geller, D., and Stutter, E., 1981. Nucl. Acids Res., 9:2335–2349.
30. Reinert, K. E., 1981. Biophysical Chemistry, 13:1–14.
31. Reinert, K. E., Zimmer, C. h., and Arcamone, F., 1996. J. Biomolec Struct. & Dyn., 14:245–253.
32. Steinmetzer, K., and Reinert, K. E., 1998. J. Biomolec. Struct. & Dyn., 15:779–791.
33. Benfante, R., Landsberger, N., Tubiello, G., and Badaracco, G., 1989. Nucl. Acids Res., 17:8273–8282.
34. Beridze, T., Tsirekidze, N. T., and Roytberg, M. A., 1992. Biochimie, 74:187–194.
35. Brukner, I., Belmaaza, A., and Chartrand, P., 1997. Proc. Natl. Acad. Sci. USA, 94:403–406.
36. Lee, C.-H., and Charney, E., 1982. J. Mol. Biol., 101:289–303.
37. Reinert, K. E., Geller, K., and Burckhardt, G., 1991. J. Biomolec. Struct & Dyn., 9:537–552.
38. Reinert, K. E., 1991. J. Biomolec. Struct. & Dyn., 9:331–352.
39. Schnedl, W., Dann, O., and Schweizer, D., 1980. Eur. J. Cell. Biol., 20:290–296.
40. Reinert, K. E., 1973. “Physical Chemistry of Nucleic Acids” Edited by:Duchesne, J., Vol. 2, 319–356. London:Academic Press.
41. Schütz, H., Stutter, E., Weller, K., and Petri, I., 1984. Studia Biophysica, 104:23–34.
42. Hays, J. B., Magar, M., and Zimm, B. H., 1969. Biopolymers, 8:531–536.
43. Reinert, K. E., and Geller, K., 1974. Studia Biophysica, 45:1–11.
44. Gray, H. B., Bloomfield, V. A., and Hearst, J. E., 1967. J. Chem. Phys., 46:1494–1498.
45. Triebel, H., Reinert, K. E., and Straβburger, J., 1971. Biopolymers 10 2619–2621.
46. Hagerman, P. J., 1988. Ann. Rev. Biophys. Biophys. Chem., 17:265–286.
47. Reinert, K. E., Strassburger, J., and Triebel, H., 1971. Biopolymers, 10:285–307.
48. Reinert, K. E., Triebel, H., and Strassburger, J., 1972. Biochim. Biophys. Acta, 287:367–375.
49. Abu-Daya, A., and Fox, K. R., 1997. Nucl. Acids Res., 24:4962–4969.
50. Zimmer, C. h., Reinert, K. E., Luck, G., Wähnert, U., Löber, G., and Thrum, H., 1971. J. Mol. Biol., 58:329–3348.
51. Park, Y. W., and Breslauer, K. J., 1991. Proc. Natl. Acad. Sci. USA, 88:1551–1555.
52. Breslauer, K. J., 1991. Curr. Opin. Struct. Biol., 1:416–422.
53. Drew, H. R., and Travers, A. A., 1985. J. Mol. Biol., 186:773–790.
54. Malcolm, A. D.B., and Snounou, G., 1983. Cold Spring Habour Symp.Quant. Biol., 47:323–326.
55. Storl, K., Burckhardt, G., Lown, J. W., and Zimmer, C. h., 1993. FEBS Letters, 334:49–54.
56. Triebel, H., Bär, H., Walter, A., Burckhardt, G., and Zimmer, C. h., 1994. J. Biomolec. Struct. & Dyn., 11:1085–1105.
57. Triebel, H., Bär, H., Geuther, R., and Burckhardt, G., 1995. Progr.ColloidPolym.Sci., 99:45–54.
58. Reinert, K. E., 1983. Nucl. Acids Res., 11:3411–3430.
59. Klug, A., Jack, A., Visvamitra, M. A., Kennard, O., Shakked, Z., and Steitz, T. A., 1979. J. Mol. Biol., 131:669–680.
60. Zimmer, C. h., and Wähnert, U., 1990. Landoldt-Börnstein New Series, Group VII, Vol. 1, Nucleic Acids, Subvolume d. Physical Data II 61–193. Berlin:Springer-Verlag.
61. S, H., Koo, H.-M. Wu, and Crothers, D. M., 1986. Nature, 302:501–506.
62. Guerri, A., Simpson, I. J., and Neidle, S., 1998. Nucl. Acids Res., 26:2873–2878.
63. Ptashne, M., 1988. Nature, 335:683–689.
64. Schleif, R., 1992. Ann. Rev. Biochem., 61:199–223.
65. Claverie-Martin, F., and Magasanik, B., 1992. J. Mol. Biol., 227:996–1008.
66. Rippe, K., von Hippel, P. H., and Langowski, J., 1995. TIBS, 20:500–506.
67. Rippe, K., Guthold, M., von Hippel, P. H., and Bustamante, C., 1997. J. Mol.Biol., 270:125–138.
68. Brahms, G., Brahms, S., and Magasanik, B., 1995. J. Mol. Biol., 246:35–42.
69. Laundon, C. H., and Griffith, J. D., 1987. Biochemistry, 26:3759–3762.
70. Low, C. M.L., Drew, H. M., and Waring, M. J., 1986. Nucleic Acids Res., 14:6785–6801.
71. Travers, A., and Muskhelishvili, G., 1998. J. Mol. Biol., 279:1027–1043.
72. Kratky, O., and Porod, G., 1949. Revue Travaux Chim., 68:1106–1122.
73. Ye. Eizner, Y. u., and Ptitsyn, O. B., 1962. Vysokomol.Soedin., 4:1725
74. Hearst, J. E., and Stockmayer, W. H., 1962. J. Chem.Phys., 37:1425–1433.
75. Crothers, D. M., and Zimm, B. H., 1965. J. Mol. Biol., 12:525–536.
76. Ullman, R., 1968. J. Chem. Phys., 49:5486–5498.
77. Yamakava, H., and Fujii, M., 1974. Macromolecules, 7:128–135.
78. Marini, J. C., Levene, S. D., Crothers, D. M., and Englund, P. T., 1982. Proc. Natl. Acad. Sci. USA, 79:7664–7668.
79. Trifonov, E. N., 1985. CRC Crit. Revs. Biochem., 19:89–106.
80. Hagerman, P. J., 1990. Ann. Rev. Biochem., 59:755–781.
81. Schütz, H., and Reinert, K. E., 1991. J. Biomolec. Struct. & Dyn., 9:315–329.
82. Birshtein, T. M., 1966. Vysokomolek. Soedinen., 8:168–194.
83. Schellman, J. A., and Harvey, S. C., 1995. Biophysical Chemistry, 55:95–114.
84. Trifonov, E. N., Tan, R. K.-Z., and Harvey, S. C., 1987. Structure & Expression, Vol.3:DNA Bending and Curvature Edited by:Olson, W. K., Sarma, M. H., Sarma, R. H., and Sundaralingam, M., 243–253. Adenine Press.
85. Bednar, J., Furrer, P., Katritch, V., Stasiak, A. Z., Dubochet, J., and Stasiak, A., 1995. J. Mol. Biol., 254:579 594
86. Marini, J. C., Effron, P., Goodman, T., Singleton, C., Wells, R., Wartell, R., and Englund, P., 1984. J. Biol. Chem., 259:8974–8979.
87. Diekmann, S., 1987. Nucl. Acids Res., 15:247–265.
88. Shlyaktenko, L. S., Lyubchenko, Yu. L., Chernov, B. K., and Zhurkin, V. B., 1990. Molet Biol., 24:79–95.
89. Drew, H. R., and Dickerson, R. E., 1981. J. Mol. Biol., 151:535–556.
90. Alexeev, D. G., Lipanov, A. A., and Skuratovskii, I. Ya., 1987. Nature, 325:821–823.
91. Geller, K., and Reinert, K. E., 1980. Nucl. Acids Res., 8:2807–2822.
92. Lyubchenko, Yu. L., and Shlyaktenko, L. S., 1997. Proc. Natl. Acad. Sci. USA, 94:496–501.
93. Kielkopf, C. L., Baird, E. E., Dervan, P. B., and Rees, D. C., 1998. Nature Struct.Biol., 5:104–108.
94. Müller, W., and Crothers, D. M., 1968. J. Mol. Biol., 35:251–290.
95. Bloomfield, V. A., Crothers, D. M., and Tinoco, I., Jr. 1974. Physical Chemistry of Nucleic Acids 445New York:Harper & Row.
96. Cohen, G., and Eisenberg, H., 1969. Biopolymers 45–55.
97. +, however, it is conspicuously smaller (26,38)
98. The “relative solution viscosity” of Pilch et al. is an approximation for y = 1 + Δ y