Influence of Drug Binding on DNA Hydration: Acoustic and Densimetric Characterizations of Netropsin Binding to the Poly(dAdT)·Poly(dAdT) and Poly(dA)·Poly(dT) Duplexes and the Poly(dT)·Poly(dA)·Poly(dT) Triplex at 25 °C

Biochemistry

Volumn 33, Issue 29, 1994, Pages 8629-8640

  Chalikian, Tigran V ^a   Plum, G Eric ^a   Sarvazyan, Armen P ^a   Breslauer, Kenneth J ^a  

^a RUTGERS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONGOCIDINE; POLY(DEOXYADENYLATE DEOXYTHYMIDYLATE);

ARTICLE; CONFORMATIONAL TRANSITION; DNA CONFORMATION; DRUG DNA BINDING; HYDRATION; LIGAND BINDING; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; STRUCTURE ANALYSIS;

BIOPHYSICS; CIRCULAR DICHROISM; DNA; NETROPSIN; NUCLEIC ACID CONFORMATION; POLY DA-DT; POLYDEOXYRIBONUCLEOTIDES; SUPPORT, U.S. GOV'T, P.H.S.; WATER;

EID: 0028142863     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi00195a003     Document Type: Article

References (61)

1. Abraham, M. H., Liszi, J., & Papp, E. (1982) J. Chem. Soc., Faraday Trans. 1 78, 197–211.
2. Alexeev, D. G., Lipanov, A. A., & Skuratovskii, I. Ya. (1987) Nature 325, 821–823.
3. Barnatt, S. (1952) J. Chem. Phys. 20, 278–279.
4. Beveridge, D. L., Swaminathan, S., Ravishanker, G., Withka, J. M., Srinivasan, J., Prevost, C., Louise-May, S., Langley, D. R., DiCapua, F. M., & Bolton, P. H. (1993) in Topics in Molecular and Structural Biology, Vol. 17, Water and Biological Macromolecules (Westhof, E., Ed.) pp 165–225, The MacMillan Press, Ltd., London.
5. Bondi, A. (1964) J. Phys. Chem. 68, 441–451.
6. Breslauer, K. J. (1991) Curr. Opin. Struct. Biol. 1, 416–422.
7. Breslauer, K. J., Remeta, D. P., Chou, W.-Y., Ferrante, R., Curry, J., Zaunczkowski, D., Snyder, J. G., & Marky, L. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 8922–8926.
8. Breslauer, K. J., Ferrante, R., Marky, L. A., Dervan, P. B., & Youngquist, R. S. (1988) in Structure and Expression, Vol. 2: DNA and Its Drug Complexes (Sarma, R. H., & Sarma, M. H., Eds.) pp 273–289, Adenine Press, New York.
9. Buckin, V. A. (1987) Mol. Biol. (USSR) 21, 512–525.
10. Buckin, V. A., Sarvazyan, A. P., & Kharakoz, D. P. (1989) in Water in Disperse Systems (Deryagin, B. V., Churayev, N. V., & Ovcharenko, F. D., Eds.) pp 45–63, Chemistry, Moscow (in Russian).
11. Chalikian, T. V., & Sarvazyan A. P. (1991) in Sensors and Probes for Physico-Chemical Biology (Gaziev, A. I., Ed.) pp 104–114, Pushchino Research Center Publication, Pushchino, Russia (in Russian).
12. Chalikian, T. V., Sarvazyan, A. P., & Breslauer, K. J. (1993) J. Phys. Chem. 97, 13017–13026.
13. Chalikian, T. V., Sarvazyan, A. P., Funck, Th., & Breslauer, K. J. (1994a) Biopolymers 34, 541–553.
14. Chalikian, T. V., Sarvazyan, A. P., Plum, G. E., & Breslauer, K. J. (1994b) Biochemistry 33, 2394–2401.
15. Chalikian, T. V., Sarvazyan, A. P., & Breslauer, K. J. (1994c) Biophys. Chem. (in press).
16. Chevrier, B., Dock, A. C., Hartman, B., Leng, M., Moras, D., Thuong, M. T., & Westhof, E. (1986) J. Mol. Biol. 188, 707–719.
17. Chuprina, V. P. (1985) FEBS Lett. 186, 98–102.
18. Conway, B. E. (1978) J. Solution Chem. 7, 721–770.
19. Desnoyers, J. E., Verrall, R. E., & Conway, B. E. (1965) J. Chem. Phys. 43, 243–249.
20. Drew, H. R., & Dickerson, R. E. (1981) J. Mol. Biol 151, 535–556.
21. Eggers, F. (1992) Acustica 76, 231–240.
22. Eggers, F., & Funck, Th. (1973) Rev. Sci. Instrum. 44, 969–978.
23. Falk, M., Poole, A. G., & Goymour, C. G. (1970) Can. J. Chem. 48, 1536–1542.
24. Herrera, J. E., & Chaires, J. B. (1989) Biochemistry 28, 1993–2000.
25. Hirata, F., & Arakawa, K. (1973) Bull. Chem. Soc. Jpn. 46, 3367–3369.
26. Kennard, O., Cruse, W. B. T., Nachman, J., Prange, T., Shakked, Z., & Rabinovich, D. (1986) J. Biomol. Struct. Dyn. 3, 623–647.
27. Kharakoz, D. P. (1992) J. Solution Chem. 21, 569–595.
28. Kopka, M. L., Yoon, C., Goodsell, D., Pjura, P., & Dickerson, R. E. (1985) Proc. Natl. Acad. Sci. U.S.A. 82, 1376–1380.
29. Lawson, C. L., & Carey, J. (1993) Nature 366, 178–182.
30. Leslie, A. G. W., Arnott, S., Chandrasekaran, R., & Ratliff, R. L. (1980) J. Mol. Biol. 143, 49–72.
31. Marky, L. A., & Breslauer, K. J. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 4359–4363.
32. Marky, L. A., & Kupke, D. W. (1989) Biochemistry 28, 9982–9988.
33. Marky, L. A., & Macgregor, R. B., Jr. (1990) Biochemistry 29, 4805–4811.
34. Marky, L. A., Curry, J., & Breslauer, K. J. (1985) in Molecular Basis of Cancer (Rein, R., Ed.) pp 155–173, Liss, New York.
35. Mathieson, J. G., & Conway, B. E. (1974) J. Solution Chem. 3, 455–477.
36. Millero, F. J. (1972) in Water and Aqueous Solutions (Horne, R. A., Ed.) pp 519–595, John Wiley & Sons, Inc., New York.
37. Otwinowski, Z., Schevitz, R. W., Zhang, R.-G., Lawson, C. L., Joachimiak, A., Marmorstein, R. Q., Luisi, B. F., & Sigler, P. B. (1988) Nature 335, 321–329.
38. Owen, B. B., & Simons, H. L. (1957) J. Phys. Chem. 61, 479–482.
39. Park, Y.-W. (1992) Ph. D. Dissertation, Rutgers University, Piscataway, NJ.
40. Park, Y.-W., & Breslauer, K. J. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 6653–6657.
41. Patel, D. J. (1982) Proc. Natl. Acad. Sci. U.S.A. 79, 6424–6428.
42. Pilet, J., Blicharski, J., & Brahms, J. (1975) Biochemistry 14, 1869–1876.
43. Remeta, D. P., Mudd, C. P., Berger, R. L., & Breslauer, K. J. (1993) Biochemistry 32, 5064–5073.
44. Sarvazyan, A. P. (1982) Ultrasonics 20, 151–154.
45. Sarvazyan, A. P. (1991) Annu. Rev. Biophys. Biophys. Chem. 20, 321–342.
46. Sarvazyan, A. P., & Kharakoz, D. P. (1977) in Molecular and Cellular Biophysics (Frank, G. M., Ed.) pp 93–106, Publ. “Nauka”, Moscow (in Russian).
47. Sarvazyan, A. P., & Chalikian, T. V. (1991) Ultrasonics 29, 119–124.
48. Schneider, B., Cohen, D., & Berman, H. M. (1992) Biopolymers 32, 725–750.
49. Shiio, H., Ogawa, T., & Yoshihashi, H. (1955) J. Am. Chem. Soc. 77, 4980–4982.
50. Snell, F. D., & Snell, C. T. (1949) Colorimetric Methods of Analysis, Vol. 2, p 671, Van Nostrand, New York.
51. Takenaka, N., & Arakawa, K. (1989) Bull. Chem. Soc. Jpn. 62, 2880–2884.
52. Teplukhin, A. V., Poltev, V. I., & Chuprina, V. P. (1992) Biopolymers 32, 1445–1453.
53. Texter, J. (1978) Prog. Biophys. Mol. Biol. 33, 83–97.
54. Thomas, G. A., & Peticolas, W. L. (1983) J. Am. Chem. Soc. 105, 993–995.
55. Tunis, M.-J.B., & Hearst, J. E. (1968a) Biopolymers 6, 1325–1344.
56. Tunis, M.-J.B., & Hearst, J. E. (1968b) Biopolymers 6, 1345–1353.
57. Vesnaver, G., & Breslauer, K. J. (1990) in Proceedings of the 45th Calorimetry Conference, Ann Arbor, MI, July 22–27, 1990, p 60, University of Michigan Press, Ann Arbor, MI.
58. Wartell, R. M., Larson, J. E., & Wells, R. D. (1974) J. Biol. Chem. 249, 6719–6731.
59. Westhof, E. (1988) Annu. Rev. Biophys. Biophys. Chem. 17, 125–144.
60. Westhof, E., & Beveridge, D. L. (1989) in Water Science Reviews, Vol. 5 (Franks, F., Ed.) pp 24–136, Cambridge University Press, Cambridge, U.K.
61. Zimmer, C., & Wahnert, U. (1986) Prog. Biophys. Mol. Biol. 47, 31–112.