Molecular Recognition between Oligopeptides and Nucleic Acids: Influence of van der Waals Contacts in Determining the 3'-Terminus of DNA Sequences Read by Monocationic Lexitropsins

Journal of the American Chemical Society

Volumn 110, Issue 11, 1988, Pages 3641-3649

  Lee, Moses ^a   Krowicki, Krzysztof ^a   Hartley, John A ^a   Lown, J William ^a   Pon, Richard T ^b  

^a UNIVERSITY OF ALBERTA   (Canada)

^b UNIVERSITY OF CALGARY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DECADEOXYNUCLEOTIDE; LEXITROPSIN; UNCLASSIFIED DRUG;

DNA BINDING; NONBIOLOGICAL MODEL; NONHUMAN; NUCLEAR MAGNETIC RESONANCE;

EID: 0023933991     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja00219a045     Document Type: Article

References (30)

1. (a) Caruthers, M. H. Acc. Chem. Res. 1980, 13, 155. (b) Frederick, C. A.; Grable, J.; Melia, M.; Samudzi, C.; Jen-Jacobson, L.; Wang, B. C.; Greene, P.; Boyer, H. W.; Rosenberg, J. W. Nature (London) 1984, 309, 327. (c) Gurskii, G. V.; Tumanyan, V. G.; Zavedatelev, A. S.; Zhyze, A. L.; Grokhovsky, S. L.; Gottikh, B. P. In Nucleic Acid-Protein Recognition; Vogel, H. J., Ed.; Academic: New York, 1977; p 189. (d) Kime, S. H.; Sussman, J. L.; Church, G. M. In Structure and Conformation of Nucleic Acids and Protein-Nucleic Acid Interactions; Sundaralingam, M., Rao, S. T., Eds.; University Park Press: Baltimore, MD, 1974; pp 571–575. (e) Takeda, Y.; Ohlendorf, D. H.; Anderson, W. F.; Matthews, B. W. Science 1983, 221, 1020.
2. (a) Lown, J. W.; Kowicki, K.; Bhat, U. G.; Skorobogaty, A.; Ward, B.; Dabrowiak, J. C. Biochemistry 1986, 25, 7408. (b) Patel, D. J.; Shapiro, L. J. Biol. Chem. 1986, 261, 1230. (c) Klevit, R. E.; Wemmer, D. E.; Reid, B. R. Biochemistry 1986, 25, 3296.
3. (a) Hahn, F. E. In Antibiotics III. Mechanism of Action of Antimicrobial and Antitumor Agents; Corcoran, J. W., Hahn, F. E., Eds.; Springer-Verlag: New York, 1975; pp 79–100. (b) Zimmer, C. Prog. Nucl. Acid Res. Mol. Biol. 1975, 15, 285. (c) Zimmer, C.; Wahnert, U. Prog. Biophys. Mol. Biol. 1986, 47, 31.
4. (a) Kopka, M. L.; Yoon, C.; Goodsell, D.; Pjurra, P.; Dickerson, R. E. Proc. Natl. Acad. Sci. U.S.A. 1985, 82, 1376. (b) Kopka, J. L.; Yoon, C.; Goodsell, D.; Pjurra, P.; Dickerson, R. E. J. Mol. Biol. 1985, 183, 553.
5. Pullman, B.; Pullman, A. Stud. Biophys. 1981, 86, 95.
6. Krowicki, K.; Lown, J. W. J. Org. Chem. 1987, 52, 3493.
7. Lee, M.; Chang, D.-K.; Hartley, J. A.; Pon, R. T.; Krowicki, K.; Lown, J. W. Biochemistry 1988, 27, 445.
8. (a) Patel, D. J. Proc. Natl. Acad. Sci. U.S.A. 1982, 79, 6424. (b) Gupta, G.; Sarma, M. H.; Sarma, R. H. J. Biomol. Struct. Dyn. 1984, 1, 1457.
9. Pullman, B.; Pullman, A.; Lavery, R. In Structure, Dynamics, Interactions and Evolution of Biological Macromolecules; Helene, C., Ed.; Reidel Publishing Co.: 1983; pp 23–44.
10. Kissinger, K.; Krowicki, K.; Dabrowiak, J. C.; Lown, J. W. Biochemistry 1987, 26, 5590.
11. Lee, M.; Hartley, J. A.; Pon, R. T.; Krowicki, K.; Lown, J. W. Nucleic Acids Res. 1988, 16, 665.
12. Lown, J. W.; Krowicki, K. J. Org. Chem. 1985, 50, 3774.
13. 6
14. Aue, W. P.; Bartholdt, E.; Ernst, R. R. J. Chem. Phys. 1976, 71, 2229.
15. (a) Macura, S.; Ernst, R. R. Mol. Phys. 1980, 41, 95. (b) Only certain of the NOESY correlations (CH5-CH6) of the complexes are observed at 21 °C. This is probably due to the increase in correlation time and cross-relaxation between many protons (see ref 24) and the exchange processes (see Discussion section).
16. Noggle, J. H.; Schirmer, R. D. The Nuclear Overhauser Effect: Chemical Applications; Academic: New York, 1971.
17. Lown, J. W.; Hanstock, C. C.; Imbach, J.-L.; Rayner, B.; Vasseur, J. J. J. Biomol. Struct. Dyn. 1985, 2, 1125.
18. (a) Hore, P. J. J. Magn. Reson. 1983, 55, 283. (b) Arnott, S.; Campbell-Smith, P. J.; Chandrasakasan, R. In Handbook of Biochemistry and Molecular Biology; Fassman, O. D., Ed.; CRC Press: Cleveland, Ohio, 1976; p 411.
19. James, T. L. Nuclear Magnetic Resonance in Biochemistry; Academic Press: New York, 1975; p 220.
20. (a) All results listed as data not shown are available on request from the authors, (b) Debart, F.; Rayner, B.; Imbach, J.-L.; Chang, D. K.; Lown, J. W. J. Biomol. Struct. Dyn. 1986, 4, 343.
21. Patel, D. J.; Pardi, A.; Itakura, K. Science 1982, 216, 581.
22. Marky, L. A.; Snyder, J. G.; Remeta, D. P.; Breslauer, K. J. In Biomolecular Stereodynamics; Sarma, R. H., Ed.; Academic Press: New York, 1983; Vol. 1, p 487.
23. Borah, B.; Roy, S.; Zon, G.; Cohen, J. S. Biochem. Biophys. Res. Commun. 1985, 133, 380.
24. (a) Kalk, A.; Berendsen, H. C. J. J. Magn. Reson. 1976, 24, 343. (b) All of the observed NOEs were assigned but some of them are not labeled so as to avoid crowding in Figure 4. The additional assignments are available for the interested reader, upon request, to the authors.
25. Frechet, D.; Cheng, D. M.; Kan, L. S.; Ts'O, P. O. P. Biochemistry 1983, 22, 5194.
26. 26afor a DNA belonging to the B family of conformations.
27. Hare, D. R.; Wemmer, D. E.; Chou, S. H.; Drobyn, G.; Reid, B. R. J. Mol. Biol. 1983, 171, 319.
28. Kearns, D. R. C. R. C. Crit. Rev. Biochem. 1984, 15, 237.
29. (a) Dalling, D. K.; Grant, D. M.; Johnson, L. F. J. Am. Chem. Soc. 1971, 93, 3678. (b) Shaw, D. Fourier Transform NMR Spectroscopy: Elsevier Scientific Publishing Co.: New York, 1976; pp 231–233.
30. Patel, D. J.; Canuel, L. L. Eur. J. Biochem. 1979, 96, 267.