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Antitumour drug–DNA interactions: NMR studies of echinomycin and chromomycin complexes

Published online by Cambridge University Press:  17 March 2009

Xiaolian Gao  and
Dinshaw J. Patel
Xiaolian Gao
Affiliation:
Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons, Columbia University, New York, New York 10032
Dinshaw J. Patel
Affiliation:
Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons, Columbia University, New York, New York 10032
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Extract

The intelligent design of new families of DNA-binding antitumour agents must await an understanding at the molecular level of the structure, dynamics and energetics of drug-DNA interactions on currently available systems. Recent progress in this area has been significant and reflects the interplay between footprinting methods that identify the sequence specificity of drug binding, structural approaches that define conformational features in the crystalline and solution states, hydrogen exchange techniques that monitor transient base pair opening and calorimetric methods that partition the enthalpic and entropic contributions to the binding isotherm.

Type
Research Article
Information
Quarterly Reviews of Biophysics , Volume 22 , Issue 2 , May 1989 , pp. 93 - 138
Copyright
Copyright © Cambridge University Press 1989

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References

Baguley, B. C. (1982). Nonintercalative DNA-binding antitumour agents. Molec. and Cell Biochem. 43, 167–181.CrossRefGoogle Scholar
Behr, W., Hinkel, K. & Hartmann, G. (1969). Interaction of RNA polymerase inhibitor Chromomycin with DNA. Eur. J. Biochem. 9, 82–92.CrossRefGoogle ScholarPubMed
Berman, E., Brown, S. C., James, T. L. & Shaker, R. H. (1985). NMR Studies of Chromomycin A3 interaction with DNA. Biochemistry, 24, 6887–6893.CrossRefGoogle ScholarPubMed
Delbarre, A., Delepierre, M., D'Estaintot, B. L., Igolen, J. & Roques, B. P. (1987). Bisintercalation of Ditercalinium into a d(C-G-C-G) minihelix: Structure and dynamics aspects – A 400 MHz NMR study. Biopolymers 26, 1001–1033.CrossRefGoogle Scholar
Feigon, J., Denny, W. A., Leupin, W. & Kearns, D. R. (1984). Interactions of Antitumour Drugs with Natural DNA: Proton NMR study of binding mode and kinetics. J. mednl. Chem. 27, 450–465.CrossRefGoogle Scholar
Fox, K. R. & Howarth, M. R. (1985). Investigations into the sequence-selective binding of mithramycin and related ligands to DNA. Nucl. Acids Res. 13, 8695–8714.CrossRefGoogle ScholarPubMed
Fox, K. R. & Waring, M. J. (1986). Nucleotide sequence binding preferences of nogalamycin investigated by DNase I footprinting. Biochemistry 25, 4349–4356.CrossRefGoogle ScholarPubMed
Gao, X. & Patel, D. J. (1988). NMR studies of Echinomycin bisintercalation complexes with d(A1-C2-G3-T4) and d(Ti-C2-G3-A4) duplexes in aqueous solution: Sequence-dependent formation of Hoogsteen A1 T4 and Watson-Crick T1 A4 base pairs flanking the bisintercalation site. Biochemistry 27, 1744–1751.CrossRefGoogle Scholar
Gao, X. & Patel, D. J. (1989 a). NMR studies of Echinomycin bisintercalation complexes with the d(Gi-C2-G3-C4) duplex in solution. pH dependent switch between Watson-Crick and Hoogsteen G1-C4 base pairs flanking the bisintercalation site. Biochemistry, submitted for publication.Google Scholar
Gao, X. & Patel, D. J. (1989 b). NMR studies of the Echinomycin bisintercalation complex with the d(A-A-A-C-G-T-T-T) duplex in solution. Biochemistry, submitted for publication.Google Scholar
Gao, X. & Patel, D. J. (1989 c). Solution structure of the chromomycin-DNA complex. Biochemistry 28, 751–762.CrossRefGoogle ScholarPubMed
Gao, X. & Patel, D. J. (1989 d). NMR studies of site selectivity in chromomycin-DNA oligomer complexes. Biochemistry, submitted for publication.Google Scholar
Gause, G. F. (1975). Olivomycin, chromomycin and mithramycin. Antibiotics III (eds. Corcoran, J. W. & Hahn, F. E.), pp. 197–202. New York: Springer.Google Scholar
Haasnoot, C. A., Waterink, H. P., Van Der Marel, G. A. & Van Boom, J. H. (1984). Discrimination between A- and B-type conformations of double helical nucleic acid fragments in solution by two dimensional nuclear Overhauser experiments. J. Biomol. Str. Dyn. 2, 345–360.CrossRefGoogle ScholarPubMed
Kaziro, T. & Kamiyama, M. (1987). Mechanism of action of chromomycin A3. J. Biochem. 62, 424–439.CrossRefGoogle Scholar
Keller-Schierlein, W., Mihailovic, M. L. & Prelog, V. (1959). On the structure of echinomycin. Helv. chim. Acta. 42, 305–322.Google Scholar
Keniry, B. A., Brown, S.C., Berman, E. & Shafer, R. H. (1987). NMR studies of the interaction of Chromomycin A3 with small DNA duplexes. Biochemistry 26, 1058–1067.CrossRefGoogle ScholarPubMed
Kissinger, K., Krowicki, K., Dabrowiak, J. C. & Lown, J. W. (1987). Molecular recognition between oligopeptides and nucleic acids. Monocationic imidazole lexitropsins that display enhanced GC sequence dependent DNA binding. Biochemistry 26, 5590–5595.CrossRefGoogle ScholarPubMed
Klevitt, R. E., Wemmer, D. E. & Reid, B. R. (1985). Proton NMR studies of the interaction between distamycin A and a symmetrical DNA dodecamer. Biochemistry 25. 3296–3303.CrossRefGoogle Scholar
Kopka, M. L., Pjura, P. E., Goodsell, D. S. & Dickerson, R. E. (1987). Drugs and Minor Groove binding in B-DNA: Netropsin and Hoechst 33258. In Nucleic Acids and Molecular Biology, Vol. 1 (ed. Eckstein, F. and Lilley, D. M.) pp. 1–24. Berlin: Springer.CrossRefGoogle Scholar
Kopka, M. L., Yoon, C., Goodsell, D., Pjura, P. & Dickerson, R. E. (1985). Binding of an antitumour drug to DNA. Netropsin and C-G-C-G-A-A-T-T-brC-G-C-G. J. molec. Biol. 183, 553–563.CrossRefGoogle Scholar
Krugh, T. R. & Nuss, M. E. (1979). Nuclear magnetic resonance studies of drugnucleic acid complexes. In Biological Applications of Magnetic Resonance (ed. Shulman, R. G.), pp. 113–175. New York: Academic Press.CrossRefGoogle Scholar
Low, C. M., Drew, H. R. & Waring, M. J. (1984). Sequence-specific binding of echinomycin to DNA: Evidence for conformational changes affecting flanking sequences. Nucl. Acids Res. 12, 4865–4879.CrossRefGoogle ScholarPubMed
Mendel, D. & Dervan, P. (1987). Hoogsteen base pairs proximal and distal to echinomycin binding sites on DNA. Proc. natn. Acad. Sci. U.S.A. 84, 910–914.CrossRefGoogle ScholarPubMed
Miyamoto, M., Morita, K., Kawamatu, Y., Noguchi, S., Marumato, R., Tanaka, K., Tatsuoka, S., Nakanishi, K., Nakadaira, Y. & Bhacca, N. S. (1964). The structure of chromomycin A3. Tet. Lett. 2355–2377.CrossRefGoogle Scholar
Neidle, S. & Abraham, A. (1984). Structural and sequence dependent aspects of drug intercalation into nucleic acids. CRC Critical Reviews in Biochemistry 17, 73–121.CrossRefGoogle ScholarPubMed
Pabo, C. B. & Sauer, R. T. (1984). Protein-DNA recognition. A. Rev. Biochem. 53, 293–321.CrossRefGoogle ScholarPubMed
Patel, D. J. (1974). NMR investigations of complex formation between actinomycin D and d(A-T-G-C-A-T) in aqueous solution. Biochemistry 13, 2396–2402.CrossRefGoogle Scholar
Patel, D. J. (1979). NMR studies of drug-nucleic acid interactions at the synthetic DNA level in solution. Acct. chem. Res. 12, 118–125.CrossRefGoogle Scholar
Patel, D. J. (1982). Antibiotic-DNA interactions: Intermolecular nuclear Overhauser effects in the netropsin-d(C-G-C-G-A-A-T-T-C-G-C-G) complex in solution. Proc. natn. Acad. Sci. U.S.A. 79, 6424–6428.CrossRefGoogle ScholarPubMed
Patel, D. J. (1989). NMR studies of drug-DNA complexes in solution. In Nucleic Acids and Molecular Biology, Vol 4 (ed Eckstein, F. and Lilley, D. M.). Berlin: Springer, submitted for publication.Google Scholar
Patel, D. J. & Shapiro, L. (1985). Molecular recognition in noncovalent antitumour agent-DNA complexes: NMR studies of the base and sequence dependent recognition of the DNA minor groove by netropsin. Biochemie 67, 887–915.CrossRefGoogle Scholar
Patel, D. J., Kozlowski, S. A., Nordheim, A. & Rich, A. (1982). Right-handed and left-handed DNA: Studies of B- and Z-DNA using proton nuclear Overhauser effect and phosphorus NMR. Proc. natn. Acad. Sci. U.S.A. 79, 1413–1417.CrossRefGoogle Scholar
Patel, D. J., Shapiro, L. & Hare, D. (1987)- DNA and RNA: NMR studies of conformations and dynamics in solution. Q. Rev. Biophys. 20, 35–112.CrossRefGoogle ScholarPubMed
Petersheim, M., Mehdi, S. & Gerlt, J. A. (1984). A general procedure for assigning phosphorus spectra of nucleic acids. J. Am. chem. Soc. 106, 439–440.CrossRefGoogle Scholar
Portugal, J., Fox, K. R., McClean, M. J., Richenberg, J. L. & Waring, M. J. (1988). Diethyl pyrocarbonate can detect a modified DNA structure induced by the binding of quinoxaline antibiotics. Nucl. Acids Res. 16, 3655–3670.CrossRefGoogle ScholarPubMed
Quigley, G. J., Wang, A. H., Ughetto, G., Van Der Marel, G., Van Boom, J. H. & Rich, A. (1980). Molecular structure of an anticancer drug-DNA complex: Daunomycin plus d(C-G-T-A-C-G). Proc. natn. Acad. Sci. U.S.A. 77, 7204–7208.CrossRefGoogle Scholar
Quigley, G. J., Ughetto, G., van der Marel, G. A., van Boom, J. H., Wang, A. H. & Rich, A. (1986). Non-Watson-Crick G-C and A T base pairs in a DNA-antibiotic complex. Science 232, 1255–1258.CrossRefGoogle Scholar
Reid, B. R. (1987). Sequence specific assignments and their use in NMR studies of DNA structure. Q. Rev. Biophys. 20, 1–34.CrossRefGoogle ScholarPubMed
Searle, M. G., Hall, J. G., Denny, W. A. & Wakelin, L. P. (1988). NMR studies of the interaction of the antibiotic nogalamycin with the hexadeoxyribonucleotide duplex d(G-C-A-T-G-C). Biochemistry 27, 4340–4349.CrossRefGoogle Scholar
Singh, U. C., Pattabiraman, N., Langridge, R. & Kollman, P. A. (1986). Molecular mechanics studies of d(CGTACG)2: Complex of triostin A with the middle A-T base pairs in either Hoogsteen or Watson-Crick pairing. 2Proc. natn. Acad. Sci. U.S.A. 83, 6402–6406.CrossRefGoogle ScholarPubMed
Skarbek, J. D. & Speedie, M. K. (1981). Antitumour antibiotics of the auerolic acid group: Chromomycin, mithramycin and olivomycin. Antitumour Compounds of Natural Origin I (ed. Aszalos, A.), pp. 191–235. Boca Raton, Florida: CRC Press.Google Scholar
Thiem, J. & Meyer, B. (1979). Studies on the structure of Chromomycin A3 by proton and carbon NMR spectroscopy. J.C.S. Perkin Transactions II 1331–1336.CrossRefGoogle Scholar
Ughetto, G., Wang, A. H., Quigley, G. J., van der Marel, G. A., van Boom, J. H. & Rich, A. (1985). A comparison of the structure of echinomycin and triostin A complexed to a DNA fragment. Nucl. Acids Res. 13, 2305–2323.CrossRefGoogle ScholarPubMed
van de Ven, F. J. & Hilbers, C. W. (1988). Nucleic Acids and Nuclear Magnetic Resonance. Eur. J. Biochem. 178, 1–38.CrossRefGoogle ScholarPubMed
van Dyke, M. W. & Dervan, P. B. (1983). Chromomycin, mithramycin and olivomycin binding sites on heterogeneous DNA. Footprinting with (methidium-propyl-EDTA) iron (II). Biochemistry 22, 2373–2377.CrossRefGoogle Scholar
van Dyke, M. W. & Dervan, P. B. (1984). Echinomycin binding sites on DNA. Science 225, 1122–1127.CrossRefGoogle ScholarPubMed
Wade, W. S. & Dervan, P. B. (1987). Alteration of sequence specificity of distamycin on DNA by replacement of an N-methylpyrrole-carboxamide with pyridine-2-carboxamide. J. Am. chem. Soc. 109, 1574–1575.CrossRefGoogle Scholar
Wang, A. H. (1987). Interactions between antitumour drugs and DNA. In Nucleic Acids and Molecular Biology. Vol. I (ed. Eckstein, F. & Lilley, D. M.), pp. 53–69. Berlin: Springer.CrossRefGoogle Scholar
Wang, A. H., Ughetto, G., Quigley, G. J., Hakoshima, T., van der Marel, G. A., van Boom, J. H. & Rich, A. (1984). Molecular structure of the DNA-triostin complex. Science 225, 1115–1121.CrossRefGoogle ScholarPubMed
Ward, D. C., Reich, E. & Goldberg, I. H. (1965). Base specificity in the interaction of polynucleotides with antibiotic drugs. Science 149, 1259–1263.CrossRefGoogle ScholarPubMed
Waring, M. J. & Fox, K. K. (1983). Molecular aspects of the interaction between quinoxaline antibiotics and nucleic acids. In Molecular Aspects of Anticancer Drug Action (eds. Neidle, S. & Waring, M. J.), pp. 127–156. London: Macmillan.CrossRefGoogle Scholar
Waring, M. J. & Wakelin, L. P. (1974). Echinomycin: a bifunctional intercalating antibiotic. Nature 252, 653–657.CrossRefGoogle ScholarPubMed
Zimmer, C. H. & Wahnert, U. (1986). Nonintercalating drug-binding ligands: Specificity of interaction and their use as tools in biophysical, biochemical and biological investigations of genetic material. Prog. Biophys. molec. Biol. 47, 31–112.CrossRefGoogle Scholar