Characterizing the DNA binding modes of a topoisomerasei-poisoning terbenzimidazole: Evidence for both intercalative and minor groove binding properties

Drug Design and Discovery

Volumn 13, Issue 3-4, 1996, Pages 115-133

  Pilch, Daniel S ^a,b,c   Xu, Zhitao ^a   Sun, Qun ^a   Lavoie, Edmond J ^a,c   Liu, Leroy F ^b,c   Geacintov, Nicholas E ^d   Breslauer, Kenneth J ^a,c  

^a RUTGERS UNIVERSITY   (United States)

^b RUTGERS ROBERT WOOD JOHNSON MEDICAL SCHOOL   (United States)

^c RUTGERS CANCER INSTITUTE OF NEW JERSEY   (United States)

^d NEW YORK UNIVERSITY   (United States)

Author keywords

DNA base drug resonance energy transfer; Flow linear dichroism; Fluorescence quenching; F rster critical distance; Mixed mode DNA binding

Indexed keywords

DNA TOPOISOMERASE; POLY(DEOXYADENYLATE DEOXYTHYMIDYLATE); TERBENZIMIDAZOLE; UNCLASSIFIED DRUG;

COMPLEX FORMATION; CONFERENCE PAPER; DNA BINDING; DRUG STRUCTURE; ENERGY TRANSFER; LINEAR DICHROISM;

BENZIMIDAZOLES; BINDING SITES; BINDING, COMPETITIVE; CIRCULAR DICHROISM; DNA TOPOISOMERASES, TYPE I; NETROPSIN; POLY DA-DT; PROTEIN BINDING; SPECTROMETRY, FLUORESCENCE; SPECTROPHOTOMETRY, ULTRAVIOLET; VISCOSITY;

EID: 0030002584     PISSN: 10559612     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (49)

1. Wang, J.C. (1985) DNA Topoisomerases. Annu. Rev. Biochem., 54, 665-697.
2. Bodley, A.L. and Liu, L.F. (1988) Topoisomerases as Novel Targets for Cancer Chemotherapy. Biol Technology, 6, 1315-1319.
3. D'Arpa, P. and Liu, L.F. (1989) Topoisomerase-Targeting Antitumor Drugs. Biochim. Biophys. Acta, 989, 163-177.
4. Liu, L.F. (1989) DNA Topoisomerase Poisons as Antitumor Drugs. Annu. Rev. Biochem., 58, 351-375.
5. Schneider, E., Hsiang, Y.-H. and Liu. L.F. (1990) DNA Topoisomerases as Anticancer Drug Targets. Adv. Pharmacol., 21, 149-183.
6. Chen, A.Y. and Liu, L.F. (1994) DNA Topoisomerases: Essential Enzymes and Lethal Targets. Annu. Rev. Pharmacol. Toxicol., 34, 191-218.
7. Wilson, W.D. and Jones, R.L. (1981) Intercalating Drugs: DNA Binding and Molecular Pharmacology. Adv. Pharmacol. Chemother., 18, 177-222.
8. Neidle, S. and Abraham, Z. (1984) Structural and Sequence-Dependent Aspects of Drug Intercalation into Nucleic Acids. CRC Crit Rev. Biochem., 17, 73-121.
9. Baguley, B.C. (1991) DNA Intercalating Anti-Tumour Agents. Anti-Cancer Drug Des., 6, 1-35.
10. Gallo, R.C., Whang-Peng, J. and Adamson, R.A.H. (1971) Studies on the Antitumor Activity, mechanism of action, and cell cycle effects of camptothecin. J. Natl. Cancer Inst., 46, 789-795.
11. Giovanella, B.C., Stehlin, J.S., Wall, M.E., Wani, M.C., Nicholas, A.W., Liu, L.F., Silber, R. and Potmesil, M. (1989) DNA Topoisomerase I-Targeted Chemotherapy of Human Colon Cancer in Xenografts. Science, 246, 1046-1048.
12. Giovanella, B.C., Hinz, H.R., Kozielski, A.J., Stehlin, A.J., Jr., Silber, R. and Potmesil, M. (1991) Complete Growth Inhibition of Human Cancer Xenografts in Nude Mice by Treatment with 20-(S)-camptothecin. Cancer Res., 51, 3052-3055.
13. Hertzberg, R.P., Caranfa, M.J., Holdem, K.G., Jakas, D.R., Gallagher, G., Mattem, M.R., Mong, S.-M., Bartus, J.O., Johnson, R.K. and Kingsbury, W.D. (1989) Modification of the Hydroxy Lactone Ring of Camptothecin: Inhibition of Mammalian Topoisomerase I and Biological Activity. J. Med. Chem., 32, 715-720.
14. Jaxel, C., Kohn, K.W., Wani, M.C., Wall, M.E. and Pommier, Y. (1989) Structure-Activity Study of the Actions of Camptothecin Derivatives on Mammalian Topoisomerase I: Evidence for a Specific Receptor Site and a Relation to Antitumor Activity. Cancer Res., 49, 4385-4389.
15. Chen, A.Y., Yu, C., Bodley, A., Peng, L.F. and Liu, L.F. (1993) A New Mammalian DNA Topoisomerase I Poison Hoechst 33342: Cytotoxicity and Drug Resistance in Human Cell Cultures. Cancer Res., 53, 1332-1337.
16. Chen, A.Y., Yu, C., Gatto, B. and Liu, L.F. (1993) DNA Minor Groove-Binding Ligands: A Different Class of Mammalian DNA Topoisomerase I Inhibitors. Proc. Natl. Acad. Sci. USA, 90, 8131-8135.
17. Pjura, P.E., Grzeskowiak, K. and Dickerson, R.E. (1987) Binding of Hoechst 33258 to the Minor Groove of B-DNA. J. Mol Biol., 197, 257-271.
18. Teng, M.-K., Usman, N., Frederick, C.A. and Wang, A.H.J. (1988) The Molecular Structure of the Complex of Hoechst 33258 and the DNA dodecamer d(CGCGAATTCGCG). Nucleic Acids Res., 16, 2671-2690.
19. 2 by Hoechst 33258: A High Field NMR Study. Biochemistry, 29, 10181-10190.
20. 2 Complex and Comparison with the X-Ray Crystal Structure. Strucrure, 1, 177-186.
21. 2 Duplex. Nucleic Acids Res., 22, 1607-1612.
22. Sun, Q., Gatto, B., Yu, C., Liu, A., Liu, L.F. and LaVoie, E.J. (1994) Structure Activity of Topoisomerase I Poisons Related to Hoechst 33342. Bioorg. Med Chem. Lett., 4, 2871-2876.
23. Sun, Q., Gatto, B., Yu, C., Liu, A., Liu, L.F. and LaVoie, E.J. (1995) Synthesis and Evaluation of Terbenzimidazoles as Topoisomerase I Inhibitors. J Med. Chem., 38, 3638-3644.
24. Geacintov, N.E., Ibanez, V., Rougée, M. and Bensasson, R.V. (1987) Orientation and Linear Dichroism Characteristics of Porphyrin-DNA Complexes. Biochemistry, 26, 3087-3092.
25. Le Pecq, J.-B. and Paoletti, C. (1967) A Fluorescent Complex Between Ethidium Bromide and Nucleic Acids: Physical-Chemical Characterization. J. Mol. Biol., 27, 87-106.
26. Förster, T. (1948) Intermolecular Energy Transference and Fluorescence. Ann. Phys., 2, 55-75.
27. Förster, T. (1965) Delocalized Excitation and Excitation Transfer. In Modern Quantum Chemistry, Part III. Action of Light and Organic Crystals, edited by O. Sinanoglu, pp. 93-137. Academic Press: New York.
28. Cheung, H.C. (1991) Resonance Energy Transfer. In Topics in Fluorescence Spectroscopy, Volume 2: Principles, edited by J.R. Lakowicz, pp. 127-176. Plenum Press: New York.
29. Paoletti, J. and Le Pecq, J.-B. (1971) Resonance Energy Transfer Between Ethidium Bromide Molecules Bound to Nucleic Acids. J. Mol. Biol., 59, 43-62.
30. Daniels, M. (1973) Recent Developments in the Fluorescence of DNA Bases and DNA at 300 °K. In Physico-Chemical Properties of Nucleic Acids, Volume 1: Electrical, Optical and Magnetic Properties of Nucleic Acids and Components, edited by J. Duchesne, pp. 99-117. Academic Press: New York.
31. Crothers, D.M. (1971) Statistical Thermodynamics of Nucleic Acid Melting Transitions with Coupled Binding Equilibria. Biopolymers, 10, 2147-2160.
32. Snyder, J.G., Hartman, N.G., D'Estantoit, B.L., Kennard, O., Remeta, O.P. and Breslauer, K.J. (1989) Binding of Actinomycin D to DNA: Evidence for a Nonclassical High-Affinity Binding Mode that Does Not Require GpC Sites. Proc. Natl Acad. Sci. USA, 86, 3968-3972.
33. Wilson, W.D., Wang, Y.-H., Knshnamoorthy, C.R. and C., S.J. (1985) Poly(dA)• poly(dT) Exists in an Unusual Conformation Under Physiological Conditions: Propidium Binding to poly(dA)•poly(dT) and poly[d(A-T)]•poly[d(A-T)]. Biochemistry, 24, 3991-3999.
34. Breslauer, K.J., Remeta, D.P., Chou, W.-Y., Ferrante, R., Curry, J., Zaunczkowski, D., Snyder, J.G. and Marky, L.A. (1987) Enthalpy-Entropy Compensations in Drug-DNA Binding Studies. Proc. Natl. Acad. Sci USA, 84, 8922-8926
35. Herrera, J.E. and Chaires, J.B. (1989) A Premelting Conformational Transition in poly(dA)•poly(dT) Coupled to Daunomycin Binding. Biochemistry, 28, 1993-2000.
36. Scaria, P.V. and Shafer, R.H. (1991) Binding of Ethidium Bromide to a DNA Triple Helix: Evidence for Intercalation. J Biol. Chem., 266, 5417-5423.
37. Bauer, W. and Vinograd, J. (1970) Interaction of Closed Circular DNA with Intercalative Dyes: II. The Free Energy of Superhelix Formation in SV40 DNA. J. Mol. Biol., 47, 419-435.
38. Bresloff, J.L. and Crothers, D.M. (1975) DNA-Ethidium Reaction Kinetics: Demonstration of Direct Ligand Transfer Between DNA Binding Sites. J. Mol. Biol, 95, 103-123.
39. Sari, M.A., Battioni, J.P., Dupré, D, Mansuy, D. and Le Pecq, J.-B. (1986) Mode of Interaction and Apparent Binding Constants of Meso-tetraaryl Porphyrins Bearing Between One and Four Positive Charges with DNA. Biochem. Biophys Res Comm., 141, 643-649.
40. Rayner, D.M., Szabo, A.G.. Loutfy, R.O. and Yip, R.W. (1980) Singlet Energy Transfer Between Nucleic Acid Bases and Dyes in Intercalation Complexes. J. Phys. Chem., 84, 289-293.
41. Chaires, J.B. (1983) Equilibrium Studies on the Interaction of Daunomycin with Deoxypolynucleotides. Biochemistry. 22, 4204-4211.
42. Lakowicz, J.R. (1983) Principles of Fluorescence Spectroscopy. Plenum Press: New York.
43. Barton, J.K., Goldberg, J.M., Kumar, C.V. and Turro, N.J. (1986) Binding Modes and Base Specificity of Tris(phenanthroline)ruthenium(II) enantiomers with Nucleic Acids: Tuning the Stereoselectivity. J. Am. Chem. Soc., 108, 2081-2088.
44. Eftink, M.R. (1991) Fluorescence Quenching: Theory and Applications. In Topics in Fluorescence Spectroscopy, Volume 2 Principles, edited by J.R. Lakowicz, pp. 53-126. Plenum Press: New York.
45. Bloomfield, V.A., Crothers, D.M. and Tinoco, I., Jr. (1974) Physical Chemistry of Nucleic Acids, pp. 442-445. Harper & Row: New York.
46. Marky, L.A., Curry, J. and Breslauer, K.J. (1985) Netropsin Binding to polyd(AT)•polyd(AT) and to polydA•polydT: A Comparative Thermodynamic Study. In Molecular Basis of Cancer, Part B; Macromolecular Recognition, Chemotherapy, and Immunology, edited by R. Rein, pp. 155-173. Alan R. Liss, Inc : New York.
47. Zimmer, C. and Wähnert, U. (1986) Nonintercalating DNA-Binding Ligands: Specificity of the Interaction and Their Use as Tools in Biophysical, Biochemical and Biological Investigations of the Genetic Material. Prog. Biophys. Mol. Biol., 47, 31-112.
48. Marky, L.A. and Breslauer, K.J. (1987) Origins of Netropsin Binding Affinity and Specificity: Correlations of Thermodynamic and Structural Data. Proc. Natl. Acad. Sci. USA, 84. 4359-4363.
49. Durand, M., Thuong, N.T. and Maurizot, J.C. (1992) Binding of Netropsin to a DNA Triple Helix. J. Biol. Chem., 267, 24394-24399.