Association of the minor groove binding drug Hoechst 33258 with d(CGCGAATTCGCG)2: Volumetric, calorimetric, and spectroscopic characterizations

Biochemistry

Volumn 44, Issue 28, 2005, Pages 9785-9794

  Han, Feixue ^a   Taulier, Nicolas ^a   Chalikian, Tigran V ^a  

^a UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CALORIMETRY; DNA SEQUENCES; OLIGOMERS; SPECTROSCOPY; THERMODYNAMIC PROPERTIES; TITRATION; ULTRASONIC VELOCITY MEASUREMENT;

GROOVE BINDING; HIGH-PRECISION DENSIMETRY; ISOTHERMAL TITRATION; OLIGOMERIC DUPLEX;

DRUG PRODUCTS;

4 [5 (4 METHYL 1 PIPERAZINYL)[2,5' BI 1H BENZIMIDAZOL] 2' YL]PHENOL; DOUBLE STRANDED DNA;

ARTICLE; CIRCULAR DICHROISM; DENSITOMETRY; DNA DRUG COMPLEX; DRUG DNA BINDING; DRUG STRUCTURE; ENTHALPY; ENTROPY; FLUORESCENCE SPECTROSCOPY; HYDRATION; ISOTHERMAL TITRATION CALORIMETRY; PRIORITY JOURNAL; TEMPERATURE DEPENDENCE; THERMODYNAMICS; VOLUMETRY;

BINDING SITES; BISBENZIMIDE; CALORIMETRY; CIRCULAR DICHROISM; DENSITOMETRY; DNA; ENTROPY; MODELS, CHEMICAL; NUCLEIC ACID CONFORMATION; NUCLEIC ACID HETERODUPLEXES; OLIGONUCLEOTIDES; SPECTROMETRY, FLUORESCENCE; SPECTROPHOTOMETRY, ULTRAVIOLET; THERMODYNAMICS; ULTRASONICS;

EID: 22244467382     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi047374f     Document Type: Article

References (72)

1. Wemmer, D. E. (2000) Designed sequence-specific minor groove ligands, Annu. Rev. Biophys. Biomol. Struct. 29, 439-461.
2. Wemmer, D. E. (1999) Ligands recognizing the minor groove of DNA: Development and applications, Biopolymers 52, 197-211.
3. Haq, I., and Ladbury, J. (2000) Drug-DNA recognition: energetics and implications for design, J. Mol. Recognit. 13, 188-197.
4. Lohman, T. M., and Mascotti, D. P. (1992) Thermodynamics of ligand-nucleic acid interactions, Methods Enzymol. 212, 400-424.
5. Chaires, J. B. (1997) Energetics of drug-DNA interactions, Biopolymers 44, 201-215.
6. Latt, S. A., and Wohlleb, J. C. (1975) Optical studies of the interaction of 33258 Hoechst with DNA, chromatin, and metaphase chromosomes, Chromosoma 52, 297-316.
7. Wemmer, D. E., and Dervan, P. B. (1997) Targeting the minor groove of DNA, Curr. Opin. Struct. Biol. 7, 355-361.
8. 2 studied in solution by NMR spectroscopy, Eur. J. Biochem. 211, 437-447.
9. Neidle, S. (2001) DNA minor-groove recognition by small molecules, Nat. Prod. Rep. 18, 291-309.
10. 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.
11. Abu-Daya, A., Philip, M. B., and Fox, K. R. (1995) DNA sequence preferences of several AT-selective minor groove binding ligands, Nucleic Acids Res. 23, 3385-3392.
12. Jin, R., and Breslauer, K. J. (1988) Characterization of the minor groove environment in a drug-DNA complex: bisbenzimide bound to the poly[d(AT)]poly[d(AT)]duplex, Proc. Natl. Acad. Sci. U.S.A. 85, 8939-8942.
13. Steiner, R. F., and Sternberg, H. (1979) The interaction of Hoechst 33258 with natural and biosynthetic nucleic acids, Arch. Biochem. Biophys. 197, 580-588.
14. Loontiens, F. G., Regenfuss, P., Zechel, A., Dumortier, L., and Clegg, R. M. (1990) Binding characteristics of Hoechst 33258 with calf thymus DNA, poly[d(A-T)], and d(CCGGAATTCCGG): multiple stoichiometries and determination of tight binding with a wide spectrum of site affinities, Biochemistry 29, 9029-9039.
15. 2 duplex: calorimetric and spectroscopic studies, J. Mol. Biol. 271, 244-257.
16. Bailly, C., Colson, P., Henichart, J. P., and Houssier, C. (1993) The different binding modes of Hoechst 33258 to DNA studied by electric linear dichroism, Nucleic Acids Res. 21, 3705-3709.
17. 2, Nucleic Acids Res. 24, 4882-4889.
18. Teng, M., Usman, N., Frederick, C. A., and Wang, A. H. (1988) The molecular structure of the complex of Hoechst 33258 and the DNA dodecamer d(CGCGAATTCGCG), Nucleic Acids Res. 16, 2671-2690.
19. 2 duplex, Nucleic Acids Res. 22, 1607-1612.
20. 1H NMR, Biochemistry 30, 11377-11388.
21. Bunkenborg, J., Behrens, C., and Jacobsen, J. P. (2002) NMR characterization of the DNA binding properties of a novel Hoechst 33258 analogue peptide building block, Bioconjugate Chem. 13, 927-936.
22. Harshman, K. D., and Dervan, P. B. (1985) Molecular recognition of B-DNA by Hoechst 33258, Nucleic Acids Res. 13, 4825-4835.
23. Filfil, R., and Chalikian, T. V. (2003) The thermodynamics of protein-protein recognition as characterized by a combination of volumetric and calorimetric techniques: the binding of turkey ovomucoid third domain to á-chymotrypsin, J. Mol. Biol. 326, 1271-1288.
24. Filfil, R., and Chalikian, T. V. (2003) Volumetric and spectroscopic characterizations of glucose-hexokinase association, FEBS Lett. 554, 351-356.
25. Han, F., and Chalikian, T. V. (2003) Hydration changes accompanying nucleic acid intercalation reactions: Volumetric characterizations, J. Am. Chem. Soc. 125, 7219-7229.
26. Filfil, R., Ratavosi, A., and Chalikian, T. V. (2004) Binding of bovine pancreatic trypsin inhibitor to trypsinogen: spectroscopic and volumetric studies, Biochemistry 43, 1315-1322.
27. Lohman, T. M., and Mascotti, D. P. (1992) Nonspecific ligand-DNA equilibrium binding parameters determined by fluorescence methods, Methods Enzymol. 212, 424-458.
28. Qu, X., and Chaires, J. B. (2000) Analysis of drug-DNA binding data, Methods Enzymol. 321, 353-369.
29. Wiseman, T., Williston, S., Brandts, J. F., and Lin, L.-N. (1989) Rapid measurement of binding constants and heats of binding using a new titration calorimeter, Anal. Biochem. 179, 131-137.
30. Jelesarov, I., and Bosshard, H. R. (1999) Isothermal titration calorimetry and differential scanning calorimetry as complementary tools to investigate the energetics of biomolecular recognition, J. Mol. Recognit. 12, 3-18.
31. Ladbury, J. E., and Chowdhry, B. Z. (1996) Sensing the heat: the application of isothermal titration calorimetry to thermodynamic studies of biomolecular interactions, Chem. Biol. 3, 791-801.
32. Millero, F. J. (1971) The partial molal volumes of electrolytes in aqueous solutions, in Water and Aqueous Solutions (Home, R. A., Ed.) pp 519-595, John Wiley & Sons, New York.
33. Eggers, F., and Funck, T. (1973) Ultrasonic measurements with milliliter liquid samples in the 0.5-100 MHz range, Rev. Sci. Instrum. 44, 969-977.
34. Sarvazyan, A. P. (1982) Development of methods of precise ultrasonic measurements in small volumes of liquids, Ultrasonics 20, 151-154.
35. Eggers, F. (1992) Ultrasonic velocity and attenuation measurements in liquids with resonators, extending the MHz frequency-range, Acustica 76, 231-240.
36. Eggers, F., and Kaatze, U. (1996) Broad-band ultrasonic measurement techniques for liquids, Meas. Sci. Technol. 7, 1-19.
37. Chalikian, T. V., Plum, G. E., Sarvazyan, A. P., and Breslauer, K. J. (1994) 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 33, 8629-8640.
38. Barnatt, S. (1952) The velocity of sound in electrolytic solution, J. Chem. Phys. 20, 278-279.
39. Owen, B. B., and Simons, H. L. (1957) Standard partial molal compressibilities by ultrasonics. 1. Sodium chloride and potassium chloride at 25 °C, J. Phys. Chem. 61, 479-482.
40. Haq, I., Jenkins, T. C., Chowdhry, B. Z., Ren, J., and Chaires, J. B. (2000) Parsing free energies of drug-DNA interactions, Methods Enzymol. 323, 373-405.
41. Chaires, J. B. (1997) Possible origin of differences between van't Hoff and calorimetric enthalpy estimates, Biophys. Chem. 64, 15-23.
42. Manning, G. S. (1978) The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides, Q. Rev. Biophys. 11, 179-246.
43. Record, M. T., Anderson, C. F., and Lohman, T. M. (1978) Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity, Q. Rev. Biophys. 11, 103-178.
44. Chaires, J. B. (1996) Dissecting the free energy of drug binding to DNA, Anti-Cancer Drug Des. 11, 569-580.
45. Misra, V. K., Sharp, K. A., Friedman, R. A., and Honig, B. (1994) Salt effects on ligand-DNA binding. Minor groove binding antibiotics, J. Mol. Biol. 238, 245-263.
46. Mathieson, J. G., and Conway, B. E. (1974) Partial molal compressibilities of salts in aqueous solution and assignment of ionic contribution, J. Solution Chem. 3, 455-477.
47. Conway, B. E. (1978) Evaluation and use of properties of individual ions in solution, J. Solution Chem. 7, 721-770.
48. Pierotti, R. A. (1965) Aqueous solutions of nonpolar gases, J. Phys. Chem. 69, 281-288.
49. Stillinger, F. H. (1973) Structure in aqueous solutions of nonpolar solutes from the standpoint of scaled-particle theory, J. Solution Chem. 2, 141-158.
50. Pierotti, R. A. (1976) Scaled particle theory of aqueous and non-aqueous solutions, Chem. Rev. 76, 717-726.
51. Kharakoz, D. P. (1992) Partial molar volumes of molecules of arbitrary shape and the effect of hydrogen-bonding with water, J. Solution Chem. 21, 569-595.
52. Sarvazyan, A. P. (1991) Ultrasonic velocimetry of biological compounds, Annu. Rev. Biophys. Biophys. Chem. 20, 321-342.
53. Chalikian, T. V., Sarvazyan, A. P., and Breslauer, K. J. (1994) Hydration and partial compressibility of biological compounds, Biophys. Chem. 51, 89-107.
54. Chalikian, T. V., and Breslauer, K. J. (1998) Volumetric properties of nucleic acids, Biopolymers 48, 264-280.
55. Chalikian, T. V. (2003) Volumetric properties of proteins, Annu. Rev. Biophys. Biomol. Struct. 32, 207-235.
56. Buckin, V. A. (1987) Experimental studies of DNA-water interaction, Mol. Biol. 21, 512-525.
57. Chalikian, T. V., and Breslauer, K. J. (1998) Thermodynamic analysis of biomolecules: a volumetric approach, Curr. Opin. Struct. Biol. 8, 657-664.
58. Edward, J. T., and Farrell, P. G. (1975) Relation between van der Waals and partial molal volumes of organic-molecules in water, Can. J. Chem. 53, 2965-2970.
59. 2O, J. Am. Chem. Soc. 121, 1156-1163.
60. Richards, F. M. (1977) Areas, volumes, packing, and protein structure, Annu. Rev. Biophys. Bioeng. 6, 151-176.
61. Richards, F. M. (1985) Calculation of molecular volumes and areas for structures of known geometry. Methods Enzymol. 115, 440-464.
62. Connolly, M. L. (1983) Solvent-accessible surfaces of proteins and nucleic acids, Science 221, 709-713.
63. Dubins, D. N., Filfil, R., Macgregor, R. B., Jr., and Chalikian, T. V. (2000) Role of water in protein-ligand interactions: Volumetric characterization of the binding of 2′-CMP and 3′-CMP to ribonuclease A, J. Phys. Chem. B 104, 390-401.
64. Drew, H. R., Wing, R. M., Takano, T., Broka, C., Tanaka, S., Itakura, K., and Dickerson, R. E. (1981) Structure of a B-DNA dodecamer. Conformation and dynamics, Proc. Natl. Acad. Sci. U.S.A. 78, 2179-2183.
65. Chalikian, T. V. (2001) Structural thermodynamics of hydration, J. Phys. Chem. B 105, 12566-12578.
66. Chalikian, T. V., Völker, J., Srinivasan, A. R., Olson, W. K., and Breslauer, K. J. (1999) The hydration of nucleic acid duplexes as assessed by a combination of volumetric and structural techniques, Biopolymers 50, 459-471.
67. Sidorova, N. Y., and Rau, D. C. (1994) The osmotic sensitivity of Netropsin analogue binding to DNA, Biopolymers 35, 377-384.
68. Luque, I., and Freire, E. (1998) Structure-based prediction of binding affinities and molecular design of peptide ligands, Methods Enzymol. 295, 100-127.
69. Makhatadze, G. I., and Privalov, P. L. (1995) Energetics of protein structure, Adv. Protein Chem. 47, 307-425.
70. Rashin, A. A., and Bukatin, M. A. (1994) A view of thermodynamics of hydration emerging from continuum studies, Biophys. Chem. 51, 167-192.
71. Rashin, A. A., and Bukatin, M. A. (1994) Magnitude of hydration entropies of nonpolar and polar-molecules. J. Phys. Chem. 98, 386-389.
72. Haq, I. (2002) Thermodynamics of drug-DNA interactions, Arch. Biochem. Biophys. 403, 1-15.