Minor-groove binding drugs: Where is the second hoechst 33258 molecule?

Journal of Physical Chemistry B

Volumn 117, Issue 19, 2013, Pages 5820-5830

  Fornander, Louise H ^a   Wu, Lisha ^a   Billeter, Martin ^b   Lincoln, Per ^a   Nordén, Bengt ^a  

^a CHALMERS UNIVERSITY OF TECHNOLOGY   (Sweden)

^b UNIVERSITY OF GOTHENBURG   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

DNA SEQUENCES; LIGANDS; MEDICAL APPLICATIONS; OLIGONUCLEOTIDES;

BINDING GEOMETRIES; BINDING MECHANISMS; BIOMEDICAL APPLICATIONS; DRUG CONCENTRATION; INTERACTION STUDIES; ISOTHERMAL TITRATION CALORIMETRY; OLIGONUCLEOTIDE DUPLEXES; PROTON NUCLEAR MAGNETIC RESONANCE;

MOLECULES;

EID: 84878055580     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp400418w     Document Type: Article

References (60)

1. Zimmer, C.; Wähnert, U. 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. 1986, 47, 31-112
2. Dickinson, L. A.; Gulizia, R. J.; Trauger, J. W.; Baird, E. E.; Mosier, D. E.; Gottesfeld, J. M.; Dervan, P. B. Inhibition of RNA Polymerase II Transcription in Human Cells by Synthetic DNA-Binding Ligands Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 12890-12895
3. Neidle, S. DNA Minor-Groove Recognition by Small Molecules Nat. Prod. Rep. 2001, 18, 291-309
4. Klug, A. The Discovery of Zinc Fingers and Their Development for Practical Applications in Gene Regulation and Genome Manipulation Q. Rev. Biophys. 2010, 43, 1-21
5. Liu, L.; Maguire, K. K.; Kmiec, E. B. Genetic Re-engineering of Saccharomyces cerevisiae RAD51 Leads to a Significant Increase in the Frequency of Gene Repair in Vivo Nucleic Acids Res. 2004, 32, 2093-2101
6. Belikov, S. V.; Grokhovsky, S. L.; Isaguliants, M. G.; Surovaya, A. N.; Gursky, G. V. Sequence-Specific Minor Groove Binding Ligands as Potential Regulators of Gene Expression in Xenopus laevis Oocytes J. Biomol. Struct. Dyn. 2005, 23, 193-202
7. Grokhovsky, S. L.; Surovaya, A. N.; Burckhardt, G.; Pismensky, V. F.; Chernov, B. K.; Zimmer, C.; Gursky, G. V. DNA Sequence Recognition by Bis-linked Netropsin and Distamycin Derivatives FEBS Lett. 1998, 439, 346-350
8. Dervan, P. B. Molecular Recognition of DNA by Small Molecules Bioorg. Med. Chem. 2001, 9, 2215-2235
9. Ojha, H.; Murari, B. M.; Anand, S.; Hassan, M. I.; Ahmad, F.; Chaudhury, N. K. Interaction of DNA Minor Groove Binder Hoechst 33258 with Bovine Serum Albumin Chem. Pharm. Bull. 2009, 57, 481-486
10. Joubert, A.; Sun, X.-W.; Johansson, E.; Bailly, C.; Mann, J.; Neidle, S. Sequence-Selective Targeting of Long Stretches of the DNA Minor Groove by a Novel Dimeric Bis-benzimidazole Biochemistry 2003, 42, 5984-5992
11. Baraldi, P. G.; Bovero, A.; Fruttarolo, F.; Preti, D.; Tabrizi, M. A.; Pavani, M. G.; Romagnoli, R. DNA Minor Groove Binders as Potential Antitumor and Antimicrobial Agents Med. Res. Rev. 2004, 24, 475-528
12. Chiang, S. Y.; Welch, J.; Rauscher, F. J.; Beerman, T. a Effects of Minor Groove Binding Drugs on the Interaction of TATA Box Binding Protein and TFIIA with DNA Biochemistry 1994, 33, 7033-7040
13. Downs, T. R.; Wilfinger, W. W. Fluorometric Quantification of DNA in Cells and Tissue Anal. Biochem. 1983, 131, 538-547
14. Goracci, L.; Germani, R.; Savelli, G.; Bassani, D. M. Hoechst 33258 as a pH-Sensitive Probe to Study the Interaction of Amine Oxide Surfactants with DNA ChemBioChem 2005, 6, 197-203
15. Barooah, N.; Mohanty, J.; Pal, H.; Sarkar, S. K.; Mukherjee, T.; Bhasikuttan, A. C. pH and Temperature Dependent Relaxation Dynamics of Hoechst-33258: a Time Resolved Fluorescence Study Photochem. Photobiol. Sci. 2011, 10, 35-41
16. Moon, J. H.; Kim, S. K.; Sehlstedt, U.; Rodger, a; Nordén, B. DNA Structural Features Responsible for Sequence-Dependent Binding Geometries of Hoechst 33258 Biopolymers 1996, 38, 593-606
17. Chaires, J. B. A Thermodynamic Signature for Drug-DNA Binding Mode Arch. Biochem. Biophys. 2006, 453, 26-31
18. 2 Duplex: Calorimetric and Spectroscopic Studies J. Mol. Biol. 1997, 271, 244-257
19. 2: Volumetric, Calorimetric, and Spectroscopic Characterizations Biochemistry 2005, 44, 9785-9794
20. Buurma, N. J.; Haq, I. Calorimetric and Spectroscopic Studies of Hoechst 33258: Self-association and Binding to Non-cognate DNA J. Mol. Biol. 2008, 381, 607-621
21. 2 Complex and Comparison with the X-ray Crystal Structure Structure (Cambridge, MA, U. S.) 1993, 1, 177-186
22. Pjura, P. E.; Grzeskowiak, K.; Dickerson, R. E. Binding of Hoechst 33258 to the Minor Groove of B-DNA J. Mol. Biol. 1987, 197, 257-271
23. Sauers, R. R. An Analysis of van der Waals Attractive Forces in DNA-Minor Groove Binding Bioorg. Med. Chem. 1995, 5, 2573-2576
24. Chang, D.; Cheng, S. On the Importance of van der Waals Interaction in the Groove Binding of DNA with Ligands: Restrained Molecular Dynamics Study Int. J. Biol. Macromol. 1996, 19, 279-285
25. Stella, S.; Cascio, D.; Johnson, R. C. The Shape of the DNA Minor Groove Directs Binding by the DNA-Bending Protein Fis Genes Dev. 2010, 24, 814-826
26. Abu-Daya, A.; Brown, P. M.; Fox, K. R. DNA Sequence Preferences of Several AT-Selective Minor Groove Binding Ligands Nucleic Acids Res. 1995, 23, 3385-3392
27. Loontiens, F. G.; Mclaughlin, L. W.; Diekmann, S.; Clegg, R. M. Binding of Hoechst 33258 and 4′,6-Diamidino-2-phenylindole to Self-Complementary Decadeoxynucleotides with Modified Exocyclic Base Substituents Biochemistry 1991, 30, 182-189
28. 4 DNA Sites with Kinetic Evidence for More Than One High-Affinity Hoechst 33258-AATT Complex J. Mol. Biol. 2002, 315, 1049-1061
29. Harshman, K. D.; Dervan, P. B. EDTA-Fe(II) Nucleic Acids Res. 1985, 13, 4825-4835
30. Loontiens, F. G.; Regenfuss, P.; Zechel, A.; Dumortier, L.; Clegg, R. M. 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 1990, 29, 9029-9039
31. Bazhulina, N. P.; Nikitin, A. M.; Rodin, S. A.; Surovaya, A. N.; Kravatsky, Y. V.; Pismensky, V. F.; Archipova, V. S.; Martin, R.; Gursky, G. V. Binding of Hoechst 33258 and Its Derivatives to DNA J. Biomol. Struct. Dyn. 2009, 26, 701-718
32. Teng, M.; Usman, N.; Frederick, C. A.; Wang, A. H.-J. The Molecular Structure of the Complex of Hoechst 33258 and the DNA Dodecamer d(CGCGAATTCGCG) Nucleic Acids Res. 1988, 16, 2671-2690
33. Quintana, J. R.; Lipanov, a a; Dickerson, R. E. Low-Temperature Crystallographic Analyses of the Binding of Hoechst 33258 to the Double-Helical DNA Dodecamer C-G-C-G-A-A-T-T-C-G-C-G Biochemistry 1991, 30, 10294-10306
34. Squire, C. J.; Baker, L. J.; Clark, G. R.; Martin, R. F.; White, J. Structures of M-iodo Hoechst-DNA Complexes in Crystals with Reduced Solvent Content: Implications for Minor Groove Binder Drug Design Nucleic Acids Res. 2000, 28, 1252-1258
35. 2 Duplex Nucleic Acids Res. 1994, 22, 1607-1612
36. Vega, M. C.; García Sáez, I.; Aymamí, J.; Eritja, R.; Van der Marel, G. a; Van Boom, J. H.; Rich, A.; Coll, M. Three-Dimensional Crystal Structure of the A-Tract DNA Dodecamer d(CGCAAATTTGCG) Complexed with the Minor-Groove-Binding Drug Hoechst 33258 Eur. J. Biochem. 1994, 222, 721-726
37. Tsunoda, M.; Sakaue, T.; Naito, S.; Sunami, T.; Abe, N.; Ueno, Y.; Matsuda, A.; Takénaka, A. Insights into the Structures of DNA Damaged by Hydroxyl Radical: Crystal Structures of DNA Duplexes Containing 5-Formyluracil J. Nucleic Acids 2010, 107289
38. 4) DNA Sequences Biochim. Biophys. Acta 2002, 1576, 136-142
39. 2 Chem. Commun. 1999, 1861-1862
40. Nordén, B.; Kubista, M.; Kuruscev, T. Linear Dichroism Spectroscopy of Nucleic Acids Q. Rev. Biophys. 1992, 25, 51-170
41. Norden, B.; Kubista, M. Linear Dichroism and Induced Circular Dichroism for Studying Structure and Interactions of DNA NATO ASI Ser., Ser. C 1988, 242, 133-165
42. Guan, Y.; Shi, R.; Li, X.; Zhao, M.; Li, Y. Multiple Binding Modes for Dicationic Hoechst 33258 to DNA J. Phys. Chem. B 2007, 111, 7336-7344
43. Kiser, J. R.; Monk, R. W.; Smalls, R. L.; Petty, J. T. Hydration Changes in the Association of Hoechst 33258 with DNA Biochemistry 2005, 44, 16988-16997
44. Freyer, M. W.; Buscaglia, R.; Hollingsworth, A.; Ramos, J.; Blynn, M.; Pratt, R.; Wilson, W. D.; Lewis, E. A. Break in the Heat Capacity Change at 303 K for Complex Binding of Netropsin to AATT Containing Hairpin DNA Constructs Biophys. J. 2007, 92, 2516-2522
45. Freyer, M. W.; Buscaglia, R.; Cashman, D.; Hyslop, S.; Wilson, W. D.; Chaires, J. B.; Lewis, E. A. Binding of Netropsin to Several DNA Constructs: Evidence for at Least Two Different 1:1 Complexes Formed from an AATT-containing ds-DNA Construct and a Single Minor Groove Binding Ligand Biophys. Chem. 2007, 126, 186-196
46. Kubista, M.; Akerman, B.; Norden, B. Induced Circular Dichroism in Nonintercalative DNA-Drug Complexes: Sector Rules for Structural Applications J. Phys. Chem. 1988, 92, 2352-2356
47. Harris, S. A.; Gavathiotis, E.; Searle, M. S.; Orozco, M.; Laughton, C. A. Cooperativity in Drug-DNA Recognition: a Molecular Dynamics Study J. Am. Chem. Soc. 2001, 123, 12658-12663
48. Cantor, C. R.; Schimmel, P. R. Biophysical Chemistry, Part III: The Behavior of Biological Macromolecules; W. H. Freeman & Co.: New York, 1980.
49. Nordén, B.; Rodger, A.; Dafforn, T. Linear Dichroism and Circular Dichroism: A Textbook on Polarized-Light Spectroscopy; Royal Society of Chemistry: Cambridge, U.K., 2010.
50. 1H NMR Biochemistry 1991, 30, 11377-11388
51. 2 Studied in Solution by NMR Spectroscopy Eur. J. Biochem. 1993, 211, 437-447
52. Poulin-Kerstien, A. T.; Dervan, P. B. DNA-Templated Dimerization of Hairpin Polyamides J. Am. Chem. Soc. 2003, 125, 15811-15821
53. Nordén, B.; Tjerneld, F. Optical Studies on Complexes between DNA and Pseudoisocyanine Biophys. Chem. 1976, 6, 31-45
54. Kubista, M.; Akerman, B.; Nordén, B. Characterization of Interaction between DNA and 4′,6-Diamidino-2-phenylindole by Optical Spectroscopy Biochemistry 1987, 26, 4545-4553
55. Jansen, K.; Nordén, B.; Kubista, M. Sequence Dependence of 4′,6-Diamidino-2-phenylindole (DAPI)-DNA Interactions J. Am. Chem. Soc. 1993, 115, 10527-10530
56. 2 Studied by CD, LD, and Normal Absorption Biochemistry 1996, 35, 1187-1194
57. 2: The Exocyclic Amino Group of Guanine Prevents Minor Groove Binding J. Am. Chem. Soc. 1993, 115, 12258-12263
58. Lyng, R.; Rodger, A.; Nordén, B. The CD of Ligand-DNA Systems. 2. Poly(dA-dT) B-DNA Biopolymers 1992, 32, 1201-14
59. White, S.; Szewczyk, J. W.; Turner, J. M.; Baird, E. E.; Dervan, P. B. Recognition of the Four Watson-Crick Base Pairs in the DNA Minor Groove by Synthetic Ligands Nature 1998, 391, 468-471
60. Dervan, P. B.; Edelson, B. S. Recognition of the DNA Minor Groove by Pyrrole-Imidazole Polyamides Curr. Opin. Struct. Biol. 2003, 13, 284-299