Determination of the drug-DNA binding modes using fluorescence-based assays

Analytical Biochemistry

Volumn 422, Issue 2, 2012, Pages 66-73

  Williams, Alicia K ^a   Dasilva, Sofia Cheliout ^a   Bhatta, Ankit ^a   Rawal, Baibhav ^a   Liu, Melinda ^a   Korobkova, Ekaterina A ^a  

^a JOHN JAY COLLEGE OF CRIMINAL JUSTICE   (United States)

Author keywords

Antiprotozoal drug and antibiotic; Drug DNA interaction; Fluorescence; Food colorants; Intercalation; Minor groove; Nucleic acid; Tricyclic antidepressants

Indexed keywords

BINDING ENERGY; DRUG INTERACTIONS; FLUORESCENCE; INTERCALATION; NUCLEAR MAGNETIC RESONANCE; NUCLEIC ACIDS; QUENCHING;

DNA BINDING CONSTANT; DRUG-DNA INTERACTIONS; ENVIRONMENTAL POLLUTANTS; FOOD COLORANTS; MINOR GROOVES; NUCLEAR MAGNETIC RESONANCE(NMR); PARTITION COEFFICIENT; TRICYCLIC ANTIDEPRESSANTS;

DNA;

4',6 DIAMIDINO 2 PHENYLINDOLE; DNA; FLUORESCENT DYE; FLUORESCENT DYE TP3; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; BINDING KINETICS; CONTROLLED STUDY; DRUG DNA BINDING; FLUORESCENCE; FLUORESCENCE ANALYSIS; INTERCALATION COMPLEX; MINOR GROOVE BINDING; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PARTITION COEFFICIENT; PRIORITY JOURNAL; THYMUS;

EID: 84857924168     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2011.12.041     Document Type: Article

References (43)

1. P.R. Turner, and W.A. Denny The genome as a drug target: sequence specific minor groove binding ligands Curr. Drug Targets 1 2000 1 14
2. M. Zihlif, D.R. Catchpoole, B.W. Stewart, and L.P. Wakelin Effects of DNA minor groove binding agents on global gene expression Cancer Genet. Proteomics 7 2010 323 330
3. M.L. Kopka, C. Yoon, D. Goodsell, P. Pjura, and R.E. Dickerson The molecular origin of DNA-drug specificity in netropsin and distamycin Proc. Natl. Acad. Sci. USA 82 1985 1376 1380 (Pubitemid 15111056)
4. W.D. Wilson, L. Strekowski, F.A. Tanious, R.A. Watson, J.L. Mokrosz, A. Strekowska, G.D. Webster, and S. Neidle Binding of unfused aromatic cations to DNA: the influence of molecular twist on intercalation J. Am. Chem. Soc. 110 1988 8292 8299 (Pubitemid 19003111)
5. D.J. Patel 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. Natl. Acad. Sci. USA 79 1982 6424 6428 (Pubitemid 13207507)
6. W.D. Wilson, F.A. Tanious, H.J. Barton, R.L. Jones, L. Strekowski, and D.W. Boykin Binding of 4′,6-diamidino-2-phenylindole (DAPI) to GC and mixed sequences in DNA: intercalation of a classical groove-binding molecule J. Am. Chem. Soc. 111 1989 5008 5010 (Pubitemid 19166044)
7. D.S. Pilch, M.A. Kirolos, X. Liu, G.E. Plum, and K.J. Breslauer Berenil [1,3-bis(4′-amidinophenyl)triazene] binding to DNA duplexes and to a RNA duplex: evidence for both intercalative and minor groove binding properties Biochemistry 34 1995 9962 9976
8. K.W. Wan, T. Shibue, and M.L. Gross Non-covalent complexes between DNA-binding drugs and double-stranded oligodeoxynucleotides: a study by ESI ion-trap mass spectrometry J. Am. Chem. Soc. 122 2000 300 307 (Pubitemid 30061058)
9. H.-Z. Pan, X.-M. Wang, H.-B. Li, Q. Yang, and L.-S. Ding Interaction mode between congo red-Sm(III) complex and herring sperm DNA J. Coord. Chem. 63 2010 4347 4357
10. G. Manzini, M.L. Barcellona, M. Avitabile, and F. Quadrifoglio Interaction of diamidino-2-phenylindole (DAPI) with natural and synthetic nucleic acids Nucleic Acids Res. 11 1983 8861 8876
11. M. Kubista, B. Aakerman, and B. Norden Characterization of interaction between DNA and 4′,6-diamidino-2-phenylindole by optical spectroscopy Biochemistry 26 1987 4545 4553
12. T. Paramanathan, F. Westerlund, M.J. McCauley, I. Rouzina, P. Lincoln, and M.C. Williams Mechanically manipulating the DNA threading intercalation rate J. Am. Chem. Soc. 130 2008 3752 3753 (Pubitemid 351429832)
13. R. Krautbauer, L.H. Pope, T.E. Schrader, S. Allen, and H.E. Gaub Discriminating small molecule DNA binding modes by single molecule force spectroscopy FEBS Lett. 510 2002 154 158 (Pubitemid 34093816)
14. H. Kostrhunova, O. Vrana, and T. Suchankova Different features of the DNA binding mode of antitumor cis-amminedichlorido(cyclohexylamine)platinum(II) (JM118) and cisplatin in vitro Chem. Res. Toxicol. 23 2010 1833 1842
15. K. Bink, A. Walch, A. Feuchtinger, H. Eisenmann, P. Hutzler, H. Höfler, and M. Werner TO-PRO-3 is an optimal fluorescent dye for nuclear counterstaining in dual-colour FISH on paraffin sections Histochem. Cell Biol. 115 2001 S293 299 (Pubitemid 32323885)
16. B. Danielsson, I. Surugiu, A. Dzgoev, M. Mecklenburg, and K. Ramanathan Optical detection of pesticides and drugs based on chemiluminescence- fluorescence assays Anal. Chim. Acta 426 2001 227 234
17. D. Zink, N. Sadoni, and E. Stelzer Visualizing chromatin and chromosomes in living cells Methods 29 2003 42 50 (Pubitemid 36259911)
18. R. Dungaros, T. Turkbay, I. Surer, F. Gok, M. Denli, and V. Baltaci DNA damage in children treated with imipramine for primary nocturnal enuresis Pediatr. Int. 44 2002 617 621 (Pubitemid 35357027)
19. E.A. Korobkova, W. Ng, A. Vethatratnam, A.K. Williams, M. Nizamova, and N. Azar In vitro studies of DNA damage caused by tricyclic antidepressants: a role of peroxidase in side effects of the drugs Chem. Res. Toxicol. 23 2010 1497 1503
20. E.F. Healy Quantitative determination of DNA-ligand binding using fluorescence spectroscopy J. Chem. Educ. 84 2007 1304 1307
21. S. Rampal, M.-S. Liu, and F.-T.A. Chen Characterization of TO-PRO-3 as an intercalator for double-stranded DNA analysis with red diode laser-induced fluorescence detection J. Chromatogr. A 781 1997 357 365 (Pubitemid 27458730)
22. J. Kapuscinski, and B. Skoczylas Simple and rapid fluorimetric method for DNA microassay Anal. Biochem. 83 1977 252 257 (Pubitemid 8270706)
23. D. Suh, and J.B. Chaires Criteria for the mode of binding of DNA binding agents Bioorg. Med. Chem. 3 1995 723 728
24. H.P. Spielmann, P.A. Fagan, T.M. Bregant, R.D. Little, and D.E. Wemmer The binding modes of a rationally designed photoactivated DNA nuclease determined by NMR Nucleic Acids Res. 23 1995 1576 1583
25. H.A. Heck, N.W. Flynn, S.E. Buttrill Jr. , R.L. Dyer, and M. Anbar Determination of imipramine in plasma by high pressure liquid chromatography and field ionization mass spectrometry: increased sensitivity in comparison with gas chromatography mass spectrometry Biomed. Mass Spectrom. 5 1978 250 257 (Pubitemid 8294027)
26. M.F. Barakat, K. El-Salamawy, M. El-Banna, M. Abdel-Hamid, and A.A.-R. Taha Radiation effects on some dyes in non-aqueous solvents and in some polymeric films Radiat. Phys. Chem. 61 2001 129 136 (Pubitemid 32522426)
27. H. Waechter, D. Munzke, A. Jang, and H.-P. Loock Simultaneous and continuous multiple wavelength absorption spectroscopy on nanoliter volumes based on frequency-division multiplexing fiber-loop cavity ring-down spectroscopy Anal. Chem. 83 2011 2719 2725
28. H. Kuhn, H.-D. Försterling, and D. Hennessey Waldeck Principles of Physical Chemistry 2009 John Wiley New York
29. R. Russ, J. Rau, and A. Stolz The function of cytoplasmic flavin reductases in the reduction of azo dyes by bacteria Appl. Environ. Microbiol. 66 2000 1429 1434 (Pubitemid 30185613)
30. K.W. Ro, K. Lim, B.C. Shim, and J.H. Hahn Integrated light collimating system for extended optical-path-length absorbance detection in microchip-based capillary electrophoresis Anal. Chem. 77 2005 5160 5166 (Pubitemid 41140833)
31. N. Nikolaidis, C. Erkey, and B.F. Smets Hazardous and Industrial Wastes: Proceedings of the Thirty-first Mid-Atlantic Industrial and Hazardous Waste Conference 1999 Environmental Engineering Program University of Connecticut, Storrs, CT
32. N. Milanovich, M. Suh, R. Jankowiak, G.J. Small, and J.M. Hayes Binding of TO-PRO-3 and TOTO-3 to DNA: fluorescence and hole-burning studies J. Phys. Chem. 100 1996 9181 9186 (Pubitemid 126834634)
33. Y. Liu, and B. Danielsson Fluorometric broad-range screening of compounds with affinity for nucleic acids Anal. Chem. 77 2005 2450 2454 (Pubitemid 40562747)
34. R.P. Haugland M.T.Z. Spence, Handbook of Fluorescence Probes and Research Chemicals 1996 Molecular Probes Eugene, OR 153
35. 2 in solution studied by NMR Biochemistry 30 1991 1372 1385
36. R.D. Snyder, and M.R. Arnone Putative identification of functional interactions between DNA intercalating agents and topoisomerase II using the V79 in vitro micronucleus assay Mutat. Res. 503 2002 21 35 (Pubitemid 34614560)
37. R.D. Snyder, D.E. Ewing, and L.B. Hendry Evaluation of DNA intercalation potential of pharmaceuticals and other chemicals by cell-based and three-dimensional computational approaches Environ. Mol. Mutagen. 44 2004 163 173 (Pubitemid 39063345)
38. N.V. Hud, V. Sklenár, and J. Feigon Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending J. Mol. Biol. 286 1999 651 660 (Pubitemid 29106207)
39. G.M. Blackburn, M.J. Gait, D. Loakes, and D. Williams Nucleic Acids Chem. Biol. 2006 Royal Society of Chemistry Dorchester, UK pp. 361-370
40. M.A. Worley, M.H. Ivey, and D.C. Graves Characterization and cloning of Pneumocystis carinii nucleic acid J. Eukaryot. Microbiol. 36 1989 9S 11S (Pubitemid 19087359)
41. A. Nakabachi, A. Yamashita, H. Toh, H. Ishikawa, H.E. Dunbar, N.A. Moran, and M. Hattori The 160-kilobase genome of the bacterial endosymbiont Carsonella Science 314 2006 267 (Pubitemid 44571965)
42. Y. Cho, S. Gorina, P.D. Jeffrey, and N.P. Pavletich Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations Science 265 1994 346 355 (Pubitemid 24259959)
43. M.J. Rudolph, and J.P. Gergen DNA-binding by Ig-fold proteins Nat. Struct. Biol. 8 2001 384 386 (Pubitemid 32381279)