Effects of minor and major groove-binding drugs and intercalators on the DNA association of minor groove-binding proteins RecA and deoxyribonuclease I detected by flow linear dichroism

European Journal of Biochemistry

Volumn 243, Issue 1-2, 1997, Pages 482-492

  Tuite, Eimer ^a   Sehlstedt, Ulrica ^a   Hagmar, Per ^a   Nordén, Bengt ^a   Takahashi, Masayuki ^b  

^a CHALMERS UNIVERSITY OF TECHNOLOGY   (Sweden)

^b INSTITUT CURIE   (France)

Author keywords

Circular dichroism; Deoxyribonuclease I; Linear dichroism; Protein DNA interactions; RecA protein

Indexed keywords

4',6 DIAMIDINO 2 PHENYLINDOLE; DEOXYRIBONUCLEASE I; DISTAMYCIN A; ETHIDIUM; ETHIDIUM BROMIDE; METHYL GREEN; METHYLENE BLUE; RECA PROTEIN;

ARTICLE; CIRCULAR DICHROISM; DNA BINDING; DNA STRUCTURE; IN VITRO STUDY; LIGAND BINDING; LINEAR DICHROISM; PRIORITY JOURNAL; PROTEIN NUCLEIC ACID INTERACTION;

EID: 0031019991     PISSN: 00142956     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1432-1033.1997.0482a.x     Document Type: Article

References (77)

1. Radding, C. M. (1989) Helical RecA nucleoprotein filaments mediate homologous pairing and strand exchange. Biochim. Biophys. Acta 1008, 131-145.
2. Smith, G. R. (1989) Homologous recombination in E. coli: multiple pathways for multiple reasons, Cell 58, 807-809.
3. Roca, A. I. & Cox, M. M. (1990) The RecA protein: structure and function, Crit. Rev. Biochem. Mol. Biol. 25, 415-456.
4. Little, J. W. & Mount, D. W. (1982) The SOS regulatory system of Escherichia coli, Cell 29, 11-22.
5. Baliga, R., Singleton, J. W. & Dervan, P. B. (1995) RecA · oligonucleotide filaments bind in the minor groove of double-stranded DNA, Proc. Natl Acad. Sci. USA 92, 10 393-10 397.
6. Podyminogin, M. A., Meyer, R. B. & Gamper, H. B. (1995) Sequence-specific covalent modification of DNA by cross-linking oligonucleotides. Catalysis by RecA and implication for the mechanism of synaptic joint formation, Biochemistry 34, 13 098-13 108.
7. Ullsperger, C. J. & Cox, M. M. (1995) Quantitative RecA protein binding to the hybrid duplex product of DNA strand exchange, Biochemistry 34, 10 859-10 866.
8. Di Capua, E., Engel, A., Stasiak, A. & Koller, Th. (1982) Characterization of complexes between RecA protein and duplex DNA by electron microscopy, J. Mol. Biol. 157, 87-103.
9. Williams, R. C. & Spengler, S. J. (1986) Fibers of RecA protein and complexes of RecA protein and single-stranded φX174 DNA as visualized by negative-stain electron microscopy, J. Mol. Biol. 187, 109-118.
10. Stasiak, A. & Di Capua, E. (1982) The helicity of DNA in complexes with RecA protein, Nature 299, 185-187.
11. Chrysogelos, A., Register, J. C. III & Griffith, J. (1983) The structure of recA protein-DNA filaments, J. Biol. Chem. 258, 12 624-12 631.
12. Pugh, B. F., Schutte, B. C. & Cox, M. M. (1989) Extent of duplex DNA underwinding induced by RecA protein binding in the presence of ATP, J. Mol. Biol. 205, 487-492.
13. Leahy, M. C. & Radding, C. M. (1986) Topography of the interaction of RecA protein with single-stranded deoxyoligonucleotides, J. Biol. Chem. 261, 6954-6960.
14. Di Capua, E. & Müller, B. (1987) The accessibility of DNA to dimethylsulfate in complexes with RecA protein. EMBO J. 6, 2493-2498.
15. Dombroski, D. F., Scraba, D. G., Bradley, R. D. & Morgan, A. R. (1983) Studies of the interaction of RecA protein with DNA. Nucleic Acids Res. 11, 7487-7504.
16. Yonesaki, T. & Minagawa, T. (1988) In vitro and in vivo recombination-related reactions of Escherichia coli recA protein and glucosyl-hydroxymethyl-deoxycytidine DNA, Mol. Gen. Genet. 213, 548-550.
17. Kumar, K. A. & Muniyappa, K. (1992) Use of structure-directed DNA ligands to probe the binding of RecA protein to narrow and wide grooves of DNA and on its ability to promote homologous pairing, J. Biol. Chem. 267, 24 824-24 832.
18. Broggini, M., Ponti, M., Ottolenghi, S., D'Incalci, M., Mongelli, N. & Mantovani, R. (1989) Distamycins inhibit the binding of OTF-1 and NFE-1 transfactors to their conserved DNA elements, Nucleic Acids Res. 17, 1051-1059.
19. Park, Y.-W. & Breslauer, K. J. (1992) Drug binding to higher ordered DNA structures: netropsin complexation with a nucleic acid triplex, Proc. Natl Acad. Sci. USA 89, 6653-6657.
20. Durand, M., Thuong, N. T. & Maurizot, J. C. (1992) Binding of netropsin to a DNA triple helix, J. Biol. Chem. 267, 24 394-24 399.
21. Oakley, M. G., Mrksich, M. & Dervan, P. B. (1992) Evidence that a minor groove-binding peptide and a major groove-binding protein can simultaneously occupy a common site on DNA, Biochemistry 31, 10 969-10 975.
22. Lahm, A. & Suck, D. (1991) DNase I-induced DNA conformation. 2 Å structure of a DNase I-octamer complex, J. Mol. Biol. 221, 645-667.
23. 2 complex at 2.3 Å resolution, J. Mol. Biol. 226, 1237-1256.
24. Lomosoff, G. P., Butler, P. J. G. & Klug, A. (1981) Sequence-dependent variation in the conformation of DNA, J. Mol. Biol. 149, 745-760.
25. Drew, H. R. (1984) Structural specificities of five commonly used DNA nucleases, J. Mol. Biol. 176, 535-557.
26. Drew, H. R. & Travers, A. A. (1984) DNA structural variations in the E. coli tyrT promoter, Cell 37, 491-502.
27. Drew, H. R. & Travers, A. A. (1985) Structural junctions in DNA: the influence of flanking sequence on nuclease digestion specificities, Nucleic Acids Res. 13, 4445-4467.
28. Hogan, M. E., Roberson, M. W. & Austin, R. H. (1989) DNA flexibility variation may dominate DNase I cleavage. Proc. Natl Acad. Sci. USA 86, 9273-9277.
29. Brukner, L. Jurukovski, V. & Savic, A. (1990) Sequence-dependent structural variations of DNA revealed by DNase I, Nucleic Acids Res. 18, 891-894.
30. Takahashi, M. & Hagmar, P. (1991) Use of ion-exchange chromatography for the study of RecA-DNA interaction, FEBS Lett. 279, 270-272.
31. Kuramitsu, S., Hamagushi, K., Ogawa, T. & Ogawa, H. (1981) A large scale preparation and some physicochemical properties of RecA protein, J. Biochem. (Tokyo) 90, 1033-1045.
32. Kim, S. K., Takahashi, M., Jernström, B. & Nordén, B. (1993) Enhancement of binding rate of RecA protein to DNA by carcinogenic benzo[a.pyrene derivatives and selective change of adduct conformation, Carcinogenesis 14, 311-313.
33. Lindberg, U. (1967) Molecular mass and amino acid composition of deoxyribonuclease I, Biochemistry 6, 335-342.
34. Chou, W. Y., Marky, L. A., Zaunczkowski, D. & Breslauer, K. J. (1987) The thermodynamics of drug-DNA interactions: ethidium bromide and propidium iodide, J. Biomol. Struct. Dyn. 5, 345-359.
35. Kim, S. K. & Nordén, B. (1993) Methyl Green. A DNA major-groove-binding drug, FEBS Lett. 315, 61-64.
36. Kapuscinski, J. & Skoczylas, B. (1978) Fluorescent complexes of DNA with DAPI 4′,6-diamidine-2-phenyl indole.2HCl or DCl 4′,6-dicarboxyamide-2-phenyl indole, Nucleic Acids Res. 5, 3775-3799.
37. Tuite. E. & Kelly. J. M. (1995) The interaction of methylene blue, azure B, and thionine with DNA: formation of complexes with polynucleotides and mononucleotides as model systems. Biopolymers 35, 419-433.
38. Takahashi, M., Kubista, M. & Nordén, B. (1989a) Binding of RecA protein to Z-form DNA studied with circular and linear dichroism spectroscopy. J. Biol. Chem. 264, 8568-8574.
39. Thresher, R. J. & Griffith, J. D. (1990) Intercalators promote the binding of RecA protein to double-stranded DNA. Proc. Natl Acad. Sci. U. S. A 87, 5056-5060.
40. Tuite, E., Kim, S. K., Nordén, B. & Takahashi, M. (1995) Effects of intercalators on complexation of RecA with duplex DNA, Biochemistry 34, 16 365-16 374.
41. Record, M. T., Anderson, C. F. & 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.
42. Hagmar, P., Pierrou, S., Nielsen, P., Nordén, B. & Kubista, M. (1992) Ionic strength dependence of the binding of methylene blue to chromatin and calf thymus DNA. J. Biomol. Struct. Dyn. 9, 667-679.
43. Nordén, B., Lincoln, P., Åkerman, B. & Tuite E. (1996) DNA interactions with substitution-inert metal complexes, in Metal ions in biological systems,vol. 33, Probing of nucleic acids by metal ion complexes of small molecules (Sigel, A. & Sigel, H., eds) pp. 177-252, Marcel Dekker, New York.
44. Tuite, E. & Nordén, B. (1994) Sequence-specific interactions of methylene blue with polynucleotides and DNA, J. Am. Chem. Soc. 116, 7548-7556.
45. Tuite, E. & Nordén, B. (1995) Methylene blue intercalates with triplex poly(dT),poly(dA) · poly(dT) but not duplex poly(dA) · poly(dT), J. Chem. Soc.m Chem. Commun. 53-54.
46. Wilson, W. D., Tanious, F. A., Barton, H. J., Jones, R. L., Fox, K., Wydra, R. L. & Strekowski, L. (1990) DNA sequence dependent binding modes of 4′,6-diamidino-2-phenylindole (DAPI), Biochemistry 29, 8452-8461.
47. Howe-Grant, M. & Lippard, S. J. (1979) Binding of platinum(II) intercalation reagents to deoxyribonucleic acid. Dependence on base-pair composition, nature of the intercalator, and ionic strength. Biochemistry 18, 5762-5769.
48. Takahashi, M., Kubista, M. & Nordén, B. (1989) Binding stoichiometry and structure of RecA-DNA complexes studied by flow linear dichroism and fluorescence spectroscopy. Evidence for multiple heterogeneous DNA co-ordination. J. Mol. Biol. 205, 137-147.
49. Kim, S. K., Nordén, B. & Takahashi, M. (1993) Role of DNA intercalators in the binding of RecA to double-stranded DNA, J. Biol. Chem. 268, 14 799-14 804.
50. Nordén, B. & Tjerneld, F. (1977) Binding of methyl green to deoxyribonucleic acid analysed by linear dichroism, Chem. Phys. Lett. 50, 508-512.
51. Takahashi, M., Kubista, M. & Nordén, B. (1991) Co-ordination of multiple DNA molecules in RecA fiber evidenced by linear dichroism spectroscopy, Biochimie 73, 219-226.
52. Hagmar, P., Nordén, B., Baty, D., Chartier, M. & Takahashi, M. (1992a) Structure of DNA-RecA complexes studied by residue differential linear dichroism and fluorescence spectroscopy for a genetically engineered RecA protein, J. Mol. Biol. 226, 1 193-1 205.
53. Nordén, B., Kubista, M. & Kurcsev, T. (1992) Linear dichroism spectroscopy of nucleic acids, Q. Rev. Biophys. 25, 51-170.
54. McEntee, K., Weinstock, G. M. & Lehman, I. R. (1981) Binding of the recA protein of Escherichia coli to single- and double-stranded DNA, J. Biol. Chem. 256, 8835-8844.
55. Blaho, J. A. & Wells, R. D. (1987) Left-handed Z-DNA binding by the RecA protein from Escherichia coli. J. Biol. Chem. 262, 6082-6088.
56. Lu, C., Scheurman, R. H. & Echols, H. (1986) Capacity of RecA protein to bind preferentially to UV lesions and inhibit the editing subunit (e) of DNA polymerase III: A possible mechanism for SOS-induced targeted mutagenesis, Proc. Natl Acad. Sci. USA 83, 619-623.
57. Sinicropi, D., Baker, D. L.; Prince, W. S., Shiffer, K. & Shak, S. (1994) Colorimetric determination of DNasel activity with a DNA-methyl green substrate. Anal. Biochem. 222, 351-358.
58. Gololobov, G. V., Chernova, E. A., Schourov D. V., Smirnov, I. V., Kudelina, I. A. & Gabibov, A. G. (1995) Cleavage of supercoiled plasmid DNA by autoantibody Fab fragment: application of the flow linear dichroism technique, Proc. Natl Acad. Sci. USA 92, 254-257.
59. Takahashi, M. & Ling, C. (1991) Use of fluorescent DNA analog for fluorometric detection of DNase activity. Anal. Biochem. 198, 246-249.
60. Yonemura, K. & Maeda, H. (1982) A new assay method for DNase by fluorescence polarization and fluorescence intensity using DNA-ethidium bromide complex as a sensitive substrate, J. Biochem. (Tokyo) 92, 1297-1303.
61. Bezanilla, M., Drake, B., Nudler, E., Kashlev, M., Hansma, P. K. & Hansma, H. G. (1994) Motion and enzymatic degradation of DNA in the atomic force microscope, Biophys. J. 67, 2454-2459.
62. Dahrowiak, J. C. & Goodisman, J. (1989) Quantitative footprinting analysis of drug-DNA interactions, in Chemistry and physics of DNA-ligand interactions (Kallenbach, N. R., ed.) pp. 143-175, Adenine Press, Schenectady NY.
63. Larsen, T. A., Goodsell, D. S., Cascio, D., Grzeskowiak, K. & Dickerson, R. E. (1989) The structure of DAPI hound to DNA, J. Biomol. Struct. Dyn. 7, 477-491.
64. Portugal, J. & Waring, M. (1988) Assignment of DNA binding sites for 4′,6-diamidine-2-phenylindole and bisbenzimide (Hoechst 33258). A comparative footprinting study, Biochim. Biophys. Acta 949, 158-168.
65. 2 determined by two-dimensional NMR, J. Am. Chem. Soc. 112, 1393-1399.
66. Carlsson, C., Jonsson, M. & Åkerman, B. (1995) Double bands in DNA gel electrophoresis caused by bis-intercalating dyes, Nucleic Acids Res. 23, 2413-2420.
67. Pugh, B. F. & Cox, M. M. (1988) General mechanism for RecA protein binding to duplex DNA, J. Mol. Biol. 203, 479-493.
68. Kubista, M., Tukahshi, M & Nordén, B. (1990) Stoichiometry, base orientation, and nuclease accessibility of RecA · DNA complexes seen by polarized light in flow-oriented solution. Implications for the mechanism of genetic recombination, J. Biol. Chem. 265, 18 891-18 897.
69. Kim, S. K., Tukahashi, M. & Nordén, B. (1995) Binding of RecA to anti-parallel poly(dA) · 2poly(dT) triple helix DNA, Biochim. Biophys. Acta 1264, 129-133.
70. Maher, L. J. III, Wold, B. & Dervan, P. B. (1989) Inhibition of DNA binding proteins by oligonucleotide-directed triple helix formation. Science 245, 725-730.
71. François, J.-C., Saison-Behmoaras, T., Thuong, N. T. & Hélène, C. (1989) Inhibition of restriction endonuclease cleavage via triple helix formation by homopyrimidine oligonucleotides, Biochemistry 28, 9617-9619.
72. Nordén, B., Tjerneld, F. & Palm, E. (1978) Linear dichroism studies of binding site structures in solution. Complexes between DNA and basic arylmethane dyes, Biophys. Chem. 8, 1-15.
73. Kubista, M., Åkerman, B. & Nordén, B. (1987) Characterization of interaction between DNA and 4′,6-diamidino-2-phenyl-indole by optical spectroscopy, Biochemistry 26, 4545-4553.
74. Jeppesen, C. & Nielsen, P. E. (1989) Photofootprinting of drug-binding sites on DNA using diazo- and azido-9-acridine derivatives, Eur. J. Biochem. 182, 437-444.
75. Lee, M., Rhodes, A. L., Wyatt, M. D., Forrow, S. & Hartley, J. A. (1993) GC base specific recognition by oligo(imidazole-carboxamide) and C-terminus-modified analogues of distamycin deduced from circular dichroism, proton nuclear magnetic resonance, and methidiumpropylethylenediaminetetraacetate-iron(II) footprinting studies, Biochemistry 32, 4237-4245.
76. Bresloff, J. L. & Crothers, D. M. (1981) Equilibrium studies of ethidium-polynucleotide interactions, Biochemistry 20, 3547-3553.
77. Becker, M. M. & Dervan, P. B. (1979) Molecular recognition of nucleic acid by small molecules. Binding affinity and structural specificity of bis(methidium)spermine, J. Am. Chem. Soc. 101, 3664-3666.