Groove-binding unsymmetrical cyanine dyes for staining of DNA: Syntheses and characterization of the DNA-binding

Nucleic Acids Research

Volumn 31, Issue 21, 2003, Pages 6227-6234

  Karlsson, H Jonas ^a   Eriksson, Maja ^a   Perzon, Erik ^a   Åkerman, Björn ^a   Lincoln, Per ^a   Westman, Gunnar ^a  

^a CHALMERS UNIVERSITY OF TECHNOLOGY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

BENZOTHIAZOLE; BENZOXAZOLE DERIVATIVE; CYANINE DYE; DNA;

ARTICLE; CHEMICAL ANALYSIS; CHEMICAL INTERACTION; CHEMICAL STRUCTURE; CIRCULAR DICHROISM; CONTROLLED STUDY; DNA BINDING; DNA SEQUENCE; ELECTROPHORESIS; FLUORESCENCE ANALYSIS; PRIORITY JOURNAL; QUANTUM YIELD; STAINING;

ANIMALS; BENZOTHIAZOLES; CARBOCYANINES; CATTLE; CIRCULAR DICHROISM; DNA; DNA, SUPERHELICAL; FLUORESCENCE; FLUORESCENT DYES; MOLECULAR STRUCTURE; NUCLEIC ACID CONFORMATION; QUINOLINIUM COMPOUNDS; STAINING AND LABELING; THIAZOLES;

EID: 0344708496     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg821     Document Type: Article

References (52)

1. Dervan,P.B. (2001) Molecular recognition of DNA by small molecules. Bioorg. Med. Chem., 9, 2215-2235.
2. White,S., Szewczyk,J.W., Turner,J.M., Baird,E.E. and Dervan,P.B. (1998) Recognition of the four watson-crick base pairs in the DNA minor groove by synthetic ligands. Nature, 391, 468-471.
3. Wang,L., Bailly,C., Kumar,A., Ding,D., Bajic,M., Boykin,D.W. and Wilson,W.D. (2000) Specific molecular recognition of mixed nucleic acid sequences: An aromatic dication that binds in the DNA minor groove as a dimer. Proc. Natl Acad. Sci. USA, 97, 12-16.
4. Plouvier,B., Bailly,C., Houssin,R., Rao,K.E., Lown,W.J., Henichart,J.P. and Waring,M.J. (1991) DNA-sequence specific recognition by a thiazole analog of netropsin - a comparative footprinting study. Nucleic Acids Res., 19, 5821-5829.
5. Hurley,L.H. (2002) DNA and its associated processes as targets for cancer therapy. Nat. Rev. Cancer, 2, 188-200.
6. 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.
7. Jorgenson,K.F., Varshney,U. and van de Sande,J.H. (1988) Interaction of Hoechst 33258 with repeating synthetic DNA polymers and natural DNA. J. Biomol. Struct. Dyn., 5, 1005-1023.
8. Reddy,B.S.P., Sondhi,S.M. and Lown,J.W. (1999) Synthetic DNA minor groove-binding drugs. Pharmacol. Ther., 84, 1-111.
9. Kapuscinski,J. (1995) DAPI - a DNA-specific fluorescent-probe. Biotech. Histochem., 70, 220-233.
10. Kubista,M., Åkerman,B. and Nordén,B. (1987) Characterization of interaction between DNA and 4′,6-diamidino-2-phenylindole by optical spectroscopy. Biochemistry, 26, 4545-4553.
11. Frau,S., Bernadou,J. and Meunier,B. (1996) Hoechst 33258, a specific DNA minor groove binder. Bull. Soc. Chim. Fr., 133, 1053-1070.
12. Kapuscinski,J. (1990) Interactions of nucleic-acids with fluorescent dyes - spectral properties of condensed complexes. J. Histochem. Cytochem., 38, 1323-1329.
13. Robles,J. and McLaughlin,L.W. (1997) DNA triplex stabilization using a tethered minor groove binding Hoechst 33258 analogue. J. Am. Chem. Soc., 119, 6014-6021.
14. Darzynkiewicz,Z., Bruno,S., Delbino,G., Gorczyca,W., Hotz,M.A., Lassota,P. and Traganos,F. (1992) Features of apoptotic cells measured by flow-cytometry. Cytometry, 13, 795-808.
15. Cosa,G., Focsaneanu,K.S., McLean,J.R.N., McNamee,J.P. and Scaiano,J.C. (2001) Photophysical properties of fluorescent DNA-dyes bound to single- and double-stranded DNA in aqueous buffered solution. Photochem. Photobiol., 73, 585-599.
16. Larsson,A., Carlsson,C., Jonsson,M. and Albinsson,B. (1994) Characterization of the binding of the fluorescent dyes YO and YOYO to DNA by polarized light spectroscopy. J. Am. Chem. Soc., 116, 8459-8465.
17. Netzel,T.L., Nafisi,K., Zhao,M., Lenhard,J.R. and Johnson,I. (1995) Base-content dependence of emission enhancements, quantum yields and lifetimes for cyanine dyes bound to double stranded DNA: Photophysical properties of monomeric and bichromophoric DNA stains. J. Phys. Chem., 99, 17936-17947.
18. Rye,H.S., Yue,S., Wemmer,D.E., Quesada,M.A., Haugland,R.P., Mathies,R.A. and Glazer,A.N. (1992) Stable fluorescent complexes of double-stranded DNA with bis-intercalating asymmetric cyanine dyes: Properties and applications. Nucleic Acids Res., 11, 2803-2812.
19. Isacsson,J. and Westman,G. (2001) Solid-phase synthesis of asymmetric cyanine dyes. Tetrahedron Lett., 42, 3207-3210.
20. Kricka,L.J. (2002) Stains, labels and detection strategies for nucleic acids assays. Ann. Clin. Biochem., 39, 114-129.
21. Cosa,G., Focsaneanu,K.S., McLean,J.R.N. and Scaiano,J.C. (2000) Direct determination of single-to-double stranded DNA ratio in solution applying time-resolved fluorescence measurements of dye-DNA complexes. Chem. Commun., 689-690.
22. Gurrieri,S., Wells,K.S., Johnson,I.D. and Bustamante,C. (1997) Direct visualization of individual DNA molecules by fluorescence microscopy: Characterization of the factors affecting signal/background and optimization of imaging conditions using yoyo. Anal. Biochem., 249, 44-53.
23. Hirons,G.T., Fawcett,J.J. and Crissman,H.A. (1994) TOTO and YOYO: new very bright fluorochromes for DNA content analyses by flow cytometry. Cytometry, 15, 129-140.
24. Svanvik,N., Stahlberg,A., Sehlstedt,U., Sjoback,R. and Kubista,M. (2000) Detection of PCR products in real time using light-up probes. Anal. Biochem., 287, 179-182.
25. Svanvik,N., Westman,G., Wang,D. and Kubista,M. (2000) Light-up probes: Thiazol orange-conjugated peptide nucleic acid for detection of target nucleic acid in homogeneous solution. Anal. Biochem., 281, 26-35.
26. Petty,J.T., Bordelon,J.A. and Robertson,M.E. (2000) Thermodynamic characterization of the association of cyanine dyes with DNA. J. Phys. Chem. B, 104, 7221-7227.
27. Nygren,J., Svanvik,N. and Kubista,M. (1998) The interactions between the fluorescent dye thiazol orange and DNA. Biopolymers, 46, 39-51.
28. Rye,H.S. and Glazer,A.N. (1995) Interaction of dimeric intercalating dyes with single-stranded DNA. Nucleic Acids Res., 23, 1215-1222.
29. Lerman,L.S. (1961) Structural considerations in interaction of DNA and acridines. J. Mol. Biol., 3, 18-30.
30. Matsuzawa,Y. and Yoshikawa,K. (1994) Change of the higher-order structure in a giant DNA induced by 4′,6-diamidino-2-phenylindole as a minor-groove binder and ethidium-bromide as an intercalator. Nucleosides Nucleotides, 13, 1415-1423.
31. Perkins,T.T., Smith,D.E. and Chu,S. (1999) Flexible polymer chains in elongational flow. In Nguyen,T.Q. and Kausch,H.-H. (eds), Flexible Polymer Chains in Elongational Flow. Springer, pp. 283-334.
32. Yoshinaga,N., Akitaya,T. and Yoshikawa,K. (2001) Intercalating fluorescence dye YOYO-1 prevents the folding transition in giant duplex DNA. Biochem. Biophys. Res. Commun., 286, 264-267.
33. 2. Bioorg. Med. Chem., 11, 1035-1040.
34. Bengtsson,M., Karlsson,H.J., Westman,G. and Kubista,M. (2003) A new minor groove binding asymmetric cyanine reporter dye for real-time PCR. Nucleic Acids Res., 31, e45.
35. Eriksson,M., Karlsson,H.J., Westman,G. and Åkerman,B. (2003) Groove-binding unsymmetrical cyanine dyes for staining of DNA: dissociation rates in free solution and electrophoresis gels. Nucleic Acids Res., 31, 6235-6242.
36. Ayyangar,N.R. and Srinivasan,K.V. (1984) Effect of substituents in the formation of diacetanilides. Can. J. Chem., 62, 1292-1296.
37. Spitulnik,M.J. (1976) New general synthesis of 2-methylbenzothiazoles. Synthesis, 730-731.
38. Roche,D., Prasad,K., Repic,O. and Blacklock,T.J. (2000) Mild and regioselective oxidative bromination of anilines using potassium bromide and sodium perborate. Tetrahedron Lett., 41, 2083-2085.
39. Miyaura,N. and Suzuki,A. (1995) Palladium-catalyzed cross-coupling reactions of organoboron compounds. Chem. Rev., 95, 2457-2483.
40. West,W. and Pearce,S. (1965) The dimeric state of cyanine dyes. J. Phys. Chem., 69, 1894-1903.
41. Ogul'chansky,T.Y., Losytskyy,M.Y., Kovalska,V.B., Yashchuk,V.M. and Yarmoluk,S.M. (2001) Aggregation of monomethine cyanine dyes in presence of DNA and its manifestation in absorption and fluorescence spectra. Spectrochim. Acta A, 57, 1525-1532.
42. Nordén,B., Kubista,M. and Kurucsev,T. (1992) Linear dichroism spectroscopy of nucleic-acids. Q. Rev. Biophys., 25, 51-170.
43. Carlsson,C., Larsson,A., Jonsson,M., Albinsson,B. and Nordén,B. (1994) Optical and photophysical properties of the oxazole yellow DNA probes YO and YOYO. J. Phys. Chem., 98, 10313-10321.
44. Colson,P., Bailly,C. and Houssier,C. (1996) Electric linear dichroism as a new tool to study sequence preference in drug binding to DNA. Biophys. Chem., 58, 125-140.
45. Wilson,W.D., Tanious,F.A., Barton,H.J., Strekowski,L., Boykin,D.W. and Jones,R.L. (1989) 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, 5008-5010.
46. Lyng,R., Rodger,A. and Nordén,B. (1992) The CD of ligand-DNA systems 2. Poly(dA-dT) B-DNA. Biopolymers, 32, 1201-1214.
47. Kasatani,K., Ohashi,M., Kawasaki,M. and Sato,H. (1987) Cyanine dye-cyclodextrin systems - enhanced dimerization of the dye. Chem. Lett., 1633-1636.
48. Buss,V. (1991) Circular-dichroism of a chiral cyanine dye dimer trapped in gamma-cyclodextrin. Angew. Chem. Int. Ed. Engl., 30, 869-870.
49. Seifert,J.L., Connor,R.E., Kushon,S.A., Wang,M. and Armitage,B.A. (1999) Spontaneous assembly of helical cyanine dye aggregates on DNA nanotemplates. J. Am. Chem. Soc., 121, 2987-2995.
50. Garoff,R.A., Litzinger,E.A., Connor,R.E., Fishman,I. and Armitage,B.A. (2002) Helical aggregation of cyanine dyes on DNA templates: Effect of dye structure on formation of homo- and heteroaggregates. Langmuir, 18, 6330-6337.
51. Espejo,R.T. and Lebowitz,J. (1976) Simple electrophoretic method for determination of superhelix density of closed circular DNAs and for observation of their superhelix density heterogeneity. Anal. Biochem., 72, 95-103.
52. Keller,W. (1975) Characterization of purified DNA-relaxing enzyme from human tissue-culture cells. Proc. Natl Acad. Sci. USA, 72, 2550-2554.