Biopolym. Cell. 1999; 15(5):449-455.
Methods
Interaction of cyanine dyes with nucleic acids. 11. Synthesis and spectral properties of novel 2,6-dimcthyl-4-[(3-methyl-l,3-benzothiazol-3-ium-2-yl)methylene]-1,4-dihydro-1-pyridinium homodimer cyanine dyes
1Kocheshev I. A., 1Kovalska V. B., 1Yarmoluk S. M.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680

Abstract

A novel convenient method for cyanine homodimer dyes synthesis based on the reaction of primary amines with pirilium salts is proposed. The method allows to obtain homodimers with linkers of different length and chemical nature. Spectral-luminescent properties of the dyes synthesized and their complexes with nucleic acids, as well as a dependence of these properties on the length and nature of linker were studied. A novel homodimer K6 in complexes with DNA showed approximately 2000-fold increase in fluorescence intensity. We consider this dye to be perspective as a fluorescent probe for the nucleic acids detection.

References

[1] Gaugain B, Barbet J, Oberlin R, Roques BP, Le Pecq JB. DNA bifunctional intercalators. I. Synthesis and conformational properties of an ethidium homodimer and of an acridine ethidium heterodimer. Biochemistry. 1978;17(24):5071-8.
[2] Rye HS, Yue S, Wemmer DE, Quesada MA, Haugland RP, Mathies RA, Glazer AN. Stable fluorescent complexes of double-stranded DNA with bis-intercalating asymmetric cyanine dyes: properties and applications. Nucleic Acids Res. 1992;20(11):2803-12.
[3] Rye HS, Quesada MA, Peck K, Mathies RA, Glazer AN. High-sensitivity two-color detection of double-stranded DNA with a confocal fluorescence gel scanner using ethidium homodimer and thiazole orange. Nucleic Acids Res. 1991;19(2):327-33.
[4] Rye HS, Drees BL, Nelson HC, Glazer AN. Stable fluorescent dye-DNA complexes in high sensitivity detection of protein-DNA interactions. Application to heat shock transcription factor. J Biol Chem. 1993;268(33):25229-38.
[5] Goodwin PM, Johnson ME, Martin JC, Ambrose WP, Marrone BL, Jett JH, Keller RA. Rapid sizing of individual fluorescently stained DNA fragments by flow cytometry. Nucleic Acids Res. 1993;21(4):803-6.
[6] Carlsson C, Larsson A, Jonsson M, Norden B. Dancing DNA in capillary solution electrophoresis () Journal of the American Chemical Society. 1995;117 (13):3871-3872.
[7] Kryvorotenko D. V., Kovalska V. B., Yarmoluk S. M. The interaction of cyanine dyes with nucleic acids. 16. New fluorescent benzothiazole-4-[2,6-dimethylpyridinium] monomethyne cyanine dyes Biopolym. Cell, 2000;16(4):320-326
[8] Grinshteyn J, Vinits M. Chemistry of amino acids and peptides. Moscow: Mir, 1965. 465 p.
[9] Brooker L.G.S. Color and constitution. V. The absorption of unsymmetrical cyanines. Resonance as a basis for a classification of dyes. Journal of the American Chemical Society 1942; 64 (2):199-210.
[10] Rye HS, Glazer AN. Interaction of dimeric intercalating dyes with single-stranded DNA. Nucleic Acids Res. 1995;23(7):1215-22.
[11] Spielmann HP, Wemmer DE, Jacobsen JP. Solution structure of a DNA complex with the fluorescent bis-intercalator TOTO determined by NMR spectroscopy. Biochemistry. 1995;34(27):8542-53.
[12] Staerk D, Hamed AA, Pedersen EB, Jacobsen JP. Bisintercalation of homodimeric thiazole orange dyes in DNA: effect of modifying the linker. Bioconjug Chem. 1997;8(6):869-77.