Spectrochimica Acta Part A 60 (2004) 129–136 Luminescence spectroscopic studies of trimethinecyanines substituted in polymethine chain with nucleic acids and proteins V.B. Kovalska, M.Yu. Losytskyy, S.M. Yarmoluk ∗ Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotnogo St., 03143 Kyiv, Ukraine Received 6 December 2002; received in revised form 8 April 2003; accepted 15 April 2003 Abstract The series of symmetrical -substituted and ,-substituted trimethinecyanine dyes were studied for their absorption and fluorescent charac- teristics in unbound state and in the presence of nucleic acids and proteins. It was shown that -substituted and ,-bridged trimethinecyanines containing extended heterocyclic systems or N-phenyl as well as N-cyclohexyl substituents demonstrate increased affinity to proteins. At the same time the presence of both N-phenyl and N-cyclohexyl substituents leads to the decrease of the dye fluorescence intensity in complexes with nucleic acids. For trimethinecyanines similarly to unsymmetrical monomethines the presence of N--hydroxy alkyl substituents results in the increase of fluorescence intensity of dye–DNA complex and the emission decrease of dye–RNA complex. © 2003 Elsevier B.V. All rights reserved. Keywords: Fluorescent detection; Trimethinecyanine dye; Nucleic acid; Protein 1. Introduction Cyanine dyes are used as staining reagents for the anal- ysis of nucleic acids and proteins in gel and capillary electrophoresis [1]. As a rule these dyes are monomethines. Unsymmetrical polymethine cyanines are also proposed for the deoxyribonucleic acid (DNA) detection [1]. Earlier we reported on -substituted and ,-bridged symmetric trime- thinecyanine dyes as the promising fluorescent probes for nucleic acids detection [2,3]. It is well-known that the hete- rocycles in the molecule of symmetrical trimethinecyanine are situated on the sizable distance from each other, and fluorescent planar all-trans conformation is the basic form for such dyes [4]. This causes the highly intensive emission of the dye. It was shown that incorporation of substituents into the polymethine chain leads to the loss of coplanarity of the dye molecule heterocycles and thus to the decrease of the fluorescence intensity of the dye (Fig. 1) [5]. Under the interaction with biopolymers the dye is fixed in planar con- formation and emission intensity significantly increases [6]. Trimethinecyanines substituted in polymethine chain in- crease their fluorescence intensity up to 100 times upon ∗ Corresponding author. Tel.: +380-44-252-2389; fax: +380-44-252-2458. E-mail address: otava@carrier.kiev.ua (S.M. Yarmoluk). binding with nucleic acids. Previously, the influence of the nature of substituent on the dye interaction with biopoly- mers and its spectroscopic manifestations were analyzed. It was shown that the binding of -substituted cyanines to dsDNA could occur via either intercalation or by fix- ation in a groove, the DNA-interaction mode for these dyes significantly depending on the nature of substituent in -position [2,3,7]. As a preferable mode of interaction of bridged trimethinecyanines with double-stranded (ds) DNA we proposed the groove binding [3]. In the present paper, a new series of nine benzothiazole and naphthathiazole trimethinecyanine dyes (Table 1) are studied for their spec- troscopic properties in the presence of nucleic acids and protein. The influence of substituents in polymethine chain and in heterocycles, as well as of N-alkyl substituents on these properties of the dyes is characterized. 2. Experimental 2.1. Material Anhydrous dimethylformamide (DMF) distilled under reduced pressure and 0.05 M Tris–HCl buffer (pH 8.0) were used as solvents. We are thankful to Dr A. Bogolyubskiy (ENAMINE, Kyiv, Ukraine) and Dr Yu. Slominskii (Insti- tute of Organic Chemistry, Kyiv, Ukraine) for granting the 1386-1425/$ – see front matter © 2003 Elsevier B.V. All rights reserved. doi:10.1016/S1386-1425(03)00187-2