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The effect of various N,N ′-substituents in the molecule of benzothiazole trimethine cyanine dye on its ability to sense the amyloid aggregates of protein was studied. The dyes are low fluorescent when free and in the presence of monomeric proteins, but their emission intensity sharply increases in complexes with aggregated insulin and lysozyme, with the fluorescence quantum yield reaching up to 0.42. The dyes carrying butyl, hydroxyalkyl, and phenylalkyl groups as N,N ′-substituents possess the increased fluorescent sensitivity to fibrillar lysozyme, whereas the ones carrying quaternary amino groups are preferably sensitive to fibrillar insulin. This fluorescent sensitivity preference provided by the N,N ′-functional groups could be explained by the interaction between these groups and protein side chains. The strongest fluorescent response (up to 70 times) and the same sensitivity to aggregates of both proteins were exhibited by the dye D-51 carrying N -sulfoalkyl group. The studied cyanines allow the detection of fibrillar aggregates in the wide range up to 0.8 to 300 μg/ml and permit monitoring the protein aggregation kinetics with high reproducibility. The modification of trimethine cyanine dyes by functional substituents in N,N ′-positions is suggested as a tool for the design of fluorescent molecules with the enhanced fluorescent sensitivity to the fibrillar aggregates of proteins. [ABSTRACT FROM AUTHOR]