Formation of triplex rA/dA-containing nucleic acid helices induced by new thiazole orange analogues and their biological evaluation. H-aggregate formation conditioned by rA sequence

Abstract

A series of 3 dicationic monomethine cyanine dyes was synthesized in moderate yields, applying structural alternations with respect to both the peripheral carrier of additional possitive charge - cyclic amine (pyrrolidine or pyridine) and the introduction of a halogen atom (fluorine or chlorine) at position 6 of the benzothiazole moiety. Structural elucidation of the target fluorophores was achieved employing a combination of 1D, 2D-NMR spectroscopy and ESI mass spectrometry in both positive and negative mode.One of the main goals of current investigation was to examine the impact of the introduced steric and electronic properties on interactions with various DNA and RNA. The cyanine dyes induced the triplex formation of consecutive rA/dA-containing nucleic acid helices. In particular, the chlorinated cyanine 3 stabilized all three triplex helices (dAdTdT, rAdTdT, rArUrU) much stronger than corresponding duplex nucleic acid forms (dAdT, rAdT, rArU). The same derivative, showed a strong tendency for H-aggregate formation in the presence of rA chain in single-stranded, double-stranded, or triple-stranded forms. The three monomethines exerted a significant effect on all tumour cell lines' viability, especially towards HeLa and A549 cell lines (5–6 μM). Co-localization studies revealed that fluorophores 2 and 3 preferentially accumulate in mitochondria, which, in addition to their proven influence on cell viability, makes them promising therapeutic leads.