By simple synthetic procedures were prepared various novel conjugates of cyanine dyes linked to amino acid side chains (Cy-aa), designed for easy incorporation into any position within peptide backbone. The proof of principle was confirmed by the first peptide-bond coupling with pyrene-fluorophore, to give peptidic cyanine-pyrene (Cy-aa-Pyr) conjugates. In general, all new conjugates revealed micromolar affinities toward ds-DNA or ds-RNA, accompanied by moderate thermal stabilization of polynucleotide double helix. However, conjugates showed recognition of various DNA or RNA secondary structures by two highly sensitive methods, fluorescence and CD spectropolarimetry. Detailed analysis of all results revealed several most important structural variations, which can be used for the fine tuning of DNA/RNA selectivity. The length of a linker between cyanine and amino acid is proportional to aggregation ability of a cyanine dye within polynucleotide binding site, at variance to addition of fluorine or chlorine on cyanine core, which hampered aggregation. Furthermore, fluorine or chlorine on cyanine switched the selectivity of fluorescence response in favour of GC-DNA, in respect to non-halogenated conjugates being fluorescently selective toward AU-RNA. Change of cyanine, from thiazole orange (TO) into oxazole yellow (YO), induced an Abstract Doctoral dissertation ii inversion of the induced CD sign only for GC-DNA, as a consequence of different aggregation pattern of Cy-aa within the DNA binding site. Two newly prepared cyanine-pyrene (Cy-aa-Pyr) conjugates proved the concept of linking two FRET-paired chromophores. The FRET-system was fluorescently silent in a free solution but selectively switched-on upon binding to the target (DNA, RNA, protein). Namely, the efficiency of FRET was dependent on DNA or RNA secondary structure, as well as on the structure of Cy-aa-Pyr conjugate. Moreover, FRET was only observed for protein (BSA) binding of one conjugate linked over quinoline moiety of cyanine, while its Cy-aa-Pyr analogue linked over benzothiazole remained FRET silent. Both Cy-aa-Pyr revealed strong fluorescence changes of pyrene for protein (BSA) binding and strong emission of cyanine only for DNA/RNA binding, thus behaving as double-headed fluoro-probes. Some of new conjugates were applicable also in in vitro staining experiments due to their low cytotoxicity and showed specific staining of mitochondria within living cells.