Bioaggregachromism of Asymmetric Monomethine Cyanine Dyes as Noncovalent Binders for Nucleic Acids

Two new asymmetric monomethine cyanine dyes, featuring dimethoxy quinolinium or methyl quinolinium end groups and benzothiazole or methyl benzothiazole end groups were synthesized. The chemical structures of the two dyes-(<i>E</i>)-6,7-dimethoxy-1-methyl-4-((3-methylbenzo[d]thiazol-2(3H)-ylidene)methyl)quinolin-1-ium iodide (<b>3a</b>) and (<i>E</i>)-4-((3,5-dimethylbenzo[d]thiazol-2(3H)-ylidene)methyl)-1,2-dimethylquinolin-1-ium iodide (<b>3b</b>)-were confirmed through NMR spectroscopy and MALDI-TOF mass spectrometry. A new methodology was developed to study monocationic dyes in the absence of a matrix and cationizing compounds in MALDI-TOF mass experiments. The newly synthesized dyes contain hydrophobic functional groups attached to the chromophore, enhancing their affinity for the hydrophobic regions of nucleic acids within the biological matrix. The dyes' photophysical properties were investigated in aqueous solutions and DMSO, as well as in the presence of nucleic acids. The dyes exhibit notable aggregachromism in both pure aqueous and buffered solutions. The observed aggregation phenomena were further elucidated using computational methods. Fluorescence titration experiments revealed that upon contact with nucleic acids, the dyes exhibit bioaggregachromism-aggregachromism on the surfaces of the respective biomolecular matrix (RNA or DNA). This bioaggregachromism was further confirmed by CD spectroscopy. Given the pronounced aggregachromism detected, we conclude that the dyes investigated in this study are highly suitable for use as fluorogenic probes in biomolecular recognition techniques. The unique absorption and fluorescence spectra of these dyes make them promising fluorogenic markers for various bioanalytical methods related to biomolecular recognition.