Abstract
Asymmetric monomethine cyanines have been extensively used as probes for nucleic acids among other biological systems. Herein we report the synthesis of seven monomethine cyanine dyes that have been successfully prepared with various heterocyclic moieties such as quinoline, benzoxazole, benzothiazole, dimethyl indole, and benz[e]indole adjoining benz[c,d]indol-1-ium, which was found to directly influence their optical and energy profiles. In this study the optical properties vs. structural changes were investigated using nuclear magnetic resonance and computational approaches. The twisted conformation unique to monomethine cyanines was exploited in DNA binding studies where the newly designed sensor displayed an increase in fluorescence when bound in the DNA grooves compared to the unbound form.
Highlights
Polymethine dyes represent a class of organic molecules with absorption bands that cover a broad spectral range (430–1100 nm), larger than any other class of dye system [1]
A series of seven monomethine cyanines were synthesized in good yield with red-shifted absorbance properties in comparison to previously synthesized monomethine cyanine dyes
The benz[c,d]indolium containing monomethine cyanine dyes in this report are non-fluorescent in free flowing solvent, when the dyes are in a viscous environment their fluorescence becomes observable due to the restricted ability to rotate around the methine bridge
Summary
Polymethine dyes represent a class of organic molecules with absorption bands that cover a broad spectral range (430–1100 nm), larger than any other class of dye system [1]. Cyanine dyes consist of two terminal aza-heterocycles connected via an electron deficient polymethine bridge that allows for a push/pull system between the two heterocycles. In addition to the variable length of the conjugated system between the heterocycles, the heterocycles themselves can be altered which allows chemists to create dyes that possess ideal photophysical properties, such as high molar extinction coefficients (>105 M1 ̈ cm1 ), tunable fluorescence intensities, and narrow absorption bands. Thiazole orange (TO) and oxazole yellow (YO), are well known imaging probes in the biological sciences due to their enhanced photophysical properties which have been attributed to restricted torsional motion of the dye in the excited state upon binding to target a macromolecule (i.e., nucleic acid structure, protein) [11,12,13,14]
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