New Thiazole Orange Derivatives for Improved Fluorescence Signaling of DNA FIT Probes

Abstract

AbstractForced intercalation probes (FIT probes) are nucleic acid probes in which an intercalator dye of the thiazole orange (TO) family serves as a surrogate nucleobase. Hybridization of FIT probes is accompanied by enhancements of fluorescence. Looking for ways to increase turn-on and brightness of fluorescence, we herein report the synthesis of new fluorogenic base surrogates. In total, nine different TO derivatives were introduced into FIT probes. Fluorescence measurements in six different sequences revealed that substitution at both the quinoline and the benzothiazole part affects fluorescence turn-on upon hybridization and brightness of probe–target duplexes. A TO derivative containing a tricyclic benzothiazole provided FIT probes signaling hybridization by up to 18.6-fold enhancement of fluorescence. Improved fluorescence quantum yields (Φds up to 0.53) and high extinction coefficients (ε518 up to 91000 M–1·cm–1) make this dye an interesting, and in some sequences superior, alternative to the canonical thiazole orange used previously in FIT probes.