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Strong impact of chloro substituent on TOTO and YOYO ds-DNA/RNA sensing

Introduction of chloro-substituent at cyanine chromophore of well-known DNA stains TOTO and YOYO resulted in a significant difference of DNA and RNA recognition in respect to parent compounds (TOTO ; YOYO), as well as in respect to corresponding monomers (Cl-TO and Cl-YO). Studied novel compounds showed strong, submicromolar affinity to all ds-polynucleotides, with minor differences in binding constant between various DNA and RNA. The Cl-YOYO revealed a specific fluorimetric recognition of ds-RNA in respect to ds-DNA by the fluorimetric response at 570 nm, which was attributed to particular aggregation property of dye, not present in corresponding Cl-TOTO analogue. The Cl-TOTO, unlike YO-analogue, showed ICD band at 520 nm only upon binding to alternating DNA sequences (both, GC-GC and AT-AT), which was not observed for homo-DNA and homo-RNA. Such recognition pattern was attributed to structural differences between polynucleotides, whereby only alternating-DNAs have a typical B-helical structure in which Cl-TOTO molecule could self-fold to give particular ICD band at 520 nm. Thus, both Cl-analogues show intriguing novel recognition properties in respect to parent TOTO and YOYO, which combined with negligible cytotoxicity offer potential for development of novel dyes for biochemical and biomedical applications.

DNA and RNA recognition ; fluorescent markers ; circular dichroism ; target-aggregating dyes

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