Electronic tuning of fluorescent 8-aryl-guanine probes for monitoring DNA duplex–quadruplex exchange

Abstract

In DNA-based diagnostics, duplex–quadruplex exchange is a common strategy for target detection using fluorescent probes that turn-on during the exchange process. Typical “label” detection platforms use emissive tags that are attached via linkers to the 5′- or 3′-ends of the oligonucleotide. Alternatively, “label-free” strategies employ fluorescent molecules that bind specifically to G-quadruplex structures with enhanced emission. Here, we report the utility of two internal fluorescent 8-aryl-2′-deoxyguanine probes (8-furyl-dG (^FurdG) and 8-(4′′-cyanophenyl)-dG (^CNPhdG)) for detecting G-quadruplex folding by the 15-mer (5′-GGTTG₅G₆TG₈TGGTTGG) thrombin-binding aptamer (TBA). The 8-aryl-dG probes adopt a syn-conformation and were inserted into G₅ (syn), G₆ (anti) and G₈ (TGT loop) of TBA to study their site-specific impact on duplex and G-quadruplex folding. Our studies show the ability of 8-aryl-dG probes to preferentially stabilize the G-quadruplex structure of TBA at G₅ and their acceptance within the TG₈T loop despite their syn-preference. Our studies also demonstrate how the choice of 8-aryl substituent can be used to tune probe electronics for turn-on fluorescence in the duplex or G-quadruplex structure. Overall, our studies establish 8-aryl-dG probes as useful tools for DNA-based diagnostics.