Electronic tuning of fluorescent 8-aryl-guanine probes for monitoring DNA duplex-quadruplex exchangeElectronic supplementary information (ESI) available: Experimental section, Fig. S1-S3 described in the text, NMR spectra of synthetic samples, MS spectra of modified TBA oligonucleotides and additional computational details. See DOI: 10.1039/c3sc52625a

• Main Authors: Sproviero, Michael, Fadock, Kaila L, Witham, Aaron A, Manderville, Richard A, Sharma, Purshotam, Wetmore, Stacey D
• Format: Journal Article
• Language: English
• Published: 23.12.2013
• ISSN: 2041-6520; 2041-6539
• DOI: 10.1039/c3sc52625a

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 ( Fur dG) and 8-(4′′-cyanophenyl)-dG ( CNPh dG)) for detecting G-quadruplex folding by the 15- mer (5′-GGTTG 5 G 6 TG 8 TGGTTGG) thrombin-binding aptamer (TBA). The 8-aryl-dG probes adopt a syn -conformation and were inserted into G 5 ( syn ), G 6 ( anti ) and G 8 (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 G 5 and their acceptance within the TG 8 T 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. Design of internal fluorescent nucleobase probes as effective molecular switches for the DNA duplex-quadruplex detection system.