Length-independent and selective sensing of CCG trinucleotide repeat foldings by a monovalency-binding fluorogenic probe

Tandem CNG (N = C, T, A, G) DNA trinucleotide repeats (TNRs) are the main expansion to cause severe neurodegenerative diseases. Small molecule ligands with a capacity to sense the CNG TNRs foldings have received considerable attention because of therapeutic and diagnostic perspectives. This requires development of effectual ligands that have a preference to a particular CNG TNRs foldings. However, the previously developed ligands using hydrogen-bonding interaction as the dominantly driving force usually exhibit a multimolecular binding behavior with TNRs. This multivalency interaction usually compromises the sensing selectivity towards CNG TNRs. Herein, we reported a monovalency probe of pseudohypericin (PHP) to selectively sense only the CCG TNRs foldings by a signal-on fluorescence, while total signal-off responses were otherwise observed for CTG, CAG, and CGG TNRs. In addition, the monovalency association of PHP to CCG TNRs is independent of the repeat length. This selective sensing occurs in the loop region, in which a triad is formed between the terminal WatsonCrick CG base pair and the mismatched cytosine adopting an extrahelical conformation. We believe that the specific interaction of PHP with the triad is in charge of the selective association of CCG TNRs over other counterparts. Furthermore, the sensitivity to CCG TNRs can be strengthened by the repeat-activated photocatalysis activity of the TNRs-based DNAzymes via a singlet oxygen (1O2) pathway. Our work offers an alternative way to sense CNG TNRs with a high selectivity and promising applications in developing TNRs-based sensors.