A small unstructured nucleic acid disrupts a trinucleotide repeat hairpin

A variety of neurodegenerative disorders are associated with the expansion of trinucleotide repeat (TNR) sequences. These repetitive sequences are prone to adopting non-canonical structures, such as intrastrand stem-loop hairpins. Indeed, the formation and persistence of these hairpins during DNA replication and/or repair have been proposed as factors that facilitate TNR expansion. Given this proposed contribution of TNR hairpins to the expansion mechanism, disruption of such structures via strand invasion offers a potential means to negate the disease-initiating expansion. In this work, we investigated the strand invading abilities of a (CTG)₃ unstructured nucleic acid on a (CAG)₁₀ TNR hairpin. Using fluorescence, optical, and electrophoretic methods, instantaneous disruption of the (CAG)₁₀ hairpin by (CTG)₃ was observed at low temperatures. Additionally, we have identified three distinct duplex-like species that form between (CAG)₁₀ and (CTG)₃; these include 1, 2, or 3 (CTG)₃ sequences hybridized to (CAG)₁₀. The results presented here showcase (CTG)₃ as an invader of a TNR hairpin and suggest that unstructured nucleic acids could serve as a scaffold to design agents to prevent TNR expansion.