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Serinol Nucleic Acid with a Fluorescent Uracil Analog serves as a Quencher-free Linear Probe.

With the goal of developing a quencher-free probe composed of artificial nucleic acid, we synthesized the fluorescent nucleobase analogue 5-(perylenylethynyl)-uracil (PeU), which was incorporated into the totally artificial serinol nucleic acid (SNA) as a substitute for thymine. In the context of a 12-mer duplex with RNA, these fluorophores reduce duplex stability slightly compared to an SNA without the PeU modification, suggesting that structural distortion was not induced by the modification. When two PeUs were incorporated at separate positions in an SNA, the fluorescent emission at around 490 nm was clearly enhanced upon the hybridization with complementary RNA. We designed a quencher-free SNA linear probe containing three PeUs each separated by 6 nucleobases. We demonstrated detection of target RNA with high sensitivity and discrimination of a single-base mismatch.