Orthogonal Amplification Circuits Composed of Acyclic Nucleic Acids Enable RNA Detection.

Construction of complex DNA circuits is difficult due to unintended hybridization and degradation by enzymes under biological conditions. We herein report a hybridization chain reaction (HCR) circuit composed of left-handed acyclic d-threoninol nucleic acid (d- a TNA), which is orthogonal to right-handed DNA and RNA. Because of its high thermal stability, use of an a TNA hairpin with a short 7 base-pair stem ensured clear ON-OFF control of the HCR circuit. The a TNA circuit was stable against nucleases. A circuit based on right-handed acyclic l-threoninol nucleic acid (l- a TNA) was also designed, and high orthogonality between d- and l- a TNA HCRs was confirmed by activation of each a TNA HCR via a corresponding input strand. A dual OR logic gate was successfully established using serinol nucleic acid (SNA), which could initiate both d- and l- a TNA circuits. The d- a TNA HCR was used for an RNA-dependent signal amplification system via the SNA interface. The design resulted in 80% yield of the cascade reaction in 3000 s without a significant leak. This work represents the first example of use of heterochiral HCR circuits for detection of RNA molecules. The method has potential for direct visualization of RNA in vivo and the FISH method.