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Xenonucleic acids (XNAs), which are composed of artificial scaffolds and natural nucleobases, have unique hybridization properties that depend on the scaffold structure. Here, we functionalized the acyclic XNA serinol nucleic acid (SNA) with nonnatural nucleobases. A linear SNA probe functionalized with 5-perylenylethynyl uracil residues showed weak greenish-yellow excimer emission in the absence of target RNA and bright cyan-green monomer emission in the presence of target RNA. Probe hybridization was rapid and enabled the quantitative measurement of RNA with discrimination of single-base mismatches. We also designed a photoresponsive SNA with two 8-pyrenylvinyl adenine (PVA) residues. Irradiation with blue (455 nm) light caused [2 + 2] photocycloaddition between intrastrand PVAs, resulting in the dissociation of the SNA/RNA duplex, whereas irradiation with ultraviolet (340 nm) light induced cycloreversion of the PVA photodimer and SNA/RNA duplex reformation. Using a combination of 8-naphthylvinyl adenine (NVA) and PVA and irradiation with 465 nm, 405 nm, 340 nm, and 300 nm light, orthogonal control of the formation of SNA(NVA-NVA)/RNA and SNA(PVA-NVA)/RNA duplexes was demonstrated. Thus, nucleobase modifications further expand the utility of acyclic XNA in bionanotechnology.

Biochemical reaction networks can exhibit plastic adaptation to alter their functions in response to environmental changes. This capability is derived from the structure and dynamics of the reaction networks and the functionality of the biomolecule. This plastic adaptation in biochemical reaction systems is essentially related to memory and learning capabilities, which have been studied in DNA computing applications for the past decade. However, designing DNA reaction systems with memory and learning capabilities using the dynamic properties of biochemical reactions remains challenging. In this study, we propose a basic DNA reaction system design that acquires classical conditioning, a phenomenon underlying memory and learning, as a typical learning task. Our design is based on a simple mechanism of five DNA strand displacement reactions and two degradative reactions. The proposed DNA circuit can acquire or lose a new function under specific conditions, depending on the input history formed by repetitive stimuli, by exploiting the dynamic properties of biochemical reactions induced by different input timings.

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 acyclicd-threoninol nucleic acid (d-aTNA), which is orthogonal to right-handed DNA and RNA. Because of its high thermal stability, use of an aTNA hairpin with a short 7 base-pair stem ensured clear ON–OFF control of the HCR circuit. The aTNA circuit was stable against nucleases. A circuit based on right-handed acyclicl-threoninol nucleic acid (l-aTNA) was also designed, and high orthogonality between d- and l-aTNA HCRs was confirmed by activation of each aTNA 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-aTNA circuits. The d-aTNA 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.

A molecular robot is an intelligent molecular system. A typical control problem of molecular robots is to maintain the concentration of a specific DNA strand at the desired level, which is typically attained by a molecular feedback control mechanism. A molecular feedback system can be constructed in a bottom-up method by transforming a nonlinear chemical reaction system into a pseudo-linear system. This method enables the implementation of a molecular proportional-integral (PI) controller on a DNA reaction system. However, a DNA reaction system is driven by fuel DNA strand consumption, and without a sufficient amount of fuel strands, the molecular PI controller cannot perform normal operations as a concentration regulator. In this study, we developed a design method for a molecular PI control system to regenerate fuel strands by introducing photoresponsive reaction control. To this end, we employed a photoresponsive molecule, azobenzene, to guide the reaction direction forward or backward using light irradiation. We validated our renewable design of the PI controller by numerical simulations based on the reaction kinetics. We also confirmed the proof-of-principle of our renewable design by conducting experiments using a basic DNA circuit.