AbstractA key goal of synthetic biology is to use biological molecules to create novel biological systems. Due to their role as transmitters in such systems, RNA molecules have gained much attention from synthetic biologists to design and construct novel RNA molecules with desirable functions and properties. In recent decades, the design of RNAs, however, has been limited to RNA architecture with primitive functions: aptamer and catalysis. To expand the paradigm of RNA-based design, we herein propose a conceptual design of RNA-RNA interaction based systems, considering domain-based structures of RNAs, as well as thermodynamic properties of RNA molecules and their interactions. Two evaluation scores, namely structural score (SS) and affinity score (AS), are used as criteria for selection of proper RNA sets. We employ this concept to design various RNA sets, each of which contains three RNA strands that altogether function like a comparator device. With these criteria, we show that four out of forty RNA sets would behave like a biological comparator since they have appropriate structure (SS=1) and proper interaction order (AS>1). The proposed scores are proven to be proper criteria for selection of RNA sets with required functions. This preliminary design offers an opportunity for synthetic biologists to expand the design of RNA sequence from a single strand to multiple strands that would behave in the same manner as enzymatic reactions.