Domain-based design platform of interacting RNAs: A promising tool in synthetic biology

Interacting RNA-based devices have increasingly gained interest among synthetic biologists due to their potential applications in biotechnology and medicine. However, the effort to create novel interacting RNA-based devices has been hampered by the difficulty in designing efficient interacting RNA molecules with desired structures and functions. In this work, we propose a new computational platform that efficiently designs interacting RNAs that can fold into specific shapes. This platform combines interacting domain-based decomposition (iDoDe) and the Domain-based Design (DD) program to randomly generate both individual and hybridized RNA sequences following a user´s requirement. In addition, the platform includes the Vienna RNA package that predicts the secondary structures and the minimum free energy (MFE) of the designing sequences. In this paper, the proposed platform is demonstrated using 4 artificial models of interacting RNAs with different structures. Using the similarity and the stability scores as the design criteria, it is found that our design platform is able to randomly generate many interacting RNAs that are perfectly matched to each of the four target structures with acceptable stability. Although this platform offers a great potential for designing interacting RNAs, it still needs further development that integrates an optimization algorithm to efficiently provide optimal sets of interacting RNAs.